UNIT 1: CONCEPT OF TAXONOMY

BLOCK I: TAXONOMY

1.1 OBJECTIVES
• To define vaccines & their types
• To understand immunodiagnostics & its applications
• To describe the methods of agglutination
• To explain the principle of Complement Fixation Test
• To describe immunotherapy & its various forms

1.2 INTRODUCTION

Taxonomy, in a broad sense the science of classification, but more strictly the classification
of living and extinct organisms—i.e., biological classification. The term is derived from the
Greek taxis (“arrangement”) and nomos (“law”). Taxonomy is, therefore, the methodology
and principles of systematic botany and zoology and sets up arrangements of the kinds of
plants and animals in hierarchies of superior and subordinate groups. The term first proposed
by the Swiss originated botanist Augustin Pyramus de Candolle in 1813 for the plant
classification. He used the term in his famous book—Theory elementaire de la botanique
(Elementary Theory of Botany). So taxonomy is the arrangement of the plants and animals on
the basis of some laws.

Simpson (1961) has defined taxonomy as the theoretical study of classification including its
bases, principles, procedures and rules. Ernst Mayer also defines taxonomy as the theory and
practice of classifying organisms. So the science of classification is known as taxonomy.
Kristofferson (1995) has defined taxonomy as “the practice of recognizing, naming, and
ordering taxa into a system of words consistent with any kind of relationships among taxa
that the investigator has discovered in nature”. Popularly, classifications of living organisms
arise according to need and are often superficial. Anglo-Saxon terms such as worm and fish
have been used to refer, respectively, to any creeping thing—snake, earthworm, intestinal
parasite, or dragon—and to any swimming or aquatic thing. Although the term fish is
common to the names shellfish, crayfish, and starfish, there are more anatomical differences
between a shellfish and a starfish than there are between a bony fish and a man. Vernacular
names vary widely. The American robin (Turdus migratorius), for example, is not the
English robin (Erithacus rubecula), and the mountain ash (Sorbus) has only a superficial
resemblance to a true ash.

Biologists, however, have attempted to view all living organisms with equal thoroughness
and thus have devised a formal classification. A formal classification provides the basis for a
relatively uniform and internationally understood nomenclature, thereby simplifying cross-
referencing and retrieval of information.

The usage of the terms TAXONOMY and SYSTEMATICS with regard to biological
classification varies greatly. American evolutionist Ernst Mayer has stated that “taxonomy is
the theory and practice of classifying organisms” and “systematics is the science of the
diversity of organisms”; the latter in such a sense, therefore, has considerable interrelations
with evolution, ecology, genetics, behaviour, and comparative physiology that taxonomy
need not have.

The process of taxonomy involves two distinct steps:

(i) Correct recognition and definition of the organisms and their relationships and

(ii) Application of suitable designations for the organisms and to different groups which
include them.

The former is called classification which includes study of characters and grouping of
individuals while the latter is termed as nomenclature.

History

People who live close to nature usually have an excellent working knowledge of the elements
of the local fauna and flora important to them and also often recognize many of the larger
groups of living things (e.g., fishes, birds, and mammals). Their knowledge, however, is
according to need, and such people generalize only rarely.

However, some of the earliest forays into formal, but limited, classification were undertaken
by the ancient Chinese and ancient Egyptians. In China a catalog of 365 species of medicinal
plants became the basis of later hydrological studies. Although the catalog is attributed to the
mythical Chinese emperor Shennong who lived about 2700 bce, the catalog was likely
written about the beginning of the first millennium. Similarly, ancient Egyptian medical
papyri dating from 1700 to 1600 bcc provided descriptions of various medicinal plants, along
with directions on how they could be used to treat illnesses and injuries.

The first great generalize in Western classification was Aristotle, who virtually invented the
science of logic, of which for 2,000 years classification was a part. Greeks had constant
contact with the sea and marine life, and Aristotle seems to have studied it intensively during
his stay on the island of Lesbos. In his writings, he described a large number of natural
groups, and, although he ranked them from simple to complex, his order was not an
evolutionary one. He was far ahead of his time, however, in separating invertebrate animals
into different groups and was aware that whales, dolphins, and porpoises had mammalian
characters and were not fish. Lacking the microscope, he could not, of course, deal with the
minute forms of life.

The Aristotelian method dominated classification until the 19th century. His scheme was, in
effect, that the classification of a living thing by its nature—i.e., what it really is, as against
superficial resemblances—requires the examination of many specimens, the discarding of
variable characters (since they must be accidental, not essential), and the establishment of
constant characters. These can then be used to develop a definition that states the essence of
the living thing—what makes it what it is and thus cannot be altered; the essence is, of
course, immutable. The model for this procedure is to be seen in mathematics, especially
geometry, which fascinated the Greeks. Mathematics seemed to them the type and exemplar
of perfect knowledge, since its deductions from axioms were certain and its definitions
perfect, irrespective of whether a perfect geometrical figure could ever be drawn. But the
Aristotelian procedure applied to living things is not by deduction from stated and known
axioms; rather, it is by induction from observed examples and thus does not lead to the
immutable essence but to a lexical definition. Although it provided for centuries a procedure
for attempting to define living things by careful analysis, it neglected the variation of living
things. It is of interest that the few people who understood Charles Darwin’s ORIGIN OF
SPECIES in the mid-19th century were empiricists who did not believe in an essence of each
form.

Aristotle and his pupil in botany, Theophrastus, had no notable successors for 1,400 years. In
about the 12th century, botanical works necessary to medicine began to contain accurate
illustrations of plants, and a few began to arrange similar plants together. Encyclopaedists
also began to bring together classical wisdom and some contemporary observations. The first
flowering of the Renaissance in biology produced, in 1543, Andreas Vesalius’s treatise on
human anatomy and, in 1545, the first university botanic garden, founded in Padua, Italy.
After this time, work in botany and zoology flourished. John Ray summarized in the late 17th
century the available systematic knowledge, with useful classifications. He distinguished the
monocotyledonous plants from the dicotyledonous ones in 1703, recognized the true affinities
of the whales, and gave a workable definition of the species concept, which had already
become the basic unit of biological classification. He tempered the Aristotelian logic of
classification with empirical observation.

Levels of Taxonomy

There are three levels of taxonomy corresponding with three periods of taxonomy:

(i) Alpha taxonomy:

The level of taxonomy by which species are characterized and naming of the species is done.

(ii) Beta taxonomy:

The level of taxonomy by which the arrangement of species in their natural system of
categories is made.

(iii) Gamma taxonomy:

The level of taxonomy which deals with the intra specific variations and evolutionary
sequence and also a causal interpretation of organic diversity.

Mayer and Ashlock (1991) have divided the taxonomy into two levels:

(i) Micro taxonomy:

The level which deals only the problems related to species.

(ii) Macro taxonomy:

The level which deals with the problems and principles of higher taxa (from subgenus and
above) only.

Mayer and Ashlock (1991) recognize three schools of macro-taxonomy such as:

(i) Phonetics (or Numerical taxonomy),

(ii) Cladistics (Phylogenetic systematics) and

(iii) Evolutionary taxonomy (or Evolutionary systematics).

(i) Phenetics (or Numerical taxonomy):

It is an attempt to classify organisms based on overall characteristics rather than on evolution

from a common ancestor. Phenetics helps to draw phyletic lineage (relationship) on the basis
of similarities and dissimilarities. Pheneticists do not rely upon primitive (plesiomorphic) and
derived (apomorphic) characters.

(ii) Cladistics (Phylogenetic systematics):

The term cladistics refers to taxonomy by which the organisms are ranked and classified
according to the “recency of common descent”. The categorical status of the animal
according to this theory depends upon the position of branching points on the phylogenetic
tree.

Taxa based on entirely shared derived (synapomorphic) characters originated from a common
ancestor. It is a method of phylogenetic analysis to identify monophyletic lineages or clades.
Julian Huxley used the term ‘clade’ in 1958 and Cain and Harrison introduced the term
‘cladistic’ in 1960.

(iii) Evolutionary taxonomy (or Evolutionary systematics):

The whole concept is based on Darwinism. According to this concept each valid taxon is
derived from a common ancestor but the common characteristic features of a realm of the
biological world do not always include a common ancestry.

The evolutionary or Darwinian classification is a branch of biological classification in which

the organisms are classified using a combination of phylogenetic relationship and overall
similarity. This type of taxonomy considers taxa more important rather than single species.

Usually taxonomists agree to divide the taxonomy into two types:

(i) Classical taxonomy and

(ii) Neo-taxonomy or experimental taxonomy.

(i) Classical taxonomy:

The oldest form of taxonomy is called classical taxonomy or orthodox taxonomy. It is related
to the description, naming and classification of the animals and plants based on the morpho-
logical features (related to external features including genitalia, anatomy, embryology and
karyotype; etc.).
(ii) Experimental taxonomy or neo-taxonomy:

It is related to the genetically studies based on a common gene pool for a taxon and become
helpful to distinguish two different taxa. Some modern procedures are applied to collect the
data for morphology. The use of electron arid scanning electron microscope in different
groups of invertebrates such as protozoans, helminthes, arthropods to study the fine structures
that become helpful in morph taxonomy.

The closely related two current aspects in taxonomy are taken into consideration,
such as:

(i) Biochemical taxonomy and

(ii) Cytological taxonomy.

(i) Biochemical taxonomy:

It deals with taxonomic characters obtained from chemical analysis of enzymes, hormones,
and proteins with peptides, nucleic acids, amino acids and sugars.

The amino acid sequences of proteins become different in the different organisms and
become helpful to distinguish the different species. Numerous techniques are applied to the
study of constituent bio-molecules such as enzymes, hormones, nucleic acids, amino acids,
etc. and help in the systematics.

To study the chemical substances, various procedures such as immunological,

chromatography (paper chromatophy and column chromatography), electrophoretic method
are applied in the study of systematics. The immunological data are used to distinguish two
different taxa. The blood group genes are applied in the classification of pigeons and
primates.

Chromatography is kind of different techniques for the separation of a complex liquid

mixture such as biological fluids (e.g., amino acids, steroid, carbohydrate, etc.) that pass
through a column of adsorbing material (e.g., paper, magnesia) the components of the
mixtures are adsorbed in separate layers in the column.

This technique is applied in various groups of arthropods, snails and the data is very much
helpful in animal systematics.
(ii) Cytotaxonomy:

It deals with taxonomic characters obtained from cytological studies. Cytotaxonomy is a

branch of taxonomy dealing with the relationships and classification of organisms based on
the structure, number of chromosomes. The position of the centromere is an important feature
of chromosome structure which helps in taxonomic studies.

Periods of Taxonomy

(i) First period:

This period may be extended from the time of Aristotle (384-322 B.C.) to Linnaeus (1707-
1778). In this period Linnaeus strongly introduced binominal nomenclature for plants and
animals and followed Aristotelian and Democritus principle in classification of animals. He
also first introduced the hierarchic system of classification both in plants and animals
following class, order, genus and species categories.

(ii) Second period:

In this period the evolutionary classification was introduced by Charles Robert Darwin
(1809-82) and variation among the organisms is the main force in evolution which was
discussed extensively. Darwin published his famous book “On the Origin of Species by
Means of Natural Selection” in 1859.

In his book the theory of evolution by natural selection was his own creation although based
on the work of Lamarck, Cuvier (1768-1832) and Erasmus Darwin (1731-1802), the
grandfather of Charles Darwin. This theory helped a lot to the systematic zoology. E.
Darwin’s book Zoonomia (1794) presented the laws of organic life. He suggested the struggle
for existence in Zoonomia which was elaborated by Charles Darwin.

(iii) Third period:

This period includes the development of modern taxonomy which started about 1930. The
study of genetics and population biology was started with typical taxonomy.

This period is remarkable with the publication of New Systematics by J. S. Huxley in 1940,
intraspecific variations were studied and the science of population genetics was started in
1908 by G. H. Hardy and W. Weinberg who independently discovered a principle concerned
with the frequency of genes (alleles) in a population in the light of evolutionary theory.
Concepts of Taxonomy

In 1975 Mayer and Ashlock first put forward the concept of Micro-taxonomy. Development
of the debates on the species, centering mainly on the so-called biological species concept,
was called micro-taxonomy or the science of species by Mayr (1982).

One of the major problems of micro-taxonomy evolves around the concept of species. A
merging of different research traditions, in systematics as well as in paleontology and
genetics, prompted the development of micro-taxonomy. Micro-taxonomy involves the study
of concepts of species like Typological species concept, Nominalistic species concept,
Biological species concept, Evolutionary species concept etc.

Micro-taxonomy deals with problems like the evolution of species, estimation of the popu-
lation of species in the living world or in special groups of organisms to which any two, three
or all species definitions apply.

It also deals with geographic variation, the recognition of polytypic species, the definition of
subspecies and species, the taxonomic status of incipient species and the role of non-
morphological characters in the delimitation of species. In any case, the biological distinction
is primary and the morphological difference secondary.

Macro-taxonomy is the science of classification:

Theoretical comments ranged from a denial that supra-specific taxa were natural entities, to
vague statements that a phylogenetic classification is the more natural. How do we
reconstruct phylogeny? How do we represent it in a formal classification? These were the
problems being dealt under macro-taxonomy. Macro-taxonomy involves study of homology,
analogy, affinities, systematic status and phylogeny.

Micro-taxonomy and Macro-taxonomy are related in the sense that one is incomplete without
the other. For the science of classification of species it is very important to know the science
of species. Macro-taxonomy involves the establishment of equivalent basis of their features.
So how is grouping (Macro-taxonomy) possible without knowing the features of the object
(Micro-taxonomy). Hence one is heavily dependent on the other.
Modern Trends in Taxonomy

The term new or modern is a relative term, as what is considered new or modern today may
become old systematics in the future. The new systematics introduced by Huxley in 1940
may indeed be very old systematics today. To dispel such misinterpretation of new
systematics the words of Mayr (1964) is of immense help.

Mayr wrote “What then is the new systematics? Perhaps it is best described as a view-
point, an attitude, a general philosophy. It started primarily as a rebellion against the
nominalistic typological and thoroughly non-biological approach of certain, alas all too
many, taxonomists of the preceding period”.

The New Taxonomy, thus, is an approach of the population taxonomists that differ drastically
from the simple pigeonholing of classical Linnaean taxonomy. Workers in the new
systematics consider themselves biologists rather than filing clerks.

New Taxonomy is neither a special technique nor a special method but an attitude which can
be applied at every taxonomic level. It deals with –

1. The utilisation of an ever-increasing number of characters and a continued depreciation of

key characters — in contrast to the typological approach.

2. A ready acceptance of new tools and techniques such as —

(a) Visual analysis of sounds in insects, frogs and birds,

(b) Analysis of courtship displays and other behaviour,

(c) Utilisation of biochemical characters,

(d) Utilisation of computers.

3. A further clarification of concepts, such as

(a) Clear separation of taxon from categories,

(b) Recognition of the subspecies as a category and not as an evolutionary unit, and

(c) Clean understanding of the causes of similarities and differences between taxa.

The Linnaean system

Carolus Linnaeus, who is usually regarded as the founder of modern taxonomy and whose
books are considered the beginning of modern botanical and zoological nomenclature, drew
up rules for assigning names to plants and animals and was the first to use binomial
nomenclature consistently (1758). Although he introduced the standard hierarchy of class,
order, genus, and species, his main success in his own day was providing workable keys,
making it possible to identify plants and animals from his books. For plants he made use of
the hitherto neglected smaller parts of the flower.

Linnaeus attempted a natural classification but did not get far. His concept of a natural
classification was Aristotelian; i.e., it was based on Aristotle’s idea of the essential features of
living things and on his logic. He was less accurate than Aristotle in his classification of
animals, breaking them up into mammals, birds, reptiles, fishes, insects, and worms. The first
four, as he defined them, are obvious groups and generally recognized; the last two
incorporate about seven of Aristotle’s groups.

Frank Franklin II/AP

The standard Aristotelian definition of a form was by genus and differentia. The genus
defined the general kind of thing being described, and the differentia gave its special
character. A genus, for example, might be “Bird” and the species “Feeding in water,” or the
genus might be “Animal” and the species “Bird.” The two together made up the definition,
which could be used as a name. Unfortunately, when many species of a genus became
known, the differentia became longer and longer. In some of his books Linnaeus printed in
the margin a catch name, the name of the genus and one word from the differentia or from
some former name. In this way he created the binomial, or binary, nomenclature. Thus,
modern humans are HOMO SAPIENS, Neanderthals are HOMO NEANDERTHALENSIS,
the gorilla is GORILLA GORILLA, and so on.

Classification since Linnaeus

Classification since Linnaeus has incorporated newly discovered information and more
closely approaches a natural system. When the life history of barnacles was discovered, for
example, they could no longer be associated with mollusks because it became clear that they
were arthropods (jointed-legged animals such as crabs and insects). Jean-Baptiste Lamarck,
an excellent taxonomist despite his misconceptions about evolution, first separated spiders
and crustaceans from insects as separate classes. He also introduced the distinction, no longer
accepted by all workers as wholly valid, between vertebrates—i.e., those with backbones,
such as fishes, amphibians, reptiles, birds, and mammals—and invertebrates, which have no
backbones. The invertebrates, defined by a feature they lack rather than by the features they
have, constitute in fact about 90 percent of the diversity of all animals. The mixed group
“Infusoria,” which included all the microscopic forms that would appear when hay was let
stand in water, was broken up into empirically recognized groups by the French biologist
Felix Dujardin. The German biologist Ernst Haeckel proposed the term Protista in 1866 to
include chiefly the unicellular plants and animals because he realized that, at the one-celled
level, there could no longer be a clear distinction between plants and animals.

The process of clarifying relationships continues. Only in 1898 were agents of disease
discovered (viruses) that would pass through the finest filters, and it was not until 1935 that
the first completely purified virus was obtained. Primitive spore-bearing land plants
(Psilophyta) from the Cambrian Period, which dates from 541 million to 485 million years
ago, were discovered in Canada in 1859. The German botanist Wilhelm Hofmeister in 1851
gave the first good account of the alternation of generations in various nonflowering
(cryptogamous) plants, on which many major divisions of higher plants are based. The
phylum Pogonophora (beard worms) was recognized only in the 20th century.

The immediate impact of Darwinian evolution on classification was negligible for many
groups of organisms and unfortunate for others. As taxonomists began to accept evolution,
they recognized that what had been described as natural affinity—i.e., the more or less close
similarity of forms with many of the same characters—could be explained as relationship by
evolutionary descent. In groups with little or no fossil record, a change in interpretation rather
than alteration of classifications was the result. Unfortunately, some authorities, believing
that they could derive the group from some evolutionary principle, would proceed to
reclassify it. The classification of earthworms and their allies (Oligochaeta), for example,
which had been studied by using the most complex organism easily obtainable and by then
arranging progressively simple forms below it, was changed after the theory of evolution
appeared. The simplest oligochaete, the tiny freshwater worm AEOLOSOMA, was
considered to be most primitive, and classifiers arranged progressively complex forms above
it. Later, when it was realized that AEOLOSOMA might well have been secondarily
simplified (i.e., evolved from a more complex form), the tendency was to start in the middle
of the series and work in both directions. Biased names for the major subgroups
(Archioligochaeta, Neoligochaeta) were widely accepted when in fact there was no evidence
for the actual course of evolution of this and other animal groups. Groups with good fossil
records suffered less from this type of reclassification because good fossil material allowed
the placing of forms according to natural affinities; knowledge of the strata in which they
were found allowed the formulation of a phylogenetic tree (i.e., one based on evolutionary
relationships), or dendrite (also called a dendrogram), irrespective of theory (SEE
ALSOphylogeny).

The long-term impact of Darwinian evolution has been different and very important. It
indicates that the basic arrangement of living things, if enough information were available,
would be a phylogenetic tree rather than a set of discrete classes. Many groups are so poorly
known, however, that the arrangement of organisms into a dendrite is impossible. Extensive
and detailed fossil sequences—the laying out of actual specimens—must be broken up
arbitrarily. Many groups, especially at the species level, show great geographical variation, so
that a simple definition of species is impossible. Difficulties of classification at the species
level are considerable. Many plants show reticulate (chain) evolution, in which species form
and then subsequently hybridize, resulting in the formation of new species. And because
many plants and animals have abandoned sexual reproduction, the usual criteria for the
species—interbreeding within a pool of individuals—cannot be applied. Nothing about the
viruses, moreover, seems to correspond to the species of higher organisms.

THE TAXONOMIC PROCESS

Basically, no special theory lies behind modern taxonomic methods. In effect, taxonomic
methods depend on: (1) obtaining a suitable specimen (collecting, preserving and, when
necessary, making special preparations); (2) comparing the specimen with the known range
of variation of living things; correctly identifying the specimen if it has been described, or
preparing a description showing similarities to and differences from known forms, or, if the
specimen is new, naming it according to internationally recognized codes of nomenclature;
(4) determining the best position for the specimen in existing classifications and determining
what revision the classification may require as a consequence of the new discovery; and (5)
using available evidence to suggest the course of the specimen’s evolution. Prerequisite to
these activities is a recognized system of ranks in classifying, recognized rules for
nomenclature, and a procedure for verification, irrespective of the group being examined. A
group of related organisms to which a taxonomic name is given is called a taxon (plural taxa).

Ranks

The goal of classifying is to place an organism into an already existing group or to create a
new group for it, based on its resemblances to and differences from known forms. To this
end, a hierarchy of categories is recognized.
For example, an ordinary flowering plant, on the basis of gross structure, is clearly one of the
higher green plants—not a fungus, bacterium, or animal—and it can easily be placed in the
kingdom Plantae (or Metaphyta). If the body of the plant has distinct leaves, roots, a stem,
and flowers, it is placed with the other true flowering plants in the division Magnoliophyta
(or Angiospermae), one subcategory of the Plantae. If it is a lily, with swordlike leaves, with
the parts of the flowers in multiples of three, and with one cotyledon (the incipient leaf) in the
embryo, it belongs with other lilies, tulips, palms, orchids, grasses, and sedges in a subgroup
of the Magnoliophyta, which is called the class Liliatae (or Monocotyledones). In this class it
is placed, rather than with orchids or grasses, in a subgroup of the Liliatae, the order Liliales.

This procedure is continued to the species level. Should the plant be different from any lily
yet known, a new species is named, as well as higher taxa, if necessary. If the plant is a new
species within a well-known genus, a new species name is simply added to the appropriate
genus. If the plant is very different from any known monocot, it might require, even if only a
single new species, the naming of a new genus, family, order, or higher taxon. There is no
restriction on the number of forms in any particular group. The number of ranks that is
recognized in a hierarchy is a matter of widely varying opinion. Shown in Table 1 are seven
ranks that are accepted as obligatory by zoologists and botanists.

Obligatory hierarchy of ranks

Animals Plants

domain Eukaryota Eukaryota

kingdom Animalia Plantae

phylum Chordata Tracheophyta

class Mammalia Pteropsida

order Primates Coniferales

family Hominidae Pinaceae

Obligatory hierarchy of ranks

Animals Plants

genus Homo Pinus

species Homo sapiens (modern human) Pinus strobus (white pine)

In botany the term DIVISION is often used as an equivalent to the term PHYLUM of
zoology. The number of ranks is expanded as necessary by using the prefixes SUB-, SUPER-
, and INFRA- (e.g., subclass, superorder) and by adding other intermediate ranks, such as
brigade, cohort, section, or tribe. Given in full, the zoological hierarchy for the timber wolf of
the Canadian subarctic would be as follows:

Kingdom Animalia

Subkingdom Metazoa

Phylum Chordata

Subphylum Vertebrata

Superclass Tetrapoda

Class Mammalia

Subclass Theria

Infraclass Eutheria

Cohort Ferungulata

Superorder Ferae

Order Carnivora

Suborder Fissipeda

Superfamily Canoidea

Family Canidae

Subfamily Caninae
Tribe (none described for this group)

Genus CANIS

Subgenus (none described for this group)

Species CANIS LUPUS (wolf)

Subspecies CANIS LUPUS OCCIDENTALIS (northern timber wolf)

Although the name of the species is binomial (e.g., CANIS LUPUS) and that of the
subspecies trinomial (C. LUPUS OCCIDENTALIS for the northern timber wolf, C. LUPUS
LUPUS for the northern European wolf), all other names are single words. In zoology,
convention dictates that the names of superfamilies end in -OIDEA, and the code dictates
that the names of families end in -IDAE, those of subfamilies in -INAE, and those of tribes
in -INI. Unfortunately, there are no widely accepted rules for other major divisions of living
things, because each major group of animals and plants has its own taxonomic history and old
names tend to be preserved. Apart from a few accepted endings, the names of groups of high
rank are not standardized and must be memorized.

The discovery of a living coelacanth fish of the genus LATIMERIA in 1938 caused virtually
no disturbance of the accepted classification, since the suborder Coelacanthi was already well
known from fossils. When certain unusual worms were discovered in the depths of the oceans
about 10 years later, however, it was necessary to create a new phylum, Pogonophora, for
them since they showed no close affinities to any other known animals. The phylum
Pogonophora, as usually classified, has one class—the animals in the phylum are relatively
similar—but there are two orders, several families and genera, and more than 100 species.
Both of these examples have been widely accepted by authorities in their respective areas of
taxonomy and may be considered stable taxa.

It cannot be too strongly emphasized that there are no explicit taxonomic characters that
define a phylum, class, order, or other rank. A feature characteristic of one phylum may vary
in another phylum among closely related members of a class, order, or some lower group.
The complex carbohydrate cellulose is characteristic of two kingdoms of plants, but among
animals cellulose occurs only in one subphylum of one phylum. It would simplify the work of
the taxonomist if characters diagnostic of phylum rank in animals were always taken from
one feature, the skeleton, for example; those of class rank, from the respiratory organs; and so
on down the taxonomic hierarchy. Such a system, however, would produce an unnatural
classification.

The taxonomist must first recognize natural groups and then decide on the rank that should be
assigned them. Are sea squirts, for instance, so clearly linked by the structure of the
extraordinary immature form (larva) to the phylum Chordata, which includes all the
vertebrates, that they should be called a subphylum, or should their extremely modified adult
organization be deemed more important, with the result that sea squirts might be recognized
as a separate phylum, albeit clearly related to the Chordata? At present, this sort of question
has no precise answer.

Some biologists believe that “numerical taxonomy,” a system of quantifying characteristics

of taxa and subjecting the results to multivariate analysis, may eventually produce
quantitative measures of overall differences among groups and that agreement can be
achieved so as to establish the maximal difference allowed each taxonomic level. Although
such agreement may be possible, many difficulties exist. An order in one authority’s
classification may be a superorder or class in another. Most of the established classifications
of the better-known groups result from a general consensus among practicing taxonomists. It
follows that no complete definition of a group can be made until the group itself has been
recognized, after which its common (or most usual) characters can be formally stated. As
further information is obtained about the group, it is subject to taxonomic revision.

NOMENCLATURE

Communication among biologists requires a recognized nomenclature, especially for the

units in most common use. The internationally accepted taxonomic nomenclature is the
Linnaean system, which, although founded on Linnaeus’s rules and procedures, has been
greatly modified through the years. There are separate international codes of nomenclature in
botany (first published in 1901), in zoology (1906), and in microbiology (bacteria and
viruses, 1948). The Linnaean binomial system is not employed for viruses. There is also a
code, which was established in 1953, for the nomenclature of cultivated plants, many of
which are artificially produced and are unknown in the wild.

The codes, the authority for each of which stems from a corresponding international
congress, differ in various details, but all include the following elements: the naming of
species by two words treated as Latin; a law of priority that the first validly published and
validly binomial name for a given taxon is the correct one and that any others must become
synonyms; recognition that a valid binomen can apply to only one taxon, so that a name may
be used both in botany and in zoology but for only one plant taxon and one animal taxon; that
if taxonomic opinion about the status of a taxon is changed, the valid name can change also;
and, lastly, that the exact sense in which a name is used be determined by reference to a type.
Rules are also given for the obligate categories of the hierarchy and for what constitutes valid
publication of a name. Finally, recommendations are given on the process of deriving names.

Linnaeus believed that there were not more than a few thousand genera of living things, each
with some clearly marked character, and that the good taxonomist could memorize them all,
especially if their names were well chosen. Thus, although the naming of the species might
often involve much research, the genus at least could be easily found.

At the present time, in many taxa, the species has a definite biological meaning: it is defined
as a group of individuals that can breed among themselves but do not normally breed with
other forms. Among microorganisms and other groups in which sexual reproduction need not
occur, this criterion fails.

In botanical practice, matters more usually resemble the Linnean situation. Many sorts of
chromosomal variants (individuals with different arrangements of chromosomes, or
hereditary material, which prevent interbreeding) and marked ecotypes (individuals whose
external form is affected by the conditions of soil, moisture, and other environmental factors),
as well as other forms, that would clearly be classified as separate species by the zoologist
may be lumped together unrecognized or considered subspecies by the botanist. Botanists
commonly use the terms VARIETY and FORM to designate genetically controlled variants
within plant populations below the subspecies level.

The use of a strictly biological species definition would enormously increase rather than
reduce the number of names in use in botany. A recognized species of flowering plant may
consist of several “chromosomal races”—i.e., identical in external appearance but genetically
incompatible and, thus, effectively separate species. Such various forms are often identifiable
only by cytological examination, which requires fresh material and extensive laboratory
work. Many botanists have said that there has been so little stability in the accepted
nomenclature that further upheavals would be intolerable and render identification impossible
for many applied botanists who may not require such refinements. To postpone recognition of
such forms, however, will probably cause upheaval in the future.
Some species of birds are widespread over the archipelagos of the southwest Pacific, where
nearly every island may have a form sufficiently distinct to be given some kind of taxonomic
recognition. For example, 73 races are currently recognized for the golden whistler
(Pachycephala pectoralis). Before the realization that species could vary geographically,
each island form was named as a separate species (as many of the races of P. PECTORALIS
actually were). It is often believed—and often it is only belief rather than fact—that all of
these now genetically isolated populations arose as local differentiations of a single stock.
Thus, they are now usually classed in zoological usage as subspecies of one polytypic
species. The term POLYTYPIC indicates that a separate description (and type specimen) is
needed for each of the distinct populations, instead of one for the entire species. The use of a
trinomial designation for each subspecies (e.g., PACHYCEPHALA PECTORALIS
BOUGAINVILLEI) indicates that it is regarded as simply a local representative (in this case,
on Bougainville Island in the Solomons) of a more widely distributed species. The decision
on whether to consider such island forms as representatives of one species depends partly on
whether, in the judgment of the taxonomist, populations from adjacent islands are sufficiently
similar to allow free interbreeding.

VERIFICATION AND VALIDATION BY TYPE SPECIMENS

The determination of the exact organism designated by a particular name usually requires
more than the mere reading of the description or the definition of the taxon to which the name
applies. New forms, which may have become known since the description was written, may
differ in characteristics not originally considered, or later workers may discover, by
inspection of the original material, that the original author inadvertently confused two or
more forms. No description can be guaranteed to be exhaustive for all time. Validation of the
use of a name requires examination of the original specimen. It must, therefore, be
unambiguously designated.

At one time authors might have taken their descriptions from a series of specimens or partly
(or even wholly) from other authors’ descriptions or figures, as Linnaeus often did. Much of
the controversy over the validity of certain names in current use, especially those dating from
the late 18th century, stems from the difficulty in determining the identity of the material
used by the original authors. In modern practice, a single type specimen must be designated
for a new species or subspecies name. The type should always be placed in a reliable public
institution, where it can be properly cared for and made available to taxonomists. For many
microorganisms, type cultures are maintained in qualified institutions. Because of the short
generation time of microorganisms, however, they may actually evolve during storage.

A complex nomenclature is applied to the different sorts of type specimens. The holotype is a
single specimen designated by the original describer of the form (a species or subspecies
only) and available to those who want to verify the status of other specimens. When no
holotype exists, as is frequently the case, a neotype is selected and so designated by someone
who subsequently revises the taxon, and the neotype occupies a position equivalent to that of
the holotype. The first type validly designated has priority over all other type specimens.
Paratypes are specimens used, along with the holotype, in the original designation of a new
form; they must be part of the same series (i.e., collected at the same immediate locality and
at the same time) as the holotype.

For a taxon above the species level, the type is a taxon of the next lower rank. For a genus,
for instance, it is a species. From the level of the genus to that of the superfamily there are
rules regarding the formation of a group name from the name of the type group. The genus
HOMO (human beings) is the type genus of the family Hominidae, for example, and the code
forbids its removal from the family Hominidae as long as the Hominidae is treated as a valid
family and the name HOMO is taxonomically valid. Whatever the remainder of its contents,
the family that contains the genus HOMO must be the Hominidae.

Indiscriminate collecting is of little use today, but huge areas of Earth are still poorly known
biologically, at least as far as many groups are concerned, and there remain many groups for
which the small number of properly collected and prepared specimens precludes any
thorough taxonomic analysis. Even in well-studied groups, such as the higher vertebrates,
new methods of analyzing material often necessitate special collecting. The determination of
variation within species or populations may necessitate the study of more specimens than are
available, even when (as is usual) the specialist can utilize material from many institutions.
Usually, collecting is done to fill gaps (in geographical range, geological formations, or
taxonomic categories) already brought to light by specialists reviewing the available material.
The well-informed collector of living things knows where to go, what to look for, and how to
spot anything especially valuable or extraordinary.

The actual techniques of collecting and preserving vary greatly from one group of organisms
to another—soil protozoa, fungi, or pines are neither collected nor preserved in the same
manner as birds. Some animals can be preserved only in weak alcohol, but others macerate
(decompose) in it. Certain earthworms “preserved” in weak alcohol simply flow out of their
own skins when lifted out. Special methods are used after long experience to preserve
characters of special value in taxonomy. Some methods make specimens difficult to observe;
this is especially true of material that has to be sectioned or otherwise made into preparations
suitable for microscopic observation.

After taxonomic material has been collected and preserved, its value can be lost unless it is
accurately and completely labeled. Only rarely is unlabeled or insufficiently labeled material
of any use. The taxonomist normally must know the locality of collection of each specimen
(or lot of specimens), often the habitat (e.g., type of forest, marsh, type of seawater), the date,
the name of the collector, and the original field number given to the specimen or lot. To this
information is added the catalog number of the collection and the sex (if not already
determined in the field and if relevant). The scientific identity of the specimen, as determined
by an acknowledged specialist, is usually added to the label at the museum. Also included is
the name of the specialist who identified the specimen. Later revisions of the classification
and additional knowledge of the organism may result in later alterations of the scientific
name, but the original labels must still be kept unaltered.

Other information may also be required. For example, the males and females of some insect
groups are extremely different in appearance, and males and females of the same species may
have to be identified. The capture of a pair in the wild actually in copulation gives a strong
(but, surprisingly, not absolute) indication that the male and female belong to the same
species; the labels of each specimen (if they are separated) indicate the specimen with which
it was mating.

Evaluating taxonomic characters

Comparison of material depends to some extent on the purposes of the comparison. For mere
identification, a suitable key, with attention given only to the characters in it, may be enough
in well-known groups. If the form is likely to be a new one, its general position is determined
by observing as many characters as possible and by comparing them with the definitions and
descriptions in a natural classification. The new specimen is compared with its nearest known
relatives, usually with reference to type material. Any character may be of taxonomic use. In
general, taxonomists tend to work from preserved material, so that their findings can be
checked. For extinct forms, of course, only preserved material (fossils) is available.
Many biochemical, physiological, or behavioral characters may be at least as good as
anatomical characters for discriminating between closely related species or for suggesting
relationships. There has been a tendency to discount anatomical characters, but, when they
are obtainable in quantity (as for most plants and animals), they probably represent as large a
sample of the effects of the organism’s heredity as can be got, short of complete genetic
analysis. Enthusiasts in genetics often stress that the only real basis for classification is the
actual genotype of each organism—i.e., the hereditary information by which the organism is
formed. It is impossible to obtain such information for extinct forms, and the time required to
obtain it for most existing ones would be enormous, even if the techniques were available. An
important development, however, has been the hybridization technique employing
deoxyribonucleic acid (DNA), the substance by which hereditary information is coded. With
this technique, it has been possible to determine similarities in parts of DNA molecules from
different organisms but not the nature of their differences.

In making comparisons, resemblances resulting from convergence must be considered.

Whales and bony fishes, for example, have similar body shapes for the same function—
progression through water. Their internal features, however, are widely different. In this case,
the convergence is evident because of the large number of characters that link whales to other
mammals and not to the fishes and because the fossil record for the vertebrates provides a fair
indication of the actual evolutionary sequence from primitive fishes through primitive
amphibians to primitive reptiles, mammal-like reptiles, and mammals. In the absence of a
good fossil record, it may be difficult or impossible to positively identify a case of
convergence, yet it has been asserted that the occurrence of convergence must not be stated
unless it has been “proved.” To obey this assertion would be to make the method of analysis
dictate in part the results achieved.

In some forms, especially internal parasites, great modification has occurred in adapting to a
parasitic way of life.The parasite is unrecognizable as a close relative of the barnacles
(crustaceans not far removed from the crabs themselves) without the free-swimming larval
stage, which shows its affinities. Transient or inconspicuous characters may be of great
importance in indicating affinities; the complete life cycle of a specimen may have to be
observed before its affinities can be determined. Although such characters may be useless for
identification and for definition of a natural group if only a few forms in a group show them,
they may be of the utmost importance in understanding relationships. Characters are therefore
weighted to some extent by the taxonomist according to their utility for different purposes.
Any characters intrinsic to the organism can be used in classification. Extrinsic characters,
including the position of fossils in a geological sequence and geographical distribution of
fossil and recent forms, may force the taxonomist to look more closely at the intrinsic
characters.

Weighting or non-weighting (i.e., by the degree of importance) of characters has been a

subject of great dispute. On the one hand, it has been pointed out that weighting is often
demonstrably arbitrary and always imprecise. On the other, it has been said that if characters
were actually examined without weighting, some obvious cases of extreme convergence
would have to be classed with each other instead of in their proper place. A classification
based on un-weighted characters is called a phenetic one (based on appearances) as opposed
to a phyletic one (based on evolutionary change within a single line of descent), in which
characters are weighted by their presumed importance in indicating lines of descent. The
quarrel results in part from a misunderstanding of aims.

At present, the classification of living things is a rough, non-quantitative sketch of their

diversity. A properly surveyed map of this diversity would advance classification
enormously. If, on such a map, the diving petrels (PELECANOIDES) of the Southern
Hemisphere and the little auk (PLAUTUS) of the Northern Hemisphere were closer to each
other than to their own phylogenetic relatives (the other petrels, fulmars, and albatrosses; and
the guillemots, terns, gulls, and shorebirds, respectively), this would show the extent of their
convergence, which is certainly great, but it would not be a reason for combining them in a
separate group. In recent years numerical techniques have been developed for estimating
overall resemblance or phenetic distance. For these methods, it is necessary to use large
numbers of characters taken from each form and, as far as possible, at random; this involves
enormous labour.The mathematical techniques are not as yet wholly satisfactory, some
having been borrowed from statistical analysis and applied to taxonomic problems without
any consideration of whether they were designed to answer the questions asked by the
taxonomist.

It is worth noting that if there were a complete fossil record for any group, then simply
placing any form nearest to those most like it (which must be its immediate ancestors or
descendants) would produce an arrangement in which all cases of parallelism and
convergence would be revealed. Since evolution occurs by descent with modification, this
arrangement would presumably reflect the greatest use of the information available about the
group and thus would also be the most useful general arrangement. For such groups, the
phenetic arrangement is the phyletic one also.

Making a classification

When some idea has been obtained of the constituent forms in a group and of the similarity
and dissimilarity that they bear to each other, it is necessary to fit a hierarchical system to
them. As already indicated, for groups with good fossil records, a dendritic, or branching,
arrangement is desired, and classification must be partly arbitrary because of lack of
knowledge. If the taxonomist has two compact groups of species, those within each group
agreeing closely with each other in many characters and differing sharply from members of
the other group in others, there is no difficulty in classification except in ranking. If each
group contains a scattering of forms, any one close to another but the most divergent
members in each group less like each other than they are like certain of the other group,
breaking up the groups into definite classes becomes arbitrary.

A particularly difficult case arises when these forms also occur in time series: the present-day
dogs, cats, hyenas, and other carnivores differ greatly from each other, but at one time their
ancestors were much alike; presumably, therefore, they came from one ancestral stock.
Paleontologists trace back each taxonomic line and are inclined to carry their separations of
taxonomic groups as far backward in time as possible, until the earliest members of related
groups are far more like each other than each is to the rest of the later members of the group
to which it is assigned. This separation of groups is extreme phyletic splitting, but cutting off
a large basal group containing all the primitive members may require arbitrary breaks in the
many lines of descent and will obscure the evolutionary relationships. There is no answer to
this dilemma except to avoid extremes.

A similar difficulty arises when the same character complex has arisen independently in
related lines. The American paleontologist George Gaylord Simpson, for example, pointed
out that mammalian characters such as the single jawbone (dentary) have arisen several times
in groups of the extinct mammal-like reptiles. To use Sir Julian Huxley’s useful terminology,
the definition of the Mammalia expresses a grade of organization (the attainment of a
particular level of advancement), not a clade (a single phyletic group or line). Some
taxonomists insist that in an evolutionary classification every group must be truly
monophyletic—that is, spring from a single ancestral stock. Usually, this cannot be
ascertained; the fossil material is insufficient or, as with many soft-bodied forms, nonexistent.
Definite convergence must not be overlooked if it can be detected.

How far groups should be split to show phyletic lines and what rank should be given each
group and subgroup thus is matters for reasonable compromise. The resulting classification, if
fossils are unknown, may be frankly “natural” or phenetic, as is often explicitly the case with
the flowering plants and is actually the case with many animal groups. If sufficient fossils are
available, the resulting classification may be consonant with what is known about the
evolution of the group or with what is merely conjectured. In reality, many classifications are
conjectural or tendentious, and simpler and more natural ones might be closer to the available
facts.

Even when only mere fragments are dealt with, a classification of some sort may still be
necessary. Large numbers of leaves, some stems, trunks or roots, many seeds, and few
flowers are known as fossils and may be of interest to the evolutionist. It may be many
decades before a particular sort of fossilized leaf can be associated with a particular sort of
branch, let alone trunk, flower, or seed. It is customary to construct form groups (i.e., a genus
or species name is assigned to the fossilized material on the basis of its structure) in order to
classify fossilized remains and to give them valid binomial names. When (if ever) two or
more bits of fossil material are identified as belonging to one organism, one name only is
retained. This procedure is best known for plants, but one phylum of animals (the Conodonta)
is made up of enigmatic structures that are obviously some part of something animal.

Current systems of classification

DIVISION OF ORGANISMS INTO KINGDOMS

As long as the only known plants were those that grew fixed in one place and all known
animals moved about and took in food, the greater groups of organisms were obvious. Even
in the time of Linnaeus, however, many biologists wondered about such animal groups as
corals and sponges, which were fixed in position and in some ways even flowerlike.

A more serious problem of classification arose with the invention of the microscope and the
discovery of microscopic forms of life. It became apparent that many of these
microorganisms held both animal and plant characteristics and could not simply be classified
in either kingdom. For example, EUGLENA is a unicellular organism with
chlorophyllcharacteristic of a plant, yet with such animal features as an eyespot and
locomotion by means of a flagellum.

Some microorganisms are parasitic inside animals and ingest complicated materials as food,
while related microorganisms obtain their nutrients through photosynthesis. It has been
proposed that the unicellular forms of microorganisms be placed in a separate kingdom, the
Protista. Some biologists do not find this to be a happy solution, however, as some of the
“unicellular” plants occur in “colonies” of various numbers of cells and may even have
specialized reproductive cells.

In the mid-20th century, biologists recognized two vastly different cell types, procaryote
(prokaryote) and eucaryote (eukaryote), and based a division of the living and extinct world
on these two broad categorizations. The divisions were based primarily on the absence or
presence, respectively, of a membrane-bound nucleus containing the genetic material of the
cell, as well as on other organizational and structural features. Many classifications of living
organisms adopted such a division and further created two superkingdoms, Prokaryota and
Eukaryota. Within the Prokaryota was placed the kingdom Monera (the bacteria, blue-green
algae, and a recently described bacterial group called the Archaebacteria (also called
Archaeobacteria). The Eukaryota comprised all other living organisms.

Viruses are far more difficult to classify. They are known only as parasites; no free-living
forms have been found. They have a far simpler structure than bacteria and reproduce by
injecting their hereditary material, which is either deoxyribonucleic acid (DNA) or
ribonucleic acid (RNA) but not both (as in all other living things), into cells of other
organisms. In effect, viruses utilize the host’s protein-synthesizing mechanism to reproduce.
The individual virus particle (virion), therefore, does not grow and divide by fission as do
bacteria. Some biologists have speculated that viruses are genes that have gotten out of
control and become parasitic; others have denied that viruses can be considered living at all.
Many are highly important disease producers in plants, animals, and bacteria.

The principal characteristic shared by bacteria and viruses is that the hereditary material is
not contained within a special nuclear membrane. Such a prokaryotic condition might be
postulated by evolutionists as primitive when compared with forms with a complex nucleus,
as in eukaryotic organisms. Viruses as they now exist may be the simplest of living things,
but it is not known how much they are modified from ancestral forms that are assumed not to
have been parasitic and that were evidently on the main line of evolution; nor is their relation
to bacteria known.

Another prokaryotic group, the blue-green algae, is traditionally placed with the other algae
(e.g., seaweeds) and studied more by botanists than by microbiologists. Blue-green algae may
be either unicellular or filamentous, and they behave like true plants, photosynthesizing in a
way that resembles green plants rather than bacteria. Many move by gliding, as do some
bacteria and some true unicellular algae. They are often extremely abundant around hot
springs or at the edges of muddy ponds, and, though they are resistant to harsh environments,
blue-green algae are killed by many drugs (e.g., antibiotics) used against bacteria. Perhaps
they are best regarded as representing a group close to the main evolutionary line that gave
rise to the eukaryotic plants.

Another problem relates to the position of the fungi, a large group including such familiar
forms as mushrooms, toadstools, molds, and yeasts. (Although some authorities place the true
slime molds (Myxomycetes)with the fungi, others point to the many characteristics they share
with the protists.) The fungi are eukaryotic, lack chlorophyll (and therefore cannot
photosynthesize as do green plants), and have rigid walls to the “cells,” or filaments (hyphae)
that sometimes contain cellulose, as do green plants. Some fungi walls or filaments are made
of chitin, the major constituent of the external skeleton of insects and other arthropods, or
even of other structural compounds. A fungal “cell” usually contains many nuclei. Asexual
and sexual spores are usually produced; some produce motile spores with flagella, like the
spores of some algae. The sexual cycle is often very complex. Because fungi in general grow
and produce “fruit” like ordinary plants, they have traditionally been included with them, but
the differences between the fungi and the plants seem considerable.

The preceding considerations exemplify the difficulties inherent in producing a generally

accepted classification, even at the highest levels. Since the earliest attempts at classifying the
living world into two kingdoms, Plantae and Animalia, biologists have debated the
relationships among all organisms. Most biologists, however, accept the fundamental
differences in cell structure that separates the superkingdoms Eukaryota and Prokaryota.

The two-kingdom classification of organisms has not been a suitable alternative since the
discovery of a microscopic group of organisms. One four-kingdom classification (Table)
recognizes the kingdoms Virus, Monera, Plantae, and Animalia within the superkingdoms
Prokaryota and Eukaryota. Separate kingdoms are not recognized for the microorganisms
(Protista) or for the fungi, which are placed in the plant kingdom. Another classification
recognizes Protista (including the fungi and protozoans) rather than viruses.

The four-kingdom scheme of classification

kingdom members

Virus

Monera bacteria, blue-green algae, archaebacteria, and prochlorophytes

algae, slime molds, true fungi, bryophytes (mosses, liverworts, and hornworts),
Plantae ferns, psilophytes, lycopodiophytes, conifers, gnetophytes, ginkgophytes, cycads,
and flowering plants

protozoans, sponges, corals, flatworms, tapeworms, arthropods, mollusks, lamp

Animalia shells, annelids, bryozoans, echinoderms, hemichordates, and chordates, including
the vertebrates

A classification of living organisms

Recent advances in biochemical and electron microscopic techniques, as well as in testing

that investigates the genetic relatedness among species, have redefined previously established
taxonomic relationships and have fortified support for a five-kingdom classification of living
organisms. This alternative scheme is presented below and is used in the major biological
articles. In it, the prokaryotic Monera continue to comprise the bacteria, although techniques
in genetic homology have defined a new group of bacteria, the Archaebacteria, that some
biologists believe may be as different from bacteria as bacteria are from other eukaryotic
organisms. The eukaryotic kingdoms now include the Plantae, Animalia, Protista, and Fungi,
or Mycota.

The protists are predominantly unicellular, microscopic, nonvascular organisms that do not
generally form tissues. Exhibiting all modes of nutrition, protists are frequently motile
organisms, primarily using flagella, cilia, or pseudopodia. The fungi, also nonvascular
organisms, exhibit an osmotrophic type of heterotrophic nutrition. Although the mycelium
may be complex, they also exhibit only simple tissue differentiation, if any at all. Their cell
walls usually contain chitin, and they commonly release spores during reproduction. The
plants are multicellular, multitissued, autotrophic organisms with cellulose-containing cell
walls. The vascular plants possess roots, stems, leaves, and complex reproductive organs.
Their life cycle shows an alternation of generations between haploid (gametophyte) and
diploid (sporophyte) generations. The animals are multicellular, multitissued, heterotrophic
organisms whose cells are not surrounded by cell walls. Animals generally are independently
motile, which has led to the development of organ and tissue systems. The monerans, the
only prokaryotic kingdom in this classification scheme, is principally made up of the bacteria.
They are generally free-living unicellular organisms that reproduce by fission. Their genetic
material is concentrated in a non-membrane-bound nuclear area. Motility in bacteria is by a
flagellar structure that is different from the eukaryotic flagellum. Most bacteria have an
envelope that contains a unique cell wall, peptidoglycan, the chemical nature of which
imparts a special staining property that is taxonomically significant (i.e., gram-positive,
gram-negative, acid-fast).

The use of “division” by botanists and “phylum” by zoologists for equivalent categories leads
to a rather awkward situation in the Protista, a group of interest to both botanists and
zoologists. As used below, the terms follow prevailing usage: phylum for the primarily
animal-like protozoa and division for other protistan groups that are more plantlike and of
interest primarily to botanists.

The discussion above shows the difficulty involved in classification. For example, one
traditional classification of the Aschelminthes, presented below and in the article
aschelminth, divides the phylum Aschelminthes into five classes: Rotifera, Gastrotricha,
Kinorhyncha, Nematoda, and Nematomorpha. An alternative classification elevates these
classes to phyla, and still another classification establishes different relationships between the
groups—phylum Gastrotricha, phylum Rotifera, phylum Nematoda (containing classes
Adenophorea, Secernentea, and Nematomorpha), and phylum Introverta (containing classes
Kinorhyncha, Loricifera, Priapulida, and Acanthocephala). The true relationships between
these pseudocoelomates remain to be established.
 1.2 SIGNIFICANCE OF TAXONOMY

Taxonomy is the science of classifying organisms. At no time there has been a greater need
for taxonomists than now when the crisis facing biodiversity is escalating. Decision 11/8 of
the second meeting of the Conference of Parties to the Convention on Biological Diversity
(CBD) identified the lack of sufficient taxonomists as a significant impediment for
implementing the decisions of the convention at national as well as international levels. Over
the past half a billionyears the world lost perhaps one species per million species each
yearincluding everything from mammals to plants and today the annualrate of extinction is
estimated to be 1000 to 10000 times faster(Wilson,2003). This is really a matter of grave
concern for all thosewho think that our biodiversity is precious and should be protected. Itis
also known now that sentineling extinctions take place on manyregions of the world today
and not merely a thing of the past whichhappened in that cloud forest of the Western Ecuador
in 1978-1980.Besides we are quite ignorant of the real magnitude of the world’s bio-
diversity. The audit of biodiversity today is far short of a reality.Though opinions on the
biodiversity of the world differ from 5-100million(Wilson,2003) species, a ‘best guess’ or
mid-way on the road, places it at 14 million living species today (Cherian,2004). Amongthese
fewer than 2 million species of organisms are scientifically identified and named. At the
current pace of taxonomic research, it may require 5000 taxonomists to complete merely the
taxonomic listing of5 million species in 25-30 years if one taxonomist can deal with
1000species. Our efforts to conserve our biodiversity will be much easier ifwe know the basic
units that are species and their relationships.Taxonomy provides discovery and identification
of these basic unitsand their relationships (Narendran, 2006, 2008).Taxonomy is the basis for
all meaningful studies on biodiversity,pest management, medicine, bioprospecting, fisheries,
quarantine,defense etc. Before initiating any kind of studies, it is absolutely essential to know
the correct name of the organism on which the studies areinitiated. This is important because
the correct scientific name of theorganism is a functional label, using which various pieces of
information concerning that organism, including all the past work done on it,can be retrieved
and stored ensuing ease of reference and stored ensuring easy reference (Narendran 2000).
Taxonomy plays animportant role in pest management programmes. When natural enemies
are being sought or transferred from one region to another in bio-logical control projects, the
correct identification of both the pest andthe natural enemy species is of great importance
(Narendran2003).History and experience have already shown that absence of taxonomic
expertise have resulted in the failure of several pest managementprogrammes resulting in
tremendous loss of agricultural products as well as huge amount of money. There are several
instances in the history of pest management to show that failures resulted because
taxonomists were not consulted in the identification of the pest or its natural enemies before
starting the pest management programmes especially biological control programmes against
insect pests. Without thehelp of taxonomists biological control workers may commit
severalmistakes (Schauff & LaSalle, 1998; Narendran 2001, 2003,2006). Theymay
inadvertently import a species of natural enemy that may bealready present in the country of
introduction. They may spend sever-al days studying the biology of a species that may have
already beendone under an unpublished or published synonym of the species. Thebiological
control workers may spend a lot of money and effort in ship-ping, curation, breeding etc of
wrong species of natural enemies suchas hyperparasites or natural enemies that do not attack
target hostspecies etc. Preservation of taxonomic collections has very greatimportance since
they may prove to be of immense value in biologicalcontrol projects.

Quarantine agencies often seek help of taxonomists to determinewhether an imported plant or

animal is harmful or not and based onthe advice of taxonomists, prevent the entry of harmful
organisms. In these days of germ warfare, it is necessary to seek help of taxonomistsfor the
identification of organisms introduced to a country by enemies. Besides these, taxonomist’s
help can be made use of in many otherfields such as medicine, fisheries, academic studies
and many otheruseful fields. In spite of all these important aspects, taxonomy is stillnot
adequately developed in the underdeveloped and developing countries like India. Taxonomy
involves hard field oriented work. It needscareful observation, analytical mind and a little
above average of intelligence to analyses and in weighting of a taxon to determine it at
speciesor infraspecific level. In some cases several days or even months maybe necessary to
arrive at a proper conclusion in determining the identity of a taxon. In several other instances
wide ranging discussions andconsultations with experts working on the group or related fields
arenecessary for taking a decision in the identification process. Yet thereare many workers of
other fields of specialization who consider taxonomy is an out dated subject and not worthy
of doing. These critics havemy optic vision that has lost sight of the whole wonderful world
of unexplored fauna and flora which await discovery by taxonomists. In orderto understand
taxonomy it is absolutely essential to have an impartialnon-biased mind with a curiosity to
find the undiscovered fauna andflora and with strong will to undertake hard work. It is ironic
to notethat often the very same people who criticize taxonomy approachestaxonomists for
prompt and urgent identification of the specimensthey want to work with. There are various
subdivisions in Taxonomy and among these themost commonly used one is the Classical
Taxonomy which is the con-ventional taxonomy based mainly on external morphology which
isoften supported and supplemented by ethological and ecological data.Some taxonomists
base their classification on greater number of characters from many sets of data in order to
produce an entirely phonetic classification and this is known as Numerical Taxonomy. It is
based onphenetic similarities and maximum number of characters (morpholog-ical,
behavioral, karyological, etc) and each character is given equalweight. Molecular taxonomy
is relatively a recent research branch oftaxonomy, invaded often by prejudiced workers of
molecular biology.It includes DNA barcoding, analyses of isosymes, molecular cytogenetics
and a number of other related techniques. Recently many biologists have turned their interests
to DNA bar-coding technique for taxonom-ic identification. DNA bar coding is a taxonomic
method which uses ashort genetic marker in the mitochondrial DNA (mtDNA) of an organ-
ism so as to identify that organism as belonging to a particular species.Though molecular
taxonomy has its usefulness, it has several demeritstoo. For identifying two unknown
organisms, species or subspecies itwould be difficult to use this method. The main problem is
the distribution of variability within and between species. Long periods of independence
allow variability within groups pose a serious stumblingblock in molecular taxonomy
(Narendran, 2006). DNA bar coding does not provide reliable information above species
level. It is also now known that recently diverged species might not be distinguishable on the
basis of DNA bar coding (CO1 sequences). One of the main differences between molecular
taxonomy and classical taxonomy is that theformer uses a technique such as DNA bar coding
which is nothing butan over simplification of the science of taxonomy. Classical taxonomyon
the other hand has a holistic approach, treating each organism as awhole and it is not
described in vacuum but in comparison with otherorganisms, objects and substances
(Grimaldi and Engel, 2007). A liv-ing organism expresses its identity in the way it organizes
its variousparts and how it relates to the environment. In molecular technique(DNA bar
coding) an organism is nothing but a DNA sequence. Inorder to understand a living organism,
it is absolutely essential to havea holistic approach establishing a relationship with it and such
relationships are possible only by looking or sensing an organism as awhole and not by bar
codes (Katz, 2005). This is not to state thatmolecular taxonomy is not useful and classical
taxonomy is better.Genomic bar coding is definitely useful as a supplementary tool
toclassical taxonomy (especially in differentiating sibling species) andnot to replace it
completely. The problem, as Grimaldi and Engel(2007) point out is that high tech
descriptions (such as molecular taxonomy) are seen by some as more scientific and this view
is not accept-able to many scientists who believe that all branches of science isimportant
especially when classical taxonomy is still making startlingdiscoveries(for instance discovery
of a new insect order recently viz.Matophasmatoidea) even now. As Ogura (1964) pointed
out classicaltaxonomy will continue to reign supreme many more years to come.The article
7(a) of the convention of of Biological Diversity statesthat the countries which signed the
biodiversity document, have toundertake an inventory of biological diversity in order to
provide fundamental information on the distribution and abundance of biodiversity. Such data
are necessary for the long-term sustainable management, use and conservation of bio diverse
area. The fourth meeting onCBD held at Darwin (Australia) in 1998 stated that the various
countries which participated in the meeting, affirmed the existence of a taxonomic
impediment for the proper management and conservation ofworld’s biodiversity. Removal of
these impediments is very essentialnot only for discovering and understanding the world’s
biodiversitybut also for global efforts to conserve our biodiversity. The mainimpediments
include shortage of man power in taxonomic work, lackof adequate funding for taxonomic
research, lack of training in taxonomy from higher secondary school level, lack of library
facilities fortaxonomic studies and lack of adequate taxonomic centers not only
foridentification but also for giving adequate training in taxonomy besides many other
impediments. There are many requirements for removing these taxonomic impediments and
some of the major onesare: 1) Taxonomy (all aspects from Classical to molecular) should
beincluded as a compulsory subject in the curriculum and syllabi fromhigher secondary
school level to postgraduate levels.; 2) enough fundsshould be given to taxonomists or to
non-governmental and govern-mental organizations and institutes for meeting the cost of
publishingpapers and monographs in taxonomy) creating enough employment opportunities
for taxonomists etc are some of the major requirements to be met with by the respective
countries which signed the bio-diversity document. It is high time we set our priorities
straight for thedevelopment of all aspects of taxonomy without being prejudiced orbiased to
any any aspect of taxonomy. More and more students shouldtake up taxonomy as their
carrier. “Taxonomy... is no less attractive, challengingly difficult, satisfying and productive
than most sophisticated, spectacularly dramatic biological experiments currently in fashion-
here is an unknown and a new world, literally at our door step, fordiscovery, exploration and
conquest “ (Mani, 1989).
1.4 APPLICATIONS OF TAXONOMY

Taxonomy is a hierarchical structure for the classification and/or organization of data. In

content management and information architecture, taxonomy is used as a tool for organizing
content.A taxonomy is an organizing principle. It is a foundation on which to base any kind
of information system. It does not matter what kind of project you are involved in, it will
benefit from clearly defined, concise language and terminology.A taxonomy and controlled
vocabulary help to fine tune search tools, they creates a common language for sharing
concepts, and it allows an efficient organization of documents and content across information
sources.Taxonomy is very important in content management. It ensures that search and
navigation work properly and that content is accessible and can be found via two access
points: searching and browsing.

Taxonomy is organized by supertype-subtype relationships, also called generalization-

specialization relationships, or less formally, parent-child relationships. Once a taxonomy
tree has been created, all the items in the tree are tagged as belonging to one or more specific
taxonomy categories. This process is typically referred to as "categorization", "tagging" or
"profiling". Users can then browse and search within specific categories.

In such an inheritance relationship, the subtype by definition has the same properties,
behaviors, and constraints as the supertype plus one or more additional properties, behaviors,
or constraints. For example: a bicycle is a kind of vehicle, so any bicycle is also a vehicle, but
not every vehicle is a bicycle. Therefore a subtype needs to satisfy more constraints than its
supertype. Thus to be a bicycle is more constraint than to be a vehicle.

Historically used by biologists to classify plants or animals according to a set of natural

relationships, in content management and information architecture, taxonomy is used as a
tool for organizing content. Creating taxonomy is central to any enterprise content strategy as
means of organizing content so that it could be found by either searching or browsing.

Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists

known as "taxonomists", though enthusiastic naturalists are also frequently involved in the
publication of new taxa.Because taxonomy aims to describe and organize life, the work
conducted by taxonomists is essential for the study of biodiversity and the resulting field of
conservation biology.
Biological classification is a critical component of the taxonomic process. As a result, it
informs the user as to what the relatives of the taxon are hypothesized to be. Biological
classification uses taxonomic ranks, including among others (in order from most inclusive to
least inclusive): Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, and
Strain.

Taxonomy in Biodiversity Conservation

Taxonomy usually refers to the theory and practice of describing, calling, and categorizing
living things. Such work is necessary for the fundamental understanding of biodiversity and
its conservation. Yet the science behind delimiting the natural world into “species” is
frequently ignored, misconstrued, and even derided in some quarters.

Most people concerned about biodiversity conservation commonly utilize the term “species”
without a clear understanding of what separates one species from another, and why. This is
where the science of taxonomy plays an integral role. Species are differentiated from each
other in a number of methods.

Although the meaning of species has been the cause of the substantial historic argument, in
other words, species are organisms usually acknowledged as morphologically distinct from
other groups.

Taxonomy in Biological Control

In biological control, the insect species, its possible area of origin, and, consequently, the area
where promising natural enemies may be discovered, is determined. The close co-operation
of taxonomists throughout pre-and post-release studies of natural opponents in target areas
helps to show the native fauna present and the advancement of a biological control
programmed.

Biological control programs should budget for appropriate taxonomic research studies in
locations where the local fauna is inadequately known. Advising regional scientists on the
proper collection, preservation, and identification of appropriate indigenous and unique
species should be emphasized.

Taxonomy to Combat Invasive Alien Species

Taxonomic information is vital for firms and border authorities to find, manage, and control
Invasive Alien Species (IAS). Reliable control and management steps can just be carried out
when unique species are properly and immediately determined. Misidentifications can cost
money when rapid choices need to be taken.

Networking and sharing of experiences, details, and know-how can help in decreasing the
costs related to IAS and lower the need for elimination programs with early detection and
prevention. When elimination is required, taxonomists can provide proficiency that is central
to develop the most efficient yet economic and ecologically benign eradication procedures.

Increased capacity-building (especially for developing countries) is necessary to determine,

record, and display intrusions; provide existing and available lists of possible and recognized
IAS; determine potential risks to neighboring countries; and to access info on taxonomy,
ecology, genes, and control approaches.

It is vital that nearby nations, and all countries along a specific pathway for invasive species,
can acknowledge such species and concur on their nomenclature. Baseline taxonomic details
on native biota at the nationwide level is likewise important to make sure that IAS can be
acknowledged and distinguished from naturally present species.

Taxonomy in Agriculture and Forestry

Recently we have faced an unpleasant problem of conserving our crops and trees from the
attack of many different sorts of pests (Locusts). It is extremely important to understand the
right category names of such insects prior to their proper control.

Every species has its own different niche in nature and varies from its associated types in
food partiality, mating seasons, tolerance or resistance capability to numerous stimuli,
predators, rivals, pathogens, and so on and all these are extremely crucial for an applied
worker before applying control procedures.

All this crucial information can be quickly obtained by group screening of the insect, if the
identity of the insect is sometimes known, it is also really helpful to have a regional
observation of the process of triggering so much damage of the crop on getting proper
identification of the insect species, it ends up being simpler to collect details about its
practices which is essential for its effective control.

Taxonomy in Wildlife Management

The primary role of a taxonomist is the organization of classes of living organisms, about
which scientifically helpful indicative generalizations can be made. The primary function is
to distinguish the different sorts of organisms and by explaining their characteristics through
descriptions, keys, figures, and so on. Should need to provide names for each individual
organism, so that the info can be recorded, saved, and reclaim when needed.

To make a set of principles based on the option and importance of characters with the
ultimate objective of organizing species in the hierarchy of greater categories.

Estimate genetic and phylogenetic relationships amongst organisms.

Taxonomy in Public Health

Taxonomy plays a fantastic function in public health management. There are a variety of
different kinds of diseases that are spread by many arthropods, bugs which are disease-
specific. So, we must prepare the control strategy in such a way that only the target species is
assaulted. This is only possible if we get the correct identification of that species. For
example, some species of anopheles mosquitoes are responsible for transmitting malaria
however the other species not.

Ticks are vectors of nematodes, protozoa, rickettsia, spirochetes, other bacteria, and infection
that cause diseases in human beings and other animals.

Taxonomy plays a crucial role in the recognition of these interactions. The control system
then used just on the target species and in this a method of cash and workforce was conserved
and the loss can be stopped. This right recognition guarantees an optimum of efficient control
at minimum expense.
 UNIT 2: MODERN APPROACHES IN TAXONOMY

2.1 Objectives
2.2 Introduction
2.3 Chemotaxonomy
2.4 Cytotaxonomy
2.5 Neotaxonomy and Molecular Taxonomy
2.6 Summary
2.7 Terminal Questions and Answers

2.1 OBJECTIVES

The Study of Chemotaxonomy, Cytotaxonomy& Neotaxonomy and Molecular Taxonomy.

2.2 INTRODUCTION

Taxonomists now accept that, the morphological characters alone should not be considered
in systematic classification of plants. The complete knowledge of taxonomy is possible with
the principles of various disciplines like Cytology, Genetics, Anatomy, Physiology,
Geographical Distribution, Embryology, Ecology, Palynology, Phenology, Bio-Chemistry,
Numerical Taxonomy and Transplant Experiments. These have been found to be useful in
solving some of the taxonomical problems by providing additional characters. It has changed
the face of classification from alpha (classical) to omega (modern kind). Thus the new
systematic has evolved into a better taxonomy.

2.3 CHEMOTAXONOMY

Various medicines, spices and preservatives obtained from plant have drawn the attention of
Taxonomists. Study of various chemicals available in plants help to solve certain
taxonomical problems. Chemotaxonomy is the scientific approach of classification of plants
on the basis of their biochemical constituents. As proteins are more closely controlled by
genes and less subjected to natural selection, it has been used at all hierarchical levels of
classification starting from the rank of ‘variety’ up to the rank of division in plants. Proteins,
amino acids, nucleic acids, peptides etc. are the most studied chemicals in chemotaxonomy.
The chemical characters can be divided into three main categories.

1. Easily visible characters like starch grains, silica etc.

2. Characters detected by chemical tests like phenolic, oil, fats, waxes etc.

3. Proteins

SIGNIFICANCE OF CHEMOTAXONOMY:

The occurrence and distribution of the various types of chemical substances present in plants
prove to be of taxonomic significance. However, it should be noted that, all kinds of chemical
substances present in plants do not reveal information useful to the taxonomist.
Phytochemical characters of taxonomic significance have been classified into three types.

These include:

a. Primary constituents:

These include the macromolecular compounds directly taking part in metabolism and include
proteins, nucleic acids, chlorophyll and polysaccharides. All chemical materials synthesized
by an organism reflect the information in DNA, RNA and proteins. These latter molecules
have been termed as semantides. Semantides, thus contain useful information of taxonomy
and phylogeny.

b. Secondary constituents:
They include compounds lacking nitrogen and not involved directly in plant metabolism i.e.,
simple phenolic compounds like caffeic, benzoic and nicotinic acids and polyphenolic
compounds like flavonoids, terpenes, coumarines, alkaloids and pigments of which
flavonoids are most widely studied with respect to plant systematics.
c. Miscellaneous substances:
However, no suitable classification of the chemical characters and their use in taxonomy is
developed so far. On the basis of their molecular weight, Jones and Luchsinger (1987) have
divided the natural chemical plant products useful in taxonomy, into two major groups.
d. Micro-molecules:
They are low molecular weight compounds with a molecular weight of 1000 or less, e.g.
amino acids, alkaloids, fatty acids, terpenoids, flavonoids, etc.
e. Macromolecules:

They include the high molecular weight compounds with a molecular weight of over 1,000,
e.g. proteins, DNA, RNA, complex polysaccharides, etc.

2.4 CYTOTAXONOMY

Cytotaxonomy is a branch of taxonomy that uses the characteristics of cellular structures to

classify organisms. In cytotaxonomy, the chromosomal configuration of an organism is the
most widely used parameter to infer the relationship between two organisms. The inference
of species relationships is based on the assumption that closely related species share similar
characteristics in their chromosomal setup (referred to as karyotype). By analyzing the
similarities and differences in the chromosomes, karyotype evolution and species evolution
can be reconstructed.

The number, structure, and behavior of chromosomes is of great value in taxonomy,

with chromosome number being the most widely used and quoted character. Chromosome
numbers are usually determined at the metaphase stage during mitosis. Usually,
the diploid chromosome number (2n) is referenced, unless dealing with a polyploidy series in
which case the base number or number of chromosomes in the genome of the original haploid
is quoted. Another useful taxonomic character is the position of
the centromere. Meiotic behavior may show the heterozygosis of inversions. This may be
constant for a taxon, offering further taxonomic evidence.

Often, cytological evidence is accompanied and strengthened by other analyses,

including genomics and DNA-based phylogenies.

Cytology has contributed to tracking the evolutionary history of many organisms, especially
primates and flowering plants. As example, karyotype comparisons have largely clarified the
evolution of Arabidopsis thalianaand of saffron crocus, though there are many more studies
that deserve highlighting.

SIGNIFICANCE OF CYTOTAXONOMY:

The role of cytotaxonomy is very important in taxonomic studies. Cytotaxonomy is more

significant than physiological taxonomy because it is the comparative study of chromosomes
at the molecular level. Small changes in chromosomes can be detected among the individual.
Chromosomes are constituted by the DNA, variation in the DNA leads to change in
chromosome which ultimately causes variation among the individual, species, genus and
everything.Cytotaxonomy is a part of taxonomic biology that deals with the classification of
organisms. Cytogenetic studies represent both structural and functional homologies among
taxa based on their evolutionary conservation.

A.BIOSYSTEMATICS

Biosystematics is an “Experimental, ecological and cytotaxonomy” through which life

forms are studied and their relationships are defined. The term biosystematics was
introduced by Camp and Gilly in 1943. Many authors feel Biosystematics is closer to
Cytogenetic and Ecology and much importance given not to classification but to evolution.

B.KARYOTAXONOMY

Chromosomes are the carriers of genetic information. Increased knowledge about the
chromosomes have been used for extensive biosystematics studies and resolving many
taxonomic problems. Utilization of the characters and phenomena of cytology for the
explanation of taxonomic problem is known as cytotaxonomy or karyotaxonomy.
Thecharacters of chromosome such as number, size, morphology and behaviour during
meiosis have proved to be of taxonomic value.

C. SEROTAXONOMY (IMMUNOTAXONOMY)

Systematic serology or serotaxonomy hadits origin towards the end of twentieth century
with the discovery of serological reactions and development of the discipline of
immunology. The classification of very similar plants by means of differences in the proteins
they contain, to solve taxonomic problems is called serotaxonomy. Smith (1976) defined it
as “the study of the origins and properties of antisera.”
 2.5 NEOTAXONOMY AND MOLECULAR TAXONOMY

(MOLECULAR SYSTEMATICS / MOLECULAR PHYLOGENETICS)

Molecular Taxonomy is the branch of phylogeny that analyses hereditary molecular

differences, mainly in DNA sequences, to gain information and to establish genetic
relationship between the members of different taxonomic categories. The advent of DNA
cloning and sequencing methods have contributed immensely to the development of
molecular taxonomy and population genetics over the years. These modern methods have
revolutionized the field of molecular taxonomy and population genetics with improved
analytical power and precision.

USES OF MOLECULAR TAXONOMY

1. Molecular taxonomy helps in establishing the relationship of different plant groups at

DNA level.

2. It unlocks the treasure chest of information on evolutionary history of organisms.

NEOTAXONOMY

The aim of neo-taxonomy or systematic or biosystematics is not only to describe, identify and
arrange organisms in convenient categories but also to understand their evolutionary histories
and mechanisms. Earlier approaches were primarily based exclusively on observed or
morphological data without considering intraspecific differences. Many of the species are
thus known by single or few specimens.

Recently, however, great attention is paid to sub-groupings of the species like populations
and subspecies. The old morphological species are now called biological ones, which also
includes ecological, ethological genetically and other characters. All these new approaches
have contributed greatly in explaining the true structure of the species and their evolutionary
position and in modification of the basic system of taxonomy. However most of the new
approaches need specific methods. A brief account of some of the more important current
approaches is discussed in this unit. Some of these approaches are still developing and
provide much excitement by generating new data and information. You should, however,
bear in mind that even today it is the morphological features which are used the most, as they
are most easily observed, In addition while going rough the new approaches you will realize
that data from just one approach may not be sufficient to identify organisms.

Taxonomists try as far as possible to use data from as many approaches as possible for
accurate identification. Thus today taxonomy is usually called biosystematics or systematic or
evolutionary taxonomy or neotaxonomy as it tends to place organisms which share a common
ancestor (monophyletic ancestory) within the same group. Inference of ancestory is based
upon similarity and difference among organisms. These differences and similarities are not
limited to morphological traits alone. They include a wide variety of similarities and
differences in behavior, embryological structures, and fine morphological details with the
help of electron microscopes, biochemistry, ecology, cytogenetically data and statistical data.

NEW SYSTEMATICS (NEO-SYSTEMATICS, BIO-SYSTEMATICS)

It is a concept of systematics that considers a species to the product of evolution. It takes into
consideration all the known characteristics of organisms and all the known evidence from
different fields of biology. The concept of new systematics was developed by Sir Julian
Huxley in 1940. Nonsystematic is also called biosystematics. Biosystematics is the science
through which life forms are discovered. Identified, described, named, classified and
catalogued with their diversity, life histories, living habitats, roles in an ecosystem, and
spatial and geographical distributions recorded. In essence, it is biosystematics, the science
that provides indispensable information to support many fields of research and beneficially
applied programs. The important features are:
♦ Species are not isolated. They are related amongst themselves by common descent and
differ from them due to the accumulation of different variations.
♦ The main stress is laid upon subspecies and populations instead of species. It has given rise
to the concept of population systematics.
♦ Statistical data are used to determine primitiveness or advancement of species.
♦ Morphological definition of species is replaced by biological definition. Besides
morphology, biosystematics or new systematics considers traits from cytology, genetics,
ecology, biochemistry and physiology. This has led to the origin of many branches of
systematics like: Morpho taxonomy (based on morphological traits), Cytotaxonomy (based
on cytological on biochemical studies), Chemotaxonomy (based on specific chemicals like
secondary metabolites), Numerical taxonomy (using statistical methods in taxonomy) and
Experimental taxonomy (based on experimental determination of genetic interrelationships
and effect of environment).
♦ A large number, sometimes thousands of specimens are studied to record variations before
deciding the limits of species.
♦ The basic unit in new systematics is population.
♦ The new systematics is scientific and very useful academically as well as economically.
♠ Numerical taxonomy is also called phonetic or Adansonia taxonomy (Adanson, 1763).
Turril (1938) used the term Omega (ω) taxonomy for biosystematics or new systematics. His
Alpha (α) taxonomy (Turril, 1938) deals with collection and identification of organisms on
the basis of gross morphology, a compilation of flora and monographs.
Difference between Systematics and New Systematics.

BASICS TO TAXONOMY

Classification means the ordering of organisms into groups. The branch of science that deals
with the study of principles and procedures of biological classification are called taxonomy
(A.P. de Candolle, 1813). Taxonomy enfolds the following fundamental elements:
♦Identification: Identification is determining the correct place in a system of classification
and finding out the correct name of an organism. It is done with the help of keys. It is just like
locating a title in the library on the basis of knowledge of its subject, title and name of the
author. This is carried out for an organism by determining its similarity with an already
known organism. Suppose there are three plants say a, b, c. All represent different species.
Another plant, say d resembles b. The recognition of the plant d as identical to the already
known plant b is its identification. Identification not only assigns the organisms to a
particular group and locate its correct name but also provides information if the organism is
new to systematics and requires giving a name.
♦ Nomenclature (L nomen: name; calare: call): It is the science of providing distinct and
proper specific names to organisms as per the established universal practices and rules so that
they can be easily recognised and differentiated from others.

♦ Classification: Classification is the arrangement of organisms into groups on the basis of

their affinities or relationships. It involves the placing of a kind of organisms or a group of
different kinds of organisms in particular categories depending upon the system of
classification but in conformity with nomenclature system.
NOMENCLATURE
♠ The science of giving names to living beings is called nomenclature. Two types of names
are given to the organisms, common and scientific.

COMMON OR VERNACULAR NAMES

♠ The naming of organisms has been started with the appearance of language in human
civilisation. Common names are local names, which are given to the animals and plants in a
particular language and region of the world by local persons. The vernacular or common
names are based on some peculiarity of the organisms. They are brief and easier to pronounce
and remember by the residents of an area. They give an immediate idea to the residents as to
identify the organisms. Natives become familiar with the names since childhood. Even then
the Vernacular names cannot be used by biologists due to the following reasons:
♦ Common names differ from region to region and language to language. An organism may
have several names in a given language.

♦ A common name may have different meanings in different areas.

♦ An organism may have several names in a given language.

♦ A single common name is often given to more than one organism.

♦ There is no uniformity in common names.
♦ Certain common names are misleading and insignificant. For example silverfish (Lepisma,
an arthropod), cuttlefish (Sepia, a mollusc), Jellyfish (Aurelia, a coelenterate), starfish
(Asterias, an echinoderm), etc., create confusion in identifying exactly the desired organism.
The common names ‘kiss me quick’ for Euphorbia Milli, ‘widow’s tear’ for Tradescantia and
‘love in mist’ for the plant Nigella damascena are simply fantastic and also without
significance.
♦ A wrong common name cannot be easily corrected.

SCIENTIFIC OR TECHNICAL NAMES

♠ Organisms must have a scientific name, which is acceptable all over the world. Such
naming must be based on agreed principles and criteria.
♠ The scientific names ensure that only one name is given to an organism and description of
the organism should help the other people to arrive at the same name in any part of the world.
Each kind of organism, representing a species, is given a different name to distinguish it from
the other. One has to ensure that such a name has not been used earlier for any other
organism. The following have been the practices of providing scientific names to the
organisms.

♦ Polynomial nomenclature: It was the first attempt of the scientists to provide scientific
names to organisms: Before 1750 (medieval periods), scholars used to add a series of
descriptive words to designate a particular species. This can be illustrated with the example
of Caryophyllum. The name given was Caryophyllum saxatile folis gramineous umbellate
corymbs meaning Caryophyllum growing on rocks having grasslike leaves and umbellate
corymb arrangement of flowers. Such long names cannot be easily remembered. These names
also varied with a selection of different characters by different taxonomists.
♦ Binomial nomenclature: The scientific names were developed by Linnaeus (Philosophia
Botanica, 1751). The standard references recognised for this are Species Plantarum (1753)
and tenth edition of Systema Naturae (1758).
The technical names recognised internationally are thus the ones given by Linnaeus in the
10th edition of his book Systema Naturae published in 1758. The system developed by
Linnaeus is known as binomial nomenclature. Binomial nomenclature is the system of
scientific naming using ‘genus’ as the first part and ‘species’ as the second part, e.g.,
Mangifera indica (mango), Apis mellifera (honey bee), Pisum sativum (garden pea), etc.

TRINOMIAL NOMENCLATURE:

Occasionally, three words are also used for naming an organism, especially the animals.
These include generic, specific and sub-species part, for example, the modern man is called
Homo sapiens sapiens. Other examples are Gorilla gorilla gorilla, Acacia ni loti ca indicia,
Ascaris lumbricoides humans, Corvus splendens insolence (Burmese crow), etc.

RULES OF BINOMIAL NOMENCLATURE

♠ To provide uniformity, and to avoid confusion, 12th International Congress at Leningrad in

1975, laid down certain principles that were published in 1978 in the form of International
Code of Botanical Nomenclature (ICBN) and International Code of Zoological Nomenclature
(ICZN). The names of bacteria and viruses are decided by International Code of
Bacteriological Nomenclature (ICBacN or ICBN) and International Code of Viral
Nomenclature (ICVN). Similarly, there is a separate International Code of Nomenclature of
Cultivated Plants (ICNCP). The important rules are:
♦ A scientific name consists of two words, first genus and second species. They should not
have less than three letters and more than twelve letters.

♦ A general term for the word identifying the species is the specific descriptor. In zoology,
the word identifying the species is called the specific name, and in botany, the specific
epithet.
♦ The generic name is always written first, which is a noun having its first letter in capital
form. The generic name is always unique for a living organism.
♦ The specific name is written after the generic name, which is an adjective having its all
letters in small form. A botanical specific name may begin with a capital letter if it denotes a
person or a place, e.g., Pentoxylon Shanii, Tolypella Jwelli, etc. A species can be named only
if it is assigned to a genus. The same specific name can be assigned to two genera but two
species of the same genus cannot have the same specific name, e.g., Mangifera indica,
Holoptalea indica (chilbil). It can be single or compound (e.g., Hibiscus rosa-Sinensis)
♦ The gender of the specific name follows the gender of the generic name, e.g., Mangifera
indica, Tamarindus in the discus.

♦ The biological or scientific name is always printed in italics whereas it is underlined when
handwritten.
♦ All taxa at ranks above species have a name composed of one word only, a “unit nominal
name”.
♦ When used with a common name, the scientific name usually follows in parentheses, e.g.
the house sparrow (Passer domesticus).

♦ The scientific name should generally be written in full. The exception to this is when
several species from the same genus are being listed or discussed in the same paper or report;
in that case the genus is written in full when it is first used, but may then be abbreviated to an
initial for successive species name, e.g. Cycas revoluta, C. Rumph ii, C. circinalis, etc. In rare
cases, this abbreviated form has spread to more general use; for example, the bacterium
Escherichia coli is often referred to as E. coli, and Tyrannosaurus Rex is better known simply
as T. rex, these two both often appearing even where they are not part of any list of species of
the same genus.

♦ The abbreviation “sp.” is used when the actual specific name cannot or need not be
specified, e.g., Pinus sp. The abbreviation “spp.” (plural) indicates “several species”. These
are not italicised or underlined.

♦ The two-word scientific names are generally followed by the name of the discoverer or
author in scholarly texts. The author’s name can be a full or abbreviated form (i.e., Mangifera
indica L., Homo sapiens Linn., Cycas circinalis Linnaeus) in the Roman script without a
comma. Author’s name is not italicised.

♦ The abbreviation “cf” is used when the identification is not confirmed. For example,
Corvus cf. splendens indicates a bird similar to the House Crow but not certainly identified as
this species.

♦ The scientific names are derived from the Latin language as it is a dead language. When
words are used from other languages, they are Latinized with the suitable ending, e.g.,
Mangifera indica.

♦ The name of categories higher than the rank of the genus is not printed in italic so or
underlined when handwritten. Bold letters, however, can be used. e.g., Phanerogams,
Spermatophyta, Mammalia, etc.

♦ No names are recognised prior to those used by Linnaeus in 1758 in the 10th edition of
Systema Naturae.The names of subfamilies and families should be based on the name of the
type genus e.g., family Gramineae is changed to Poaceae, Compositae is changed to
Asteraceae, etc.

♦ When a species is transferred or revised, the name of the original author is retained but in
parentheses, e.g., Syzygium cumin (Linn).
♦ When a species is transferred or revised, the name of the original author is retained but in
parentheses, e.g., Syzygium cumin (Linn).

♦ In case an organism has been given more than one name, the earlier legitimate one is
recognized to be valid (not prior to 1.5.1753 for plants or 1.8.1758 for animals). This is called
the law of priority.
 UNIT 3: DIMENSION OF SPECIATION AND
TAXONOMIC CHARACTERS

3.1 Objectives
3.2 Introduction
3.3 Dimension of Speciation
3.4 Mechanism of Speciation
3.5 Species Concept
3.5.1 Species
3.6 Theories of Biological Classification
3.7 Taxonomic Characters

3.1 OBJECTIVES
We will study the following point
• Taxonomic Characters
• Dimension of Speciation
• Mechanism of Speciation
• Species Concept

3.2 INTRODUCTION

Speciation is the evolutionary process by which populations evolve to become distinct

species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting
of lineages, as opposed to anagenesis, phyletic evolution within lineages. Charles Darwin was
the first to describe the role of natural selection in speciation in his 1859 book On the Origin
of Species. He also identified sexual selection as a likely mechanism, but found it
problematic. There are four geographic modes of speciation in nature, based on the extent to
which speciating populations are isolated from one another: allopatric, peripatric, parapatric,
and sympatric. Speciation may also be induced artificially, through animal husbandry,
agriculture, or laboratory experiments. Whether genetic drift is a minor or major contributor
to speciation is the subject of much ongoing discussion. Rapid sympatric speciation can take
place through polyploidy, such as by doubling of chromosome number; the result is progeny
which are immediately reproductively isolated from the parent population. New species can
also be created through hybridization followed—if the hybrid is favoured by natural selection
by reproductive isolation.

Speciation is the process of formation of a new genetically independent group of organisms,

called species, through the course of evolution.

• The process of splitting of genetically homogenous population into two or more

populations that undergo genetic differentiation and eventual reproductive isolation is
called speciation.
• The entire course of evolution depends upon the origin of new populations (species)
that have greater adaptive efficiency than their ancestors.

Speciation occurs in two ways.

1. Transformation of old species into new species over time.

2. Splitting of a single species into several, that is the multiplication of species.

Speciation occurs as a result of several factors which are:

1. Natural selection

• As explained by Charles Darwin, different individuals in a species might develop

specific distinct characteristics which are advantageous and affect the genetic makeup
of the individual.
• Under such conditions, these characteristics will be conserved, and over time, new
species might be formed.
• However, in this case, the essential aspect of this factor is that speciation occurs only
when a single species splits into several species resulting in the multiplication of
species.

2. Genetic drift

• Genetic drift is the change in the allele frequencies in a population as a result of

“sampling error” while selecting the alleles for the next generation from the gene pool
of the current population.
• It has been, however, argued that genetic drift doesn’t result in speciation and just
results in evolution, that is, change from one species to another, which cannot be
considered speciation.

3. Migration

• When a certain number of species from a population migrate from one geographical
region to another, the species might accumulate characteristics which are different
from that of the original population.
• Migration usually results in geographical isolation and ultimately leads to speciation.

4. Chromosomal Mutations

• Chromosomal mutations have the potential to serve as (or contribute to) isolating
mechanisms, and the locking up and protection of a particularly favorable gene
complement through a chromosomal mutation.
• These mutations, when preserved from one generation to another, might result in the
formation of new species.

5. Natural causes

• Sometimes, natural events imposed by the environment like a river or a mountain

range might cause the separation of what once a continuous population is divided into
two or smaller populations.
• These events result in geographical isolation of the incipient species followed by
reproductive isolation leading to speciation.

6. Reduction of gene flow

• Speciation might also occur in the absence of some extrinsic physical barriers.
• There might be a reduced gene flow over a broad geographical range where
individuals in the Far East would have zero chance of mating with individuals in the
far western end of the range.
• In addition, if there are some selective mechanisms like genetic drift at the opposite
ends of the range, the gene frequencies would be altered, and speciation would be
ensured.
Classically, speciation has been observed as a three-stage process:

1. Isolation of populations.
2. Divergence in traits of separated populations (e.g. mating system or habitat use).
3. Reproductive isolation of populations that maintains isolation when populations come
into contact again (secondary contact).

• Recent research shows that steps one and two may take place simultaneously in the
same place, and often the third step does not occur.
• The process of speciation begins with the isolation of subpopulation of a species
which could either occur through physical isolation (allotropic speciation) or genetic
isolation (sympatric speciation).
• Once the population is separated, a gradual accumulation of small genetic changes
results in a subpopulation of a species that eventually accumulate so many changes
that the subpopulations become different species.
• Over time, the subpopulation now becomes genetically independent and will continue
to diverge by mutation, selection, and genetic drift.
• The genetic differentiation might cause a slight change in the mating dance or even a
small change in the shape of the male genitalia or some changes in the habitat or
feeding habits of the subpopulation, which results in reproductive isolation.
• Eventually, the genetic differentiation between the subpopulation becomes so high
that the formation of hybrids between them would be physiologically,
developmentally, or behaviorally impossible even if the modes of the separation were
abolished.

TYPES OF SPECIATION/MODES OF SPECIATION

• The classification of the modes or types of speciation is based on how much the
geographical separation of the original population contributes to the reduced gene
flow and ultimately, the formation of new species.

The modes of speciation are:

• Allopatric speciation is the mode of speciation in which the original population is

divided into two by a barrier resulting in reproductive isolation.
 • The model for allopatric speciation was presented by Mayr.
• It is based on the concept that new species arise when some physical geographic
barrier divides the large population of a species into two or more small populations.
• The individuals of these isolated populations cannot interbreed because of their
physical isolation.
• Physical isolation might occur either due to physical barriers like vast expanses of
ocean, high mountains, glaciers, deep river valleys, wide rivers or deserts, or a
considerable distance due to a larger geographical range.
• Each isolated population starts to adapt to their separated environments while
accumulating differences and evolving independently into new species.
• Allopatric speciation can occur even in cases in which the barrier allows some
individuals to cross the barrier to mate with the members of the other groups.
• For speciation even to be considered “allopatric,” gene flow between the soon-to-be
species must be significantly reduced—but it doesn’t have to be entirely reduced to
zero.

Examples

• The classic example of allopatric speciation is that of Darwin’s finches. The divergent
populations of finches inhabiting the Galapagos Islands were observed to have
differences in features such as body size, color, and beak length or shape. The
differences resulted because of the different types of food available in various Islands.
• Another example is of Grand Canyon Squirrels which were separated during the
formation of the Grand Canyon and resulted in two different species of squirrels.

PERIPATRIC SPECIATION

• Peripatric speciation is a special condition of allopatric speciation which occurs when

the size of the isolated subpopulation is small.
• In this case, in addition to geographic separation, genetic drift also plays an important
as genetic drift acts more quickly in small populations.
• The small isolated subpopulation might carry some rare genes which upon reaching
the new geographical region become fixed over the course of a few generations as a
result of genetic drift.
• As a result, the entire population of the new region ends up having these rare genes.
 • Over time, new genetic characters, as well as natural selection, cause the survival of
individuals which are better suited to the climate and food of the new region.
• Finally, under the influence of all these factors, new species are formed.
• However, it is very difficult to explain what role genetic drift played in the divergence
of the two populations, which makes gathering evidence to support or refute this
mode very challenging.

Examples

• The Australian bird PETROICA MULTICOLOUR and LONDON UNDERGROUND

MOSQUITO , a variant of the mosquito CULEX PIPIENS, which entered in the London
Underground in the 19th century, are the examples of Petripatric speciation.

PARAPATRIC SPECIATION

• Parapatric speciation is a mode of speciation in which there is no extrinsic barrier

between the populations but, the large geographic range of the population causes the
individuals to mate with the neighboring individuals than with the individuals in a
different part of the geographical range.
• In this case, the population is continuous, but the population doesn’t mate randomly.
• Here, the genetic variation occurs as a result of reduced gene flow within the
population and varying selection pressures across the population’s range.
• This occurs in population which is distributed over a large geographical range. Thus,
the individuals in the far west region cannot mate with the individuals in the Far East
region.
• Through a few generations, new species might be formed within the existing
population.

Examples

• The grass species ANTHOXANTHUM ODORATUM where some species living near the
mine have become tolerant to heavy metals; however, other plants that don’t live
around the mines are not tolerant.
• But because the plants are close together, they could fertilize each other and result in a
new species.
SYMPATRIC SPECIATION

• Sympatric speciation is the process of the formation of new species from an original
population that are not geographically isolated.
• It is based on the establishment of new populations of a species in different ecological
niches and the reproductive isolation of founders of the new population from the
individuals of the source population.
• Gene flow between daughter and parental population during sympatric speciation is
postulated to be inhibited by intrinsic factors, such as chromosomal changes and non-
random mating.
• Exploiting a new niche might automatically reduce gene flow with individuals
exploiting a different niche.
• This mode of speciation is common in herbivore insects when they begin feeding and
mating on a new plant or when a new plant is introduced within the geographical
range of the species.
• The gene flow is then reduced between the species that specialize in a particular plant
which might ultimately lead to the formation of new species.
• The selection resulting in specialization needs to be really strong for the population to
diverge.
• Thus, sympatric speciation is a sporadic event in multicellular organisms or randomly
mating populations.

Examples

• Sympatric speciation is observed in apple maggot flies which 200 years ago laid eggs
and bred only on hawthorns but now lays eggs on both hawthorns and domestic
apples.
• As a result, gene flow between parts of the population that mate on different types of
fruit is reduced, and in fewer than 200 years, some genetic differences between these
two groups of flies have evolved.
3.3 DIMENSION OF SPECIATION

All forms of natural speciation have taken place over the course of evolution; however,
debate persists as to the relative importance of each mechanism in driving biodiversity.

One example of natural speciation is the diversity of the three-spined stickleback, a marine
fish that, after the last glacial period, has undergone speciation into new freshwater colonies
in isolated lakes and streams. Over an estimated 10,000 generations, the sticklebacks show
structural differences that are greater than those seen between different genera of fish
including variations in fins, changes in the number or size of their bony plates, variable jaw
structure, and color differences.

ALLOPATRIC

Allopatric (from the ancient Greek allos, "other" + patrā, "fatherland") speciation, a
population splits into two geographically isolated populations (for example, by habitat
fragmentation due to geographical change such as mountain formation). The isolated
populations then undergo genotypic or phenotypic divergence as: (a) they become subjected
to dissimilar selective pressures; (b) they independently undergo genetic drift; (c) different
mutations arise in the two populations. When the populations come back into contact, they
have evolved such that they are reproductively isolated and are no longer capable of
exchanging genes. Island genetics is the term associated with the tendency of small, isolated
genetic pools to produce unusual traits. Examples include insular dwarfism and the radical
changes among certain famous island chains, for example on Komodo. The Galápagos
Islands are particularly famous for their influence on Charles Darwin. During his five weeks
there he heard that Galápagos tortoises could be identified by island, and noticed that finches
differed from one island to another, but it was only nine months later that he reflected that
such facts could show that species were changeable. When he returned to England, his
speculation on evolution deepened after experts informed him that these were separate
species, not just varieties, and famously that other differing Galápagos birds were all species
of finches. Though the finches were less important for Darwin, more recent research has
shown the birds now known as Darwin's finches to be a classic case of adaptive evolutionary
radiation.
PERIPATRIC

In peripatric speciation, a subform of allopatric speciation, new species are formed in

isolated, smaller peripheral populations that are prevented from exchanging genes with the
main population. It is related to the concept of a founder effect, since small populations often
undergo bottlenecks. Genetic drift is often proposed to play a significant role in peripatric
speciation.

Case studies include Mayr's investigation of bird fauna; the Australian bird Petroica
multicolor; and reproductive isolation in populations of Drosophila subject to population
bottlenecking.

In parapatric speciation, there is only partial separation of the zones of two diverging
populations afforded by geography; individuals of each species may come in contact or cross
habitats from time to time, but reduced fitness of the heterozygote leads to selection for
behaviours or mechanisms that prevent their interbreeding. Parapatric speciation is modelled
on continuous variation within a "single," connected habitat acting as a source of natural
selection rather than the effects of isolation of habitats produced in peripatric and allopatric
speciation.[32]

Parapatric speciation may be associated with differential landscape-dependent selection. Even

if there is a gene flow between two populations, strong differential selection may impede
assimilation and different species may eventually develop. Habitat differences may be more
important in the development of reproductive isolation than the isolation time. Caucasian
rock lizards Darevskia rudis, D. valentini and D. portschinskii all hybridize with each other in
their hybrid zone; however, hybridization is stronger between D. portschinskii and D. rudis,
which separated earlier but live in similar habitats than between D. valentini and two other
species, which separated later but live in climatically different habitats.

Ecologists refer to parapatric and peripatric speciation in terms of ecological niches. A niche
must be available in order for a new species to be successful. Ring species such as Larus gulls
have been claimed to illustrate speciation in progress, though the situation may be more
complex. The grass Anthoxanthum odoratum may be starting parapatric speciation in areas of
mine contamination.
SYMPATRIC

Sympatric speciation is the formation of two or more descendant species from a single
ancestral species all occupying the same geographic location.

Often-cited examples of sympatric speciation are found in insects that become dependent on
different host plants in the same area.

The best known example of sympatric speciation is that of the cichlids of East Africa
inhabiting the Rift Valley lakes, particularly Lake Victoria, Lake Malawi and Lake
Tanganyika. There are over 800 described species, and according to estimates, there could be
well over 1,600 species in the region. Their evolution is cited as an example of both natural
and sexual selection. A 2008 study suggests that sympatric speciation has occurred in
Tennessee cave salamanders. Sympatric speciation driven by ecological factors may also
account for the extraordinary diversity of crustaceans living in the depths of Siberia's Lake
Baikal.

Budding speciation has been proposed as a particular form of sympatric speciation, whereby
small groups of individuals become progressively more isolated from the ancestral stock by
breeding preferentially with one another. This type of speciation would be driven by the
conjunction of various advantages of inbreeding such as the expression of advantageous
recessive phenotypes, reducing the recombination load, and reducing the cost of sex.

The hawthorn fly (Rhagoletis pomonella), also known as the apple maggot fly, appears to be
undergoing sympatric speciation. Different populations of hawthorn fly feed on different
fruits. A distinct population emerged in North America in the 19th century sometime after
apples, a non-native species, were introduced. This apple-feeding population normally feeds
only on apples and not on the historically preferred fruit of hawthorns. The current hawthorn
feeding population does not normally feed on apples. Some evidence, such as that six out of
thirteen allozyme loci are different, that hawthorn flies mature later in the season and take
longer to mature than apple flies; and that there is little evidence of interbreeding (researchers
have documented a 4–6% hybridization rate) suggests that sympatric speciation is occurring.
METHODS OF SELECTION

REINFORCEMENT

Reinforcement, sometimes referred to as the Wallace effect, is the process by which natural
selection increases reproductive isolation. It may occur after two populations of the same
species are separated and then come back into contact. If their reproductive isolation was
complete, then they will have already developed into two separate incompatible species. If
their reproductive isolation is incomplete, then further mating between the populations will
produce hybrids, which may or may not be fertile. If the hybrids are infertile, or fertile but
less fit than their ancestors, then there will be further reproductive isolation and speciation
has essentially occurred (e.g., as in horses and donkeys).

The reasoning behind this is that if the parents of the hybrid offspring each have naturally
selected traits for their own certain environments, the hybrid offspring will bear traits from
both, therefore would not fit either ecological niche as well as either parent. The low fitness
of the hybrids would cause selection to favor assortative mating, which would control
hybridization. This is sometimes called the Wallace effect after the evolutionary biologist
Alfred Russel Wallace who suggested in the late 19th century that it might be an important
factor in speciation. Conversely, if the hybrid offspring are more fit than their ancestors, then
the populations will merge back into the same species within the area they are in contact.

Reinforcement favoring reproductive isolation is required for both parapatric and sympatric
speciation. Without reinforcement, the geographic area of contact between different forms of
the same species, called their "hybrid zone," will not develop into a boundary between the
different species. Hybrid zones are regions where diverged populations meet and interbreed.
Hybrid offspring are very common in these regions, which are usually created by diverged
species coming into secondary contact. Without reinforcement, the two species would have
uncontrollable inbreeding. Reinforcement may be induced in artificial selection experiments
as described below.

ECOLOGICAL

Ecological selection is "the interaction of individuals with their environment during resource
acquisition". Natural selection is inherently involved in the process of speciation, whereby,
"under ecological speciation, populations in different environments, or populations exploiting
different resources, experience contrasting natural selection pressures on the traits that
directly or indirectly bring about the evolution of reproductive isolation". Evidence for the
role ecology plays in the process of speciation exists. Studies of stickleback populations
support ecologically-linked speciation arising as a by-product, alongside numerous studies of
parallel speciation, where isolation evolves between independent populations of species
adapting to contrasting environments than between independent populations adapting to
similar environments. Ecological speciation occurs with much of the evidence,
"...accumulated from top-down studies of adaptation and reproductive isolation".

SEXUAL SELECTION

It is widely appreciated that sexual selection could drive speciation in many clades,
independently of natural selection. However the term "speciation", in this context, tends to be
used in two different, but not mutually exclusive senses. The first and most commonly used
sense refers to the "birth" of new species. That is, the splitting of an existing species into two
separate species, or the budding off of a new species from a parent species, both driven by a
biological "fashion fad" (a preference for a feature, or features, in one or both sexes, that do
not necessarily have any adaptive qualities). In the second sense, "speciation" refers to the
wide-spread tendency of sexual creatures to be grouped into clearly defined species, rather
than forming a continuum of phenotypes both in time and space – which would be the more
obvious or logical consequence of natural selection. This was indeed recognized by Darwin
as problematic, and included in his On the Origin of Species (1859), under the heading
"Difficulties with the Theory". There are several suggestions as to how mate choice might
play a significant role in resolving Darwin's dilemma. If speciation takes place in the absence
of natural selection, it might be referred to as nonecological speciation.

ARTIFICIAL SPECIATION

New species have been created by animal husbandry, but the dates and methods of the
initiation of such species are not clear. Often, the domestic counterpart of the wild ancestor
can still interbreed and produce fertile offspring as in the case of domestic cattle, that can be
considered the same species as several varieties of wild ox, gaur, yak, etc., or domestic sheep
that can interbreed with the mouflon.
The best-documented creations of new species in the laboratory were performed in the late
1980s. William R. Rice and George W. Salt bred Drosophila melanogasterfruit flies using a
maze with three different choices of habitat such as light/dark and wet/dry. Each generation
was placed into the maze, and the groups of flies that came out of two of the eight exits were
set apart to breed with each other in their respective groups. After thirty-five generations, the
two groups and their offspring were isolated reproductively because of their strong habitat
preferences: they mated only within the areas they preferred, and so did not mate with flies
that preferred the other areas. The history of such attempts is described by Rice and Elen E.
Hostert (1993). Diane Dodd used a laboratory experiment to show how reproductive isolation
can develop in Drosophila pseudoobscura fruit flies after several generations by placing them
in different media, starch- and maltose-based media.

Alternatively, these observations are consistent with the notion that sexual creatures are
inherently reluctant to mate with individuals whose appearance or behavior is different from
the norm. The risk that such deviations are due to heritable maladaptations is very high. Thus,
if a sexual creature, unable to predict natural selection's future direction, is conditioned to
produce the fittest offspring possible, it will avoid mates with unusual habits or features.
Sexual creatures will then inevitably tend to group themselves into reproductively isolated
species.

GENETICS

Few speciation genes have been found. They usually involve the reinforcement process of
late stages of speciation. In 2008, a speciation gene causing reproductive isolation was
reported. It causes hybrid sterility between related subspecies. The order of speciation of
three groups from a common ancestor may be unclear or unknown; a collection of three such
species is referred to as a "trichotomy."

Speciation via polyploidy

Polyploidy is a mechanism that has caused many rapid speciation events in sympatry because
offspring of, for example, tetrapod x diploid matings often result in triploid sterile progeny.
However, among plants, not all polyploids are reproductively isolated from their parents, and
gene flow may still occur, such as through triploid hybrid x diploid matings that produce
tetraploids, or matings between meiotically unreduced gametes from diploids and gametes
from tetraploids (see also hybrid speciation).

It has been suggested that many of the existing plant and most animal species have undergone
an event of polyploidization in their evolutionary history. Reproduction of successful
polyploid species is sometimes asexual, by parthenogenesis or apomixis, as for unknown
reasons many asexual organisms are polyploid. Rare instances of polyploid mammals are
known, but most often result in prenatal death.

HYBRID SPECIATION

Hybridization between two different species sometimes leads to a distinct phenotype. This
phenotype can also be fitter than the parental lineage and as such natural selection may then
favor these individuals. Eventually, if reproductive isolation is achieved, it may lead to a
separate species. However, reproductive isolation between hybrids and their parents is
particularly difficult to achieve and thus hybrid speciation is considered an extremely rare
event. The Mariana mallard is thought to have arisen from hybrid speciation.

Hybridization is an important means of speciation in plants, since polyploidy (having more

than two copies of each chromosome) is tolerated in plants more readily than in animals.
Polyploidy is important in hybrids as it allows reproduction, with the two different sets of
chromosomes each being able to pair with an identical partner during meiosis. Polyploids
also have more genetic diversity, which allows them to avoid inbreeding depression in small
populations.

Hybridization without change in chromosome number is called homoploid hybrid speciation.

It is considered very rare but has been shown in Heliconiusbutterflies and sunflowers.
Polyploid speciation, which involves changes in chromosome number, is a more common
phenomenon, especially in plant species.

GENE TRANSPOSITION

Theodosius Dobzhansky, who studied fruit flies in the early days of genetic research in
1930s, speculated that parts of chromosomes that switch from one location to another might
cause a species to split into two different species. He mapped out how it might be possible for
sections of chromosomes to relocate themselves in a genome. Those mobile sections can
cause sterility in inter-species hybrids, which can act as a speciation pressure. In theory, his
idea was sound, but scientists long debated whether it actually happened in nature. Eventually
a competing theory involving the gradual accumulation of mutations was shown to occur in
nature so often that geneticists largely dismissed the moving gene hypothesis. However, 2006
research shows that jumping of a gene from one chromosome to another can contribute to the
birth of new species. This validates the reproductive isolation mechanism, a key component
of speciation.

RATES

There is debate as to the rate at which speciation events occur over geologic time. While
some evolutionary biologists claim that speciation events have remained relatively constant
and gradual over time (known as "Phyletic gradualism" – see diagram), some
palaeontologists such as Niles Eldredge and Stephen Jay Gould have argued that species
usually remain unchanged over long stretches of time, and that speciation occurs only over
relatively brief intervals, a view known as punctuated equilibrium. (See diagram, and
Darwin's dilemma.)

PUNCTUATED EVOLUTION

Evolution can be extremely rapid, as shown in the creation of domesticated animals and
plants in a very short geological space of time, spanning only a few tens of thousands of
years. Maize (Zea mays), for instance, was created in Mexico in only a few thousand years,
starting about 7,000 to 12,000 years ago. This raises the question of why the long term rate of
evolution is far slower than is theoretically possible.

Evolution is imposed on species or groups. It is not planned or striven for in some Lamarckist
way. The mutation on which the process depends are random events, and, except for the
"silent mutations" which do not affect the functionality or appearance of the carrier, are thus
usually disadvantageous, and their chance of proving to be useful in the future is vanishingly
small. Therefore, while a species or group might benefit from being able to adapt to a new
environment by accumulating a wide range of genetic variation, this is to the detriment of the
individuals who have to carry these mutations until a small, unpredictable minority of them
ultimately contributes to such an adaptation. Thus, the capability to evolve would require
group selection, a concept discredited by (for example) George C. Williams, John Maynard
Smith and Richard Dawkins as selectively disadvantageous to the individual.

The resolution to Darwin's second dilemma might thus come about as follows:

If sexual individuals are disadvantaged by passing mutations on to their offspring, they will
avoid mutant mates with strange or unusual characteristics. Mutations that affect the external
appearance of their carriers will then rarely be passed on to the next and subsequent
generations. They would therefore seldom be tested by natural selection. Evolution is,
therefore, effectively halted or slowed down considerably. The only mutations that can
accumulate in a population, on this punctuated equilibrium view, are ones that have no
noticeable effect on the outward appearance and functionality of their bearers (i.e., they are
"silent" or "neutral mutations," which can be, and are, used to trace the relatedness and age of
populations and species.[15][94]) This argument implies that evolution can only occur if mutant
mates cannot be avoided, as a result of a severe scarcity of potential mates. This is most
likely to occur in small, isolated communities. These occur most commonly on small islands,
in remote valleys, lakes, river systems, or caves, or during the aftermath of a mass
extinction.[94] Under these circumstances, not only is the choice of mates severely restricted
but population bottlenecks, founder effects, genetic drift and inbreeding cause rapid, random
changes in the isolated population's genetic composition. Furthermore, hybridization with a
related species trapped in the same isolate might introduce additional genetic changes. If an
isolated population such as this survives its genetic upheavals, and subsequently expands into
an unoccupied niche, or into a niche in which it has an advantage over its competitors, a new
species, or subspecies, will have come in being. In geological terms, this will be an abrupt
event. A resumption of avoiding mutant mates will thereafter result, once again, in
evolutionary stagnation.

In apparent confirmation of this punctuated equilibrium view of evolution, the fossil record of
an evolutionary progression typically consists of species that suddenly appear, and ultimately
disappear, hundreds of thousands or millions of years later, without any change in external
appearance. Graphically, these fossil species are represented by lines parallel with the time
axis, whose lengths depict how long each of them existed. The fact that the lines remain
parallel with the time axis illustrates the unchanging appearance of each of the fossil species
depicted on the graph. During each species' existence new species appear at random intervals,
each also lasting many hundreds of thousands of years before disappearing without a change
in appearance. The exact relatedness of these concurrent species is generally impossible to
determine. This is illustrated in the diagram depicting the distribution of hominin species
through time since the hominins separated from the line that led to the evolution of our
closest living primate relatives, the chimpanzees.

3.4 MECHANISM OF SPECIATION

How does a single species give rise to two or more different species? This concept, called
speciation, requires that a single population of organisms divide into two or more populations
that no longer interbreed. Without interbreeding, there is no gene flow between the
populations, and these populations may then evolve separately into distinct species. There are
many definitions for what a species is, but we will begin with biologist Ernst Mayr's 1940
definition, in which he states that species are groups of actually or potentially interbreeding
natural populations which are reproductively isolated from other such groups. We will extend
this to say that if two individuals of different species do mate and produce offspring, that
those offspring would not be fertile.

In the accompanying animation, we examine two mechanisms of establishing a barrier to

gene flow, leading to speciation. Speciation occurs when the gene pool of a population is
somehow reproductively isolated from other populations of the parent species and no longer
has gene flow occurred between them.

On the basis of period taken in speciation, there are two types of mechanisms of speciation:

A. Gradual speciation.

B. Instantaneous or abrupt speciation.

A. Gradual speciation:

It is the gradual divergence of populations due to the accumulation of variations over a long
period of time.

Gradual speciation occurs in two ways:

1. Geographic or allopatric speciation (Gr. alio = other; patria = naHve land):

When an original population becomes separated spatially because of geographic barriers, into
two or more groups, these are termed as allopatric populations.

The geographical barriers (e.g. a creeping glacier, a land bridge (e.g. Isthmus of Panama) or
ocean or mountain or migration of some individuals to a new habitat which is geographical
isolated from original range) impose the restriction on the gene flow between populations, so
that the latter become reproductively isolated.

These groups become more and more different and finally become different species, called
allopatric species, e.g. Darwin’s finches of Galapagos Islands are geographically isolated
from related birds of South American mainland; and adaptive radiations in the Australian
marsupials to form new species.

2. Sympatric speciation (Gr. sym = together; patria = native land):

It occurs within same geographical area and’ within original population but two elementary
species occupy different etiological or ecological niches and are reproductively isolated by
the development of biological isolating barriers.

Differences between Allopatric and Sympatric speciation.

Allopatric speciation Sympatric speciation

1. In this, subpopulations are separated by 1. In this, subpopulations occur in same geo-
certain geographical barriers. graphical area but in different ecological
nitches.
2. It occurs in different populations.
2. It occurs within original population.
3. These are geographically isolated.
3. These are ecologically or ethologically iso-
4. Darwin’s finches on Galapagos islands.
lated.

4. Pig frog and Gopher frog occur in different

habitats.
B. Abrupt of instantaneous speciation:

It is defined as the sudden development of new species which is reproductively and

ecologically isolated from the parental species. This mechanism operates through individuals
and thus, not a population phenomenon.

It may occur by:

1. Mutations:

Mutations are large, sudden and inheritable changes while individuals with mutations are
called mutants. Mutations are called fountain head of variations as these form the main types
of sources of variations.

Significance:

Such mutations can produce sibling species which are morphologically similar but
ecologically and reproductively isolated. For example, the production of two sibling species
of Drosophila pseudo-obscura and D. persimilis.

2. Hybridization and Polyploidy:

Hybridization involves the interbreeding of two genetically different – individuals of two

same or different species to produce hybrids while polyploidy means presence of more than
two sets of chromosomes.

Occasionally, the interspecific hybrids are produced naturally or artificially. Such hybrids are,
however, sterile due to incompatibility between the chromosomes of two different species
and their failure to pair in meiosis.

But the doubling of chromosomes may produce fertile offsprings. Doubling of chromosome
number allows normal meiosis and formation of normal but diploid gametes so hybridization
followed by polyploidy can lead to the formation of new species very rapidly. This results in
the production of new species.
3.5 SPECIES CONCEPT

The following points highlight the four important groups of species concept. The groups
are:

1. Typological Species Concept

2. Nominalist Species Concept

3. Evolutionary Species Concept

4. Biological Species Concept.

TYPOLOGICAL SPECIES CONCEPT:

This concept says that the observed diversity of the universe reflects the existence of a
limited number of underlying “universals” or types. Individuals are considered to be merely
expressions of the same type. When two individuals or groups of individuals have sufficiently
different characters then only they should be considered as different species.

Variation results in the revealing of characters which are already present but not expressed in
each species. Thus, variation according to the typological species concept is considered to be
an irrelevant phenomenon.

This concept dates back 2,300 years to the philosophies of Plato and Aristotle, and was the
species concept of Linnaeus and his followers. Species was supposed to be a fixed or static
unit which did not change and, as such, existed permanently and forever.

Since this philosophical tradition is sometimes referred to as essentialism, the typological

definition is also sometimes called the essentialist species concept. The species can be
recognized by their essential natures or essential characters which are expressed in
accordance with their morphology.

It is, therefore, also called the morphological species concept. Taxonomists almost
unanimously accepted the essentialist species concept up to the early post-Linnaean period.
It thus includes four postulates:

(i) Species are similar individuals sharing the same essence.

(ii) Each species is separated from all others by a sharp discontinuity.

(iii) Each species is completely constant through time.

(iv) Strict limits are present to the possible variation within any one species.

Two practical reasons exist for the present universal rejection of this concept:

1. Individuals are frequently found in nature that are clearly conspecific with other
individuals in spite of striking differences in structure owing to sexual dimorphism, age
differences, polymorphism and other terms of individual variation. These were often
described originally as different species.

For example:

(i) The male and female of river duck, the mallard, were originally placed under separate
species. The males were described as Anas boscas and the females as Anas platyrhynchos.

(ii) In many groups of birds (humming bird, pea-hen etc.) females differ more from the males
of their own species than from the females of other related species.

(iii) Larval stages of several chordates and invertebrates are markedly different from their
parents or adult stage and, thus, were very often considered as separate species.

(iv) In case of the deep sea fishes the males are dwarf and attached to the body of the females.
So they were considered as separate species.

Thus, in the above cases, they should be deprived of their separate species status, regardless
of their degree of morphological differences, as soon as they are found to be numbers of the
same breeding population. Different phases that belong to the same population cannot be
considered as different species.
2. Sibling species differ hardly at all morphologically, yet are good biological species. Degree
of difference is not the decisive criterion in the ranking of taxa as species. The typological
species concept is still defended by a few writers.

In situations where there is a lack of biological information, a taxonomist may be forced to

recognize a species provisionally on the basis of morphological evidences, but such species
are subject to later reconsideration.

NOMINALISTIC SPECIES CONCEPT:

Nominalistic species concept is that of Occam and his followers, who believed that nature
produces individuals only. Species are man’s own creation and have no actual existence in
nature. They are mental concepts and nothing more. Species have been invented so that we
may refer to great numbers of individuals collectively. This concept was popular in France
during the 18th century.

The drawbacks of this concept are:

(i) No naturalist whether a primitive native or a trained population geneticist – can agree that
species are man-made, when it is an established fact that they are the products of evolution.

(ii) Nominalists misinterpreted the relation between similarity and relationship. The members
of any species are not grouped together as they are similar (as claimed by these workers),
rather they are similar to each other because of common heritage. It is just like when two
brothers are identical twins not due to their similarity but rather due to both being derived
from a single zygote.

EVOLUTIONARY SPECIES CONCEPT:

The shortcomings of Biological species concept (in uniparental organisms where

interbreeding fails), had led Meglitsch (1954), Simpson (1961), Grant (1971) and other
authors – particularly paleontologists – in formulating the evolutionary species concept.

Simpson (1961) defined it as “an evolutionary species is a lineage (an ancestral- descendant
sequence of populations) evolving separately from others and with its own unitary
evolutionary role and tendencies”. Willey (1981), on the other hand, believed that each
species is an internally similar part of a phylogenetic tree.
The drawbacks of this concept are:

(i) This definition is of a phyletic lineage and not of a species. It side-stepped the crucial role
of why phyletic lines do not interbreed with each other.

(ii) This concept ignores the core of the species problem as to the causation and maintenance
of discontinuities between contemporary species.

(iii) This concept has failed to solve the problem of how to deal with the relationship of
descendant populations in a single lineage.

BIOLOGICAL SPECIES CONCEPT:

The biological species concept is also known as the Newer Species Concept, because it was
accepted in the latter half of the nineteenth century after Darwin’s “Origin of Species” was
published (in 1859) and also due to the fact that organic evolution was established. It was
after 1750 that an entirely new species concept began to emerge. But it was in 1905 that K.
Jordan first clearly formulated the concept in all of its consequences. This concept combined
the thoughts of the typological and nominalistic concepts by stating that the species have
independent reality and are typified by the statistics of populations of individuals. It,
however, differs from both by stressing the populational aspect and genetic cohesion of the
species and also by pointing out that species receives its reality from the historically evolved,
shared information content of its gene pool.

Thus, the members of a species show the following properties:

(i) A reproductive community:

The member of an animal species recognizes each other as potential mates and seeks each
other for the purpose of reproduction.

(ii) An ecological unit:

The species members form an ecological unit which, regardless of the individuals composing
it, interacts as a unit with other species with which it shares the environment.

(iii) A genetic unit:

The species consists of a large, inter-communicating gene pool, whereas the individual is
merely a temporary vessel holding a small portion of the contents of the gene pool for a short
period of time. These three properties raise the species above the typological interpretation of
a “class of objects”. Thus, from this theoretical species concept, the species definition which
results is — A species is a group of interbreeding natural population that is reproductively
isolated from other such groups. This species concept is called biological not because it deals
with biological taxa, but because the definition itself is biological. It utilizes criteria that are
meaningless as far as the inanimate world is concerned. Biologically, a species is a potential
gene pool. It is a Mendelian population which has its own devices, that is, isolating
mechanisms which protect it against harmful gene flow from other gene pools. Gene of the
same gene pool forms harmonious combinations because they have become co-adopted by
natural selection. Mixing the genes of two different species lead to high frequency of
disharmonious gene combinations. Mechanisms that prevent this are favoured by selection.
Thus, the word species in biology is a relational term. ‘A’ is a species in relation to ‘B’ and
‘C’ because it is reproductively isolated from them. Since evolution is a regular process, the
species is an arbitrary division of the continuous and ever-changing series of individuals in
nature. Therefore, species is dynamic and multidimensional in nature. The biological species
concept has been able to solve the paradox caused by the conflict between the fixity of
species of the naturalist and the fluidity of the species of the evolutionist. It was this conflict
that made Linnaeus deny evolution and Darwin the reality of species.

The biological species concept combines the discreteness of the local species at a given time
with an evolutionary potential for continuing change. The biological species concept has its
importance in the fact that it is employed in the largest number of biological disciplines —
ecology, physiology, behaviour biology etc. Intraspecific categories designate groupings of
population’s within species. Normally, the species is the lowest category used in routine
taxonomy.
3.5.1 SPECIES

1. Morphological Species:

This is the traditional concept of species. It was originally introduced by Carolus Linnaeus in
his Systema Naturae in 1758. According to this concept, a population group of
morphologically distinct organisms constitutes a species.

The main objections to this concept are that it does not take into consideration:

(i) The range of variation in size, colour, form & weight.

(ii) The genetic diversity

(iii) The common origin of related species and

(iv) The change of species in time.

Morphological species concept does not take into account of pronounced sexual dimorphism
exhibited by different organisms. For example, the males and females of river duck, the
mallard, were originally placed under separate species. The males were described as Anas
boschas and females as A. platyrhyechos.

In many other birds like birds of paradise, humming birds, wood warblers etc. females differ
more from the males of their own species than from the females of other related species. In
many deep-sea angler fishes of the family Ceratioidei, the males are much smaller in size
than females, live as parasitic forms upon them. Such dwarf males, originally mistaken as
separate species, attach themselves by the mouth of the female and feed up their body fluids.

Insects and lower invertebrates like rotifers, echiuroids like Bonellia exhibit more
pronounced morphological differences in the two sexes. Larval stages of several vertebrates
and invertebrates are so markedly different from their parents that they were very often
placed in separate species.

2. GENETIC SPECIES:

According to Lotsy (1918) a species is a group of genetically identical individuals. This view
was supported by some geneticists. But this definition of species is incorrect because even the
off-springs of same parents have different genetic constitution. Only identical twins are
genetically similar.

3. BIOLOGICAL SPECIES:

This is the modern concept of species proposed and developed by Dobzhansky in 1937 and
Mayr in 1942. According to Dobzhansky mendelian population sharing a common gene pool
constitute a species. The most uptodate and convincing definition of species has been given
by Mayr (1942) to his book “Systematics and the origin of species”. According to him,
species are the groups of actually or potentially interbreeding natural populations that are
reproductively isolated from each such groups.

The general characters of animal species may be summarized as follows:

1. Each species possesses a common gene pool.

2. Each species is in a process of continually adjusting to its environment.

3. Each species fills an ecological niche not exactly utilized by another species.

4. Each species possesses a constellation of isolating mechanisms that indirectly or directly

prevent exchange of genes with related species.

5. Each species has the capacity to give rise to new species.

Subspecies and varieties:

Subspecies is an aggregate of local breeding populations of a given species which has

become recognizably different from another population of the same species. A subspecies
usually differ from other similar breeding groups of the same species both taxonomically and
with respect to certain gene pool characteristics.

The subspecies name is written immediately after species name. So the whole constitute a
trinominal.

The term variety was used to describe the non-genetic variants of phenotype caused by the
climatic effects. But now the term subspecies replaces the term variety.
Clines:

The term ‘cline’ was introduced by Huxley (1939). It refers to a gradient (decrease or
increase) within a continuous population. The regular or continuous variations occur for
genotypes (genocline) or phenotypes (phenocline).

One of the best examples of clinal gradation is exhibited by the meadow frog of North
America, Rana pipens. It is found throughout the Paire grass land and includes a number of
temperature adapted races, which exhibit an orderly variability and adaptability. When the
population of North and South extremes is compared the differences are pronounced, yet
between the two extremes, there is no break in variation.

Demes:

The term ‘Deme’ was introduced by Gilmour and Gregor in 1939. A deme is a community of
potentially interbreeding individuals at a given locality which share a single gene pool. The
term deme is always used with a prefix which characterizes the deme more precisely.

1. Topedeme – a group of individuals existing in a certain geographic region.

2. Ecodeme – a group of individuals associated with a specific habit

3. Phenodeme – a deme differing phenotypically from others.

4. Genodeme – a deme differing from others in genotype.

5. Plastodeme – a deme differing phenotypically from others owing to the effect of

environment.

Sibling species:

Mayr (1952) has used the term sibling species for the sympatric populations that are
morphologically similar if not identical, but are reproductively isolated.

Sibling species occur in almost all animal groups. But they are more common in insects. A
best studied example is the genus Drosophila. Drosophila pseudoobscura and D. persimilis
are so identical in their morphology that these were described as two races of the same
species (race A and race B) by Lancefield (1924).

The salivary gland chromosomes of both these differ, in the arrangement of genes and also
the banding patterns. Morphological differences also exist in the sex comb, male genitalia
and relative wing size. These two races of flies coexist in nature over a wide area without
natural hybridization.

Artificial crosses between race A and race B produce F1 hybrids, of which only females are
fertile and the males are sterile. Lancefield found that sterility is due to the differences in the
Y- chromosome. In race A, Y chromosome is sub-metacentric and in race B, Y is a
metacentric.

With these observations, these biological races are now established as two distinct species
and are described as ‘Sibling species’. In addition to morphological and chromosomal
differences, these two species exhibit differences in ecological, physiological and sexual
behaviors.

Monotypic and polytypic species:

Species containing only a single subspecies are called ‘monotypic’ while those containing
more than one species are termed ‘polytypic’.
3.6 THEORIES OF BIOLOGICAL CLASSIFICATION

Theories of Taxonomy

A theory of taxonomy establishes the principles that we use to recognize and to rank
taxonomic groups. There are two currently popular theories of taxonomy, (1) traditional
evolutionary taxonomy and (2) phylogenetic systematics (cladistics). Both are based on
evolutionary principles. We will see, however, that these two theories differ on how
evolutionary principles are used. These differences have important implications for how we
use taxonomy to study the evolutionary process. The relationship between a taxonomic group
and a phylogenetic tree or cladogram is important for both of these theories. This relationship
can take one of three forms: monophyly, paraphyly, or polyphyly. A taxon is monophyletic if
it includes the most recent common ancestor of the group and all descendants of that
ancestor. A taxon is paraphyletic if it includes the most recent common ancestor of all
members of a group and some but not all of the descendants of that ancestor. A taxon is
polyphyletic if it does not include the most recent common ancestor of all members of a
group; this condition requires that the group has had at least two separate evolutionary
origins, usually requiring independent evolutionary acquisition of similar. Both evolutionary
and cladistics taxonomy accept monophyletic groups and reject polyphyletic groups in their
classifications. They differ on the acceptance of paraphyletic groups, however, and this
difference has important evolutionary implications.
Traditional Evolutionary Taxonomy

Traditional evolutionary taxonomy incorporates two different evolutionary principles for

recognizing and ranking higher taxa: (1) common descent and (2) amount of adaptive
evolutionary change, as shown on a phylogenetic tree. Evolutionary taxa must have a single
evolutionary origin, and must show unique adaptive features.
The mammalian paleontologist George Gaylord Simpson (Figure 10-5) was highly influential
in developing and formalizing the procedures of evolutionary taxonomy. According to
Simpson, a particular branch on the evolutionary tree is given the status of a higher taxon if it
represents a distinct adaptive zone. Simpson describes an adaptive zone as “a characteristic
reaction and mutual relationship between environment and organism, a way of life and not a
place where life is led.” By entering a new adaptive zone through a fundamental change in
organismal structure and behavior, an evolving population can use environmental resources
in a completely new way. A taxon that comprises a distinct adaptive zone is termed a grade.
Simpson gives the example of penguins as a distinct adaptive zone within birds. The lineage
immediately ancestral to all penguins underwent fundamental changes in the form of the
body and wings to permit a switch from aerial to aquatic locomotion. Aquatic birds that can
fly both in the air and underwater are somewhat intermediate in habitat, morphology, and
behavior between aerial and aquatic adaptive zones. Nonetheless, the obvious modifications
of the wings and body of penguins for swimming represent a new grade of organization.
Penguins are therefore recognized as a distinct taxon within the birds, the family
Spheniscidae.

PHYLOGENETIC SYSTEMATICS/CLADISTICS

A second and stronger challenge to evolutionary taxonomy is one known as phylogenetic

systematics or cladistics. As the first name implies, this approach emphasizes the criterion of
common descent and, as the second name implies, it is based on the cladogram of the group
being classified. This approach to taxonomy was first proposed in 1950 by the German
entomologist, Willi Hennig (Figure 10-8) and therefore is sometimes called “Hennigian
systematics.” All taxa recognized by Hennig’s cladistic system must be monophyletic. We
saw how evolutionary taxonomists’ recognition of the primate families Hominidae and
Pongidae distorts genealogical relationships to emphasize adaptive uniqueness of the
Hominidae. Because the most recent common ancestor of the paraphyletic family Pongidae is
also an ancestor of the Hominidae, recognition of the Pongidae is incompatible with cladistic
taxonomy. To avoid paraphyly, cladistic taxonomists have discontinued use of the traditional
family Pongidae, placing chimpanzees, gorillas, and orangutans with humans in the family
Hominidae. We adopt the cladistic classification in many sections.

The disagreement on the validity of paraphyletic groups may seem trivial at first, but its
important consequences become clear when we discuss evolution. For example, claims that
amphibians evolved from bony fish, that birds evolved from reptiles, or that humans evolved
from apes may be made by an evolutionary taxonomist but are meaningless to a cladist. We
simply by these statements that a descendant group (amphibians, birds, or humans) evolved
from part of an ancestral group (bony fish, reptiles, and apes, respectively) to which the
descendant does not belong. This usage automatically makes the ancestral group
paraphyletic, and indeed bony fish, reptiles, and apes as traditionally recognized are
paraphyletic groups. How are such paraphyletic groups recognized? Do they share
distinguishing features that are not shared by the descendant group?

Paraphyletic groups are usually defined in a negative manner. They are distinguished only by
features absent from a particular descendant group, because any traits that they share from
their common ancestry are present also in the excluded descendants (unless secondarily lost).
For example, apes are those “higher” primates that are not humans. Likewise, fish are those
vertebrates that lack the distinguishing characteristics of tetrapod’s (amphibians and
amniotes). What does it mean then to say that humans evolved from apes? To the
evolutionary taxonomist, apes and humans are different adaptive zones or grades of
organization; to say that humans evolved from apes states that bipedal, tailless organisms of
large brain capacity evolved from arboreal, tailed organisms of smaller brain capacity. To the
cladist, however, the statement that humans evolved from apes says essentially that humans
evolved from something that they are not, a trivial statement that contains no useful
information. To the cladist, any statement that a particular monophyletic group descends from
a paraphyletic one is nothing more than a claim that the descendant group evolved from
something that it is not. Extinct ancestral groups are always paraphyletic because they
exclude a descendant that shares their most recent common ancestor. Although many such
groups have been recognized by evolutionary taxonomists, none are recognized by cladists.

Zoologists often construct paraphyletic groups because they are interested in a terminal,
monophyletic group (such as humans), and they want to ask questions about its ancestry. It is
often convenient to lump together organisms whose features are considered approximately
equally distant from the group of interest and to ignore their own unique features. It is
significant in this regard those humans have never been placed in a paraphyletic group,
whereas most other organisms have been. Apes, reptiles, fishes, and invertebrates are all
terms that traditionally designate paraphyletic groups formed by combining various “side
branches” that are found when human ancestry is traced backward through the tree of life.
Such a taxonomy can give the erroneous impression that all of evolution is a progressive
march toward humanity or, within other groups, a progressive march toward whatever species
humans designate as being the most “advanced.” Such thinking is a relic of preDarwinian
views that there is a linear scale of nature having “primitive” creatures at the bottom and
humans near the top just below angels. Darwin’s theory of common descent states, however,
that evolution is a branching process with no linear scale of increasing perfection along a
single branch. Nearly every branch will contain its own combination of ancestral and derived
features. In cladistics, this perspective is emphasized by recognizing taxa only by their own
unique properties and not grouping organisms only because they lack the unique properties
found in related groups.

3.7 TAXONOMIC CHARACTERS

(i) Classical Taxonomy:

Classification of any group of organism uses selected stable characteristics which vary among
the taxa. These are known as taxonomic characteristics. Classically, the bacteria have been
classified on the basis of similarities in phenotypic characteristics, like morphological
features, response to Gram stain, cultural characteristics, physiological biochemical
properties, pathogenicity, antibiotic sensitivity, serological relationships etc. Taxonomically
important morphological, cultural and physiological- biochemical characteristics are shown
in Table 3.1, 2 and 3 respectively.

(ii) Molecular Taxonomy:

Approach to bacterial taxonomy has undergone drastic changes since the development of
molecular biology in the second half of the twentieth century. The concept that
macromolecules, like proteins and nucleic acids, could be used as an indicator of evolution of
living organisms was first suggested by Zuckerkandl and Pauling in 1965.

They described these macromolecules as “molecular chronometers”, because the sequences

of monomers in them have changed slowly and randomly and the number of changes in a
particular macromolecule has increased linearly with geological time scale.

A comparison of the sequence of monomers of a particular macromolecule from two

organisms should, therefore, give a measure of their phylogenetic relationship. If the
sequences differ considerably, it indicates that the two organisms are phylogenetically
distant.

This new approach has given rise to the molecular taxonomy. Although initially amino acid
sequencing of proteins was used as a parameter for determination of phylogenetic relations,
nucleic acids soon replaced proteins. Among the characteristics of nucleic acids, DNA base
composition, DNA homology, DNA sequencing, r-RNA sequence analysis etc. have been
used for solving taxonomic problems.

The principles of some of the methods are briefly described:

(a) DNA base composition:

The first characteristic that was applied in solving taxonomic problems was the base
composition of DNA. A unique feature of DNA is that the ratio of (G + C): (A + T) is more
or less constant for a biological species. The ratio is conventionally expressed as G + C moles
%. Organisms which are closely related, like the strains of a given species have close values
of G + C moles %. In bacteria; this value varies from about 25% to 80%.

Several methods are available for experimental determination of DNA base ratio. Of these,
two methods commonly employed are those by determination of melting temperature of
DNA and buoyant density. The principles are described briefly.

A characteristic feature of double-stranded DNA helix is that at a high temperature the helical
structure collapses producing two single strands due to dissolution of the H-bonds. This is
known as melting and the temperature at which melting occurs is a character of a particular
species of DNA.

Because there are three H-bonds between G and C, and two between A and T, a DNA
molecule having more of G + C melts at a higher temperature. Another important
characteristic of DNA is that molten or denatured DNA shows an increase in optical density
at 260 nm, a phenomenon known as hyperchromicity.

This means that as the double stranded DNA is dissociated into single-stranded state, its
optical density at 260 nm (OD260) gradually increases and reaches a maximum when all the
DNA present in a sample becomes denatured. This can be measured in an instrument called
UV spectrophotometer having an arrangement for gradually raising the temperature of a
DNA solution.

By plotting % increase of OD26o against temperature, a curve is obtained as shown in Fig.

3.4. The temperature at which 50% of maximum increase is reached is taken as the melting
temperature (Tm) of that particular species of DNA. From the melting temperature, the G + C
moles % can be calculated from the relation, Tm = 69.3 + 0.41(G + C) %.

Although G + C content of DNA is a useful taxonomic character, it alone may not indicate a
close relation, because two quite unrelated organisms may have by chance close G + C
content. But for two organisms resembling each other in most other phenotypic characters, a
close G + C content of DNA can be taken as a reliable indication of their phylogenetic
relatedness.

By analysis of G + C content of DNA of large number of bacteria, it has been found that
strains within a species have more or less identical values and its variation in different species
within a genus usually does not exceed by more than 10%.

It should be remembered that G + C content gives only the overall composition of DNA and
gives no information about the sequence of bases in the DNA molecule. It is this sequence in
a DNA segment that constitutes the specificity of a gene. So, G + C content of DNA does not
give any information regarding the similarity of genes of two organisms.

Another technique of determination of G + C moles % of DNA utilizes a different property of

double-stranded (ds-) DNA. The buoyant density of ds-DNA increase linearly with its G + C
content. In an equilibrium density gradient, homogeneous nucleic acid accumulates as a
symmetrical band, the width of which is inversely proportional to the square root of its
molecular weight.
Smaller molecules having a lower molecular weight tend to diffuse more rapidly than larger
molecules and, hence, have wider bands. Also, DNA samples differing in G + C content form
separate bonds, because of their difference in density.

In equilibrium density gradient centrifugation using caesium chloride (CsCl), the samples of
DNA, previously purified by removing proteins and RNA, are mixed thoroughly with a 6M
solution of the caesium salt in a PVC (polyvinyl chloride) centrifuge tube and the mixture is
subjected to high speed ultracentrifugation for a sufficiently long time to allow the formation
of a density gradient.

The highest density is at the bottom of the tube and it gradually decreases upwards. The
different components of the DNA sample collect in distinct bands at levels where the density
of a particular component equals that of the gradient.

The fractions can be collected by puncturing the PVC tube at the bottom and their density
determined. From the buoyant density of the DNA bands, their G + C moles % can be
calculated from the relation, p (buoyant density) = 1.660 + 0.98 (G + C) %.

(b) Nucleic acid hybridization:

More reliable information about the similarity of the genomes of two organisms can be
obtained by DNA-DNA hybridization, because formation of a heteroduplex between two
single stranded DNA molecules derived from two organisms depends on the degree of
complementarity of the two single strands.

A double-stranded DNA can be dissociated into single strands by application of heat. An

interesting feature of single-stranded DNA is that on cooling, the strands tend to re-associate
to form double-helix structure automatically. This process, known as annealing, occurs
optimally when the temperature is brought to about 25°C below the melting temperature in a
solution of high ionic concentration, such as 0.3M NaCl which reduces electrostatic repulsion
between the DNA strands.

Various methods have been developed for quantitative determination of heteroduplex

formation. One of the most commonly employed techniques involves binding of
comparatively long DNA molecules of one organism to nitrocellulose filter and allowing the
bound DNA molecules to hybridize with comparatively short DNA molecules of the other
organism.

For differentiating between the two species of DNA, one of them — usually the second one
32
— is made radioactive by labeling with either P or 3H. Radioactive DNA is obtained by
32
growing an organism in a medium containing a radioactive salt e.g. P labeled phosphate.
DNA becomes labeled and is then isolated and purified for use in hybridization.

For DNA-DNA hybridization, the longer non-radioactive single stranded DNA molecules are
first allowed to bind to a nitrocellulose filter, unbound DNA is removed by washing and the
filter with bound DNA is incubated with the radioactive smaller single-stranded DNA under
optimal conditions of annealing.

During incubation the smaller radioactive molecules hybridize with the longer DNA
molecules depending on their homology in the base sequences. Then the filter is washed to
remove the unbound radioactive DNA molecules and the radioactivity of the filter is
measured.

(c) Ribosomal RNA homology:

An important discovery made in 1965 revealed that in all living organisms, the DNA
segments transcribing ribosomal RNA (r-cistrons or r-DNA) have changed more slowly in
course of evolution than the rest of the genome. In other words, the r-cistrons are more
conserved in comparison to the genes encoding proteins.

This provided an instrument for comparing the phylogenetic relationships between distantly
related organisms through determination of base sequences of r-RNA or r-DNA. Among the
different r-RNAs, the 16S r-RNA of prokaryotic organisms and the analogous 18S r-RNA of
eukaryotes have been found to be most suitable for comparison of their sequences in
taxonomic studies.

The method used in the beginning for determination of r-RNA homology was oligonucleotide
cataloging. Purified r-RNA was cleaved into oligonucleotides by specific enzymes, like
bacteriophage T1 RNase, separated by two-dimensional electrophoresis, further hydrolysed
into smaller segments and again electrophoresed to determine their nucleotide sequences.
The sequence of one unique oligonucleotide of each organism was stored in computer.
Sequences of different organisms were compared to determine their similarity. Ribosomal
RNA of most of the major taxonomic group has been found to possess one or more unique
sequences which are known as their oligonucleotide signature. Such signature sequences have
been determined for most of the major taxonomic groups of bacteria.

One of the major impacts of r-RNA studies on taxonomy is the recognition of three major
domains — the Archaea, the Eucarya including all eukaryotes, and the Bacteria. It has been
claimed by Woese, Kandler and Wheelis (1990) that the three major evolutionary lines
diverged from a common ancestral form.

Advances in the molecular biological techniques have now made it possible to determine
nucleotide sequences of r-DNA for preparing phylogenetic trees with the help of computers.
Such trees are built up by comparing the sequences of two molecules by alignment. The
number of mismatches in the sequence is counted and used to calculate the evolutionary
distance. The similarity between the two molecules is expressed as similarity coefficient.

A group of closely related organisms e.g. species of the same genus, will generally have a
narrow range of similarity coefficients. Conversely, a wider range of similarity coefficients
indicates that the organisms have branched off from each other in more remote past.
 UNIT4: PROCEDURES IN TAXONOMY

4.1 Objectives
4.2 Introduction
4.3 Taxonomic procedure
4.3.1 Taxonomic collection
4.3.2 Preservation
4.3.3 Identification
4.4 International Code of Zoological Nomenclature (ICZN)
4.4.1 Principals, Application and Rules
4.4.2 Zoological Nomenclature and Formation of Scientific Names of Various Taxa

4.1 OBJECTIVES

• Study of Taxonomic procedure, Taxonomic collection, Preservation & Identification.

• Study of International Code of Zoological Nomenclature (ICZN) & Zoological

Nomenclature and Formation of Scientific Names of Various Taxa

4.2 INTRODUCTION

Taxonomy, in a broad sense the science of classification, but more strictly the classification
of living and extinct organisms—i.e., biological classification. The term is derived from the
Greek taxis (“arrangement”) and names (“law”). Taxonomy is, therefore, the methodology
and principles of systematic botany and zoology and sets up arrangements of the kinds of
plants and animals in hierarchies of superior and subordinate groups. The term first proposed
by the Swiss originated botanist Augustine Paramus de Candolle in 1813 for the plant
classification. He used the term in his famous book—Theory elementaire de la botanique
(Elementary Theory of Botany). So taxonomy is the arrangement of the plants and animals on
the basis of some laws.
 4.3 TAXONOMIC PROCEDURE

Biological collections are typically preserved plant or animal specimens along with specimen
documentation such as labels and notations. TYPES OF COLLECTIONS Most biological
collections are either dry collections or wet collections. They also may include collections
preserved at low temperatures or microscopy collections. DRY COLLECTION Dry
collections consist of those specimens that are preserved in a dry state. Some specimens can
be preserved naturally (starfish) or artificially with sufficient rigidity to accommodate normal
handling. Such specimens often are suitable for dry preservation. Specific characteristics.
Drying may provide the best available means to preserve natural colors (for example,
butterflies) or distinguishing features (such as skeletal parts or surface details). Such
specimens in a dry state may have great potential for interpretation and research.
WET COLLECTIONS: Wet collections are specimens kept in a liquid preservative to
prevent their deterioration. Certain biological specimens are preserved in a wet form due to: ·
convenience · an intent to preserve body form and soft parts for a variety of uses When color
preservation is not critical and dry preservation sacrifices qualities needed for other intended
uses, fluid preservation is beneficial. BIOLOGICAL LOW-TEMPERATURE
COLLECTIONS Specimens are maintained at low temperatures to preserve: · soft parts for
various biochemical analyses · whole organisms in a viable (able to live and grow) state.
specimens preserved at low temperatures - Some algae, Protozoa (especially parasitic
strains), Viruses, Cloned viral genomes, Bacteria,Bacteriophages,Plasmids · Animal tissues
(dissected organs, muscles),Cell lines - Blood and blood components (whole blood, serum,
plasma, antisera) - Semen,Venom - Other samples (cloned probes, isolated proteins and
nucleic acids, cell suspensions) Note: The largest organisms that can be preserved in a viable
state are some insects.
BIOLOGICAL MICROSCOPY COLLECTIONS:Scientists preserve certain specimens
as microscope preparations to preserve whole or partial organisms for various kinds of
microscopic examination & some kinds of biochemical analyses, including extraction of
DNA. Specimens prepared for microscopy may be found in all biological collections, but are
most common in these collections are like entomology, mycology, parasitology etc. It’s also
common for microscopy collections to be ancillary to more traditional collections. Examples
of such ancillary collections included histology, karyology & scales.
Value of biological collections most biological collections are highly valuable for the
following reasons. Museums are only place where extinct species are preserved. Specimens
of special historical value. Specimens rarely found in any collections. Many areas in world
are geographically inaccessible. Material from such area is invaluable & is preserved at all
costs A material is of unique value if it forms the basis of published research. It may be
needed again for verification of original data or for renewed study in the light of more recent
knowledge or by new techniques.
• METHODS OF COLLECTON Mist net Arctic tern caught in mist net
• Attracting Nocturnal Insects with UV Light Many insects can see ultraviolet light,
which has shorter wavelengths than light visible to the human eye. For this reason, a
black light will attract different insects than a regular incandescent light. . The black
light can be suspended in front of a white sheet, giving flying insects a surface on
which to land. You can then observe the insects on the sheet, and collect any
interesting specimens by hand. A black light trap is constructed by suspending a black
light over a bucket or other container, usually with a funnel inside. Insects fly to the
light, fall down through the funnel into the bucket, and are then trapped inside the
container. Black light traps sometimes contain a killing agent, but can also be used
without one to collect live specimens.
• Malaise traps A Malaise trap is a large, tent-like structure used for trapping flies and
wasps. Insects fly into the tent wall and are funneled into a collecting vessel attached
to highest point.
• Insects are collected mainly by beating and sweeping beating sweeping
• Plankton net Aquatic insects and other arthropods are collected by using dip nets &
plankton nets Dip net
• Trawling and dredging for collecting deep-sea animals Trawling Dredging
• Collecting net
• Aspirator
• Berlese funnel
• Floatation method Used to collect arthropods, eggs and pupae of insects from soil or
matted vegetation.
• Killing bottles Cyanide bottle Killing tube POISON
 • RECORDING DATA: Geographic locality Stratigraphic position (for fossils only)
Date, Stage (adult male, female or immature form) Altitude or depth, Host Name of
collector etc.
• Genitalia preserved in tiny glass vial along with specimen.
• Storage building should be Fireproof Dustproof Earthquake resistant Air-conditioned.
Special care for type specimens Type specimens should not be allowed to be handled
frequently. They should only be examined by experts. Avoid their transport as far as
possible. They should be stored separately from general collection. They should be
clearly labeled in distinct colours.
• Method of cataloguing is different from group to group. In higher vertebrates each
specimen is given separate number and catalogued separately.In case of insects this is
not done due to their large number. All specimens from one locality are catalogued
together. Only type specimens are unusually catalogued. In large museums type
catalogues are bound in book in which types are serially numbered. There are various
ways in using filing cards of collections: Some museums have elaborate card filing
system which help in easy collection of information about specimen. Some large
museums place all information about each specimen on separate IBM card.
• Museum number Original field number Scientific name Locality Date Collector
remarks

4.3.1 TAXONOMIC COLLECTION

Every taxonomist has to take the responsibility of curating collections. This requires a great
deal of expertise, knowledge and clear understanding of the function of different collections.
Preparation of Material There are certain materials which are ready for study as soon as
collected from the field e.g., bird and mammal skins. There are certain insects which should
never be placed in alcohol or any other liquid preservative whereas others are useless when
dried. Certain invertebrates are to be preserved in alcohol of formalin before their study.
Microscope slide mounts or slides of parts of organs may have tube prepared for the smaller
forms. Most insects are pinned, and the wings are spread if they are taxonomically important
as in butterflies, moths and some grasshoppers. Housing Research collections should be
housed in fireproof and dustproof buildings. Most museums keep their collections in air-
conditioned buildings. Rapid changes in temperature and humidity are harmful to museum
cases and specimens. Storage cases should be built to be insect-proof. Photographs and films
should be stored in air-conditioned rooms. Cataloging the method of cataloging depends on
the group of animals. All the specimens including vertebrates collected at a given locality or
district or by one expedition are entered in the catalog together. This greatly facilitates in
knowing the distributional data and the preparation of faunistic analyses. Cataloging is
usually done after the specimens have been identified, at least up to the genus level. In groups
where the collections consist of large numbers of specimens, it is customary to catalog the
specimens by lots. Each lot consists of a set of specimens from a given locality or region. It is
also important to note whether a lot was received as a gift or by purchase or exchange. The
names of the collector and donor are always given. When museums and their collections were
small, curators had maintained card-files which provided all sorts of information such as
collecting station, name of the collector etc.
Maintenance of computer record should never be at the cost of work on systematic
collections. Arrangement of the Collection The collection should be arranged in the same
sequence as some generally adopted classification. The sequence of orders and families is
usually standardized in many classes of animals. The contents of trays and cases should be
clearly indicated on the outside which could serve as a check list. Where specimens are of
large and unequal size, they have to be stored separately. Curating of Types the names of
species are based on type specimens. Many descriptions of classical authors are equally
applicable to several related species. Types are usually deposited in large collections in public
or private institutions which have come to be recognized as standard repositories of types.
While conducting an authoritative revision ofa given genus, a specialist should be able to see
all the existing types. If many of them are in a single institution, the specialist should travel
the read obtain scattered types.
Modern curators are quite liberal in lending type specimens to qualified specialists. It is
recommended that the type collections should be arranged alphabetically according to the
given specific name. A type collection is a reference collection rather than classification.
Type specimens assume such an important role in the taxonomy of lesser-known groups that
many workers believe that no individual should retain a type in his private collection after the
study has been completed. Exchange of Material the selecting of material for exchanges and
keeping its record is time-consuming, so the exchanges are not as popular as they used tube.
Among private collectors this practice is common. Specialists doing a monograph on a
certain genus or family can always borrow material from other institutions and return it after
completing his work. Exchanges are not desirable in groups where series of unlimited size
can be obtained and where the concerned areas are not easily accessible.
Exchanges are sometimes necessary to build up complete identification collections. Many
specialists give away excess specimens as open exchanges not expecting any return.
Improperly preserved or inadequately labeled specimens should be eliminated by the curator
.The most efficient method for the elimination of useless material is to ask specialists to pull
out such specimens while scrutinizing the material during a revision. LoansModern curators
are very generous in lending specimens to qualified experts.This is due to the fact that
systematic collections are the general property of science and not of a specific institution or
curator. Every loan, however, involves loss of time and effort, and the borrower should
refund the lender for his efforts. Research grants now include an item so as to cover the costs
of postage, selecting the specimens, recording the loan, and getting the material packed for
shipment. The modern curator, being essentially a research worker, must delegate these tasks
to hired clerical help. A request for the loan of specimens should be as specific as possible,
including a statement of the reason for the request and some indication of the length of time
for which the material is needed.
The beginner may be unable to borrow certain material except through a loan to his or her
institution or to the beginner’s major professor. If the borrower is unable to complete the
studies in the designated time, the person or institution that made the loan should be
informed. The lender should never be placed in the embarrassing position of having to write
and ask about the status of the study. If a specialist has agreed to identify a collection
provided he or she receives certain specimens, the specialist should make sure that the terms
of the agreement are well understood and should return to the lender a list of the specimens
which he or she has retained. All types and unique specimens must be returned to the lender
in such cases.

4.3.2 PRESERVATION
Specimens of insects and arthropods, if properly preserved and cared for, can last hundreds of
years. Any given specimen carries an enormous potential to inform us about itself and the
time and place of collection. Maintaining any specimen for many years carries a cost. Proper
preservation ensures a high quality specimen, which increases the quality of information the
specimen contains, and increases the value of the maintenance of the specimen. A good
specimen takes up just as much room as a bad one. The same as five dirty, rusty, junk cars
take up just as much space as five clean, shiny, perfectly restored cars.
Detailed information about general and specific types of preservation can be found within the
publications recommended on the Collecting Insects page of this wiki. Below is an overview
appropriate for general preservation and curation.

Adult:
Adult:
Temporary Immature
Permanent Comments
Order (Field) Preservatio
Preservatio *
Preservatio n
n
n

Arachnids Never
Ethanol Ethanol Ethanol
1 (Spiders, Mites, allow to
(80%) (80%) (80%)
Etc.) dry

Never
Ethanol Ethanol Ethanol
2 Protura allow to
(80%) (80%) (80%)
dry

Never
Collembola Ethanol Ethanol Ethanol
3 allow to
(springtails) (80%) (80%) (80%)
dry

Never
Ethanol Ethanol Ethanol
4 Diplura allow to
(80%) (80%) (80%)
dry

Microcoryphia Never
Ethanol Ethanol Ethanol
5 (jumping allow to
(80%) (80%) (80%)
bristletails) dry

Never
Thysanura Ethanol Ethanol Ethanol
6 allow to
(silverfish) (80%) (80%) (80%)
dry

Ephemeroptera Ethanol Ethanol Ethanol Never

7
(mayflies) (80%) (80%) (80%)
allow to
 dry

Do not kill
Odonata
Pinned or Ethanol or preserve
8 (dragonflies and Dry, kill jar
enveloped (80%) adult in
damselflies)
fluid

Dry, kill jar;

Orthoptera
ethanol Ethanol
9 (grasshoppers and Pinned
(80%), may (80%)
crickets)
fade color

Dry, kill jar;

1 Ethanol Ethanol
Grylloblattodea ethanol
0 (80%) (80%)
(80%)

1 Mantophasmatod Ethanol Ethanol Ethanol

1 ea (80%) (80%) (80%)

1 Phasmatodea Ethanol
Dry, kill jar Pinned
2 (walkingsticks) (80%)

1 Mantodea Ethanol
Dry, kill jar Pinned
3 (preying mantids) (80%)

Dry, kill jar;

1 Blattodea Ethanol
ethanol Pinned
4 (cockroaches) (80%)
(80%)

Never
1 Ethanol Ethanol Ethanol
Isoptera (termites) allow to
5 (80%) (80%) (80%)
dry

Rubbing Alcohol, also called Isopropyl Alcohol and Isopropanol is a commonly available
alcohol that can be used to preserve specimens, but it is not recommended for long term
storage. Specimens will become very brittle over a short period of time.
Ethanol, also called ethyl alcohol and grain alcohol is generally the best fluid for short and
long term preservation of specimens. Low concentrations of alcohol (below 70%) will not
properly preserve a specimen, while high concentrations (above 90%) may cause the
specimen to crush under osmotic pressure. Generally 80% (160 proof) ethanol is the best to
use. In a pinch, high alcohol distilled spirits, such as 100 proof vodka or rum, can be used,
but only for short periods of time until replaced by proper strength ethanol.

If there is a chance that the ethanol will be significantly diluted (for example, many
specimens in the same jar, specimens are large and fluid filled, etc.) it is best to replace the
ethanol once after 24-48 hours. Some large immature flies, dragonflies, beetles, and
caterpillars may begin to rot internally before they become sufficiently preserved if placed
directly in ethanol. Two common practices used to prevent this are: 1) inject the specimen
with ethanol before immersing within ethanol; 2) bring water to a boil, take it off the heat,
drop the specimen in the water and leave it for 1-2 minutes, remove specimen, pat dry, place
in ethanol. Replace ethanol once after 24-48 hours. Never allow specimens preserved in
ethanol to dry out, unless they have been removed for pinning.

4.3.3 IDENTIFICATION

Taxonomic identification is the recognition of the identity or essential character of an

organism. Taxonomists often present organized written descriptions of the characteristics of
similar species so that other biologists can identify unknown organisms. These organized
descriptions are referred to as taxonomic keys. A taxonomic key is often published with
pictures of the species it describes. However, written descriptions are usually preferred over
pictures, since pictures cannot convey the natural variation in the morphology of a species,
nor the small, yet characteristic, morphological features of a species. In addition, matching an
unidentified organism to one picture in a book of hundreds or thousands of pictures can be
very time-consuming.

4.4 INTERNATIONAL CODE OF ZOOLOGICAL NOMENCLATURE (ICZN)

The International Code of Zoological Nomenclature (ICZN) is a widely

accepted convention in zoology that rules the formal scientific naming of organisms treated
as animals. It is also informally known as the ICZN Code, for its publisher, the International
Commission on Zoological Nomenclature (which shares the acronym "ICZN"). The rules
principally regulate:

• How names are correctly established in the frame of binominal nomenclature[1]

• Which name must be used in case of name conflicts
• How scientific literature must cite names

Zoological nomenclature is independent of other systems of nomenclature, for

example botanical nomenclature. This implies that animals can have the same generic names
as plants.

The rules and recommendations have one fundamental aim: to provide the maximum
universality and continuity in the naming of all animals, except where taxonomic judgment
dictates otherwise. The code is meant to guide only the nomenclature of animals, while
leaving zoologists freedom in classifying new taxa.

In other words, whether a species itself is or is not a recognized entity is a subjective

decision, but what name should be applied to it is not. The code applies only to the latter. A
new animal name published without adherence to the code may be deemed simply
"unavailable" if it fails to meet certain criteria, or fall entirely out of the province of science
(e.g., the "scientific name" for the Loch Ness Monster).

The rules in the code determine what names are valid for any taxon in
the family group, genus group, and species group. It has additional (but more limited)
provisions on names in higher ranks. The code recognizes no case law. Any dispute is
decided first by applying the code directly, and not by reference to precedent.

The code is also retroactive or retrospective, which means that previous editions of the code,
or previous other rules and conventions have no force any more today, and the nomenclatural
acts published 'back in the old times' must be evaluated only under the present edition of the
code.

(Adopted by the 15th International Congress of Zoology (London) and published on

November 6, 1961)

The object of the code is to promote stability and universality in the scientific name of
animals, and to ensure that each name is unique and distinct.
The Swedish naturalist Carl von Linne’ (1707-1778), who changed his name to a binomen,
Carolus Linnaeus, was the father a set of rules of nomenclature published in Critica
Botanica (1737), Philosophia Botanica (1751) and in the 10th edition of Systema
Naturae (1758). The confusion that prevailed after Linnaeus was solved in the 5th
International Congress of Zoology in Berlin in 1901. The original code was, however,
adopted in 1904 in the 6th International Congress of Zoology in Bern and published in 1905
in Paris as, “Regles Internationales de la Nomenclature Zoologique.”

The most recent version (a modified version of 1961 code) was published in 1964 in parallel
French and English. It was adopted by the 16th International Congress of Zoology,
Washington (1963) with modifications in articles 11, 31, 39 and 60.

International Congress of Zoology is a legislative body, which adopts by voting the

constitution and proposals put before it by the commission.

International Commission on Zoological Nomenclature is a judicial body elected by the

International Congress of Zoology. It is protector of the code and deals with the
interpretations, disputes and implementation of the code. Amendments have to be routed
through the commission.

International Code of Zoological Nomenclature (1964) is the system of rules and

recommendations authorized by the International Congress of Zoology. The object of the
code is to promote stability and universality in the scientific names of animals and to ensure
that each name is unique and distinct. Code does not restrict the freedom of taxonomic
thought and action.

Before the present code, the following codes were prevalent in Europe and U.S.A.:

1. Strickland Code (1842) in Berlin.

2. W.H.Dall Code (1877) in USA.

3. Douville’ Code (1881) in France.

Salient features of the “Code”

The 1964 code consists of a Preamble, 86 Articles, 5 Appendices, a Glossary and a

detailed Index, in parallel English and French. Starting date of the code is 1st January 1758
(publication date of the10th edition of Systema naturae).
1. Names must either be Latin or Latinized.

2. Names of taxa higher than species should be uninominal.

3. Name of a species is binomen.

4. Name of a subspecies is a trinomen.

5. Name of a subgenus is placed in parenthesis between genus and species, e.g. Xorides
(Gonophonus) nigrus.

6. Family name should end in DAE, e.g. Tipulidae.

7. Genus name should be a noun in nominative singular or treated as such, e.g. Apis, Rana.

8. Species name should be an adjective or noun in nominative singular agreeing in gender

with the generic name, e.g. Drosophila obscura, Felis tigris etc. OR a noun standing in
opposition to the generic name, e.g. Felis leo.

9. Zoological nomenclature is independent of other systems.

10. All names given to the species from time to time should be mentioned in synoymy.

11. Author’s name is not part of the name. It’s use is optional and is suffixed, e.g. Cancer
pagurus Linnaeus.

12. Law of priority: The valid name is the oldest name published and available.

13. Synonymy: Synonyms are different names assigned to the same taxon. They should be
mentioned along with the valid taxon, e.g. Erias vitella(=Erias fabia).

14. Homonymy: Homonyms are identical names in spelling for different species of the same
genus and for different genera of a family. Junior homonym has to be rejected. Homonymy
arises when an existing species’ name is not known to the person assigning a name, or a
species with identical name is transferred to the same genus.

15. Holotype: Single specimen on which description of the species is based. Red colored
label is fixed on the specimen.

16. Allotype: Specimen of the opposite sex to holotype. Also carries a red label.

17. Paratype: All remaining specimens after the designation of holotype and allotype are
assigned the status of paratypes. They carry yellow labels.
18. Syntypes: If no holotype is designated, all specimens that the author studied for the
description of the species are called syntypes.

19. Lectotype: In the absence of a holotype, one specimen from syntypes can be designated
as Lectotype and rest of the specimens as Paralectotypes.

20. Neotype: If all type-specimens are destroyed, a neotype, that fits the description very
well, can be designated under exceptional circumstances.

4.4.1 PRINCIPALS, APPLICATION AND RULES

“Zoological nomenclature is the system of scientific names applied to taxonomic units of

animals (taxa) known to occur in nature, whether living or extinct.” The nomenclature should
fulfill the following three basic requirements:

UNIQUENESS: The name of a taxon is like the index number of a file. It gives immediate
access to all information in literature, available about a particular taxon. Every name must be
unique because it is key to the entire literature. Uniqueness has been achieved by
adopting binominal nomenclature, as proposed by Linnaeus in the X edition of Systema
Naturae in 1758.

According to binominal nomenclature, each species name should consist of the first generic
and second species name. Species name should not duplicate under any genus, e.g. Panthera
leo, Panthera tigris, Panthera pardus. A combination of the two makes the name unique.

UNIVERSALITY: Scientific names should be known to all and be universally accepted.

Vernacular names would be difficult to keep track of, and scientists will have to learn names
in several languages of the world. To avoid this, zoologists have adopted by international
agreement a single language, Latin, which is a dead language and therefore does not evolve
and is acceptable to everybody.

One need not learn Latin language in order to give name. Any word in any language, if
latinized by changing the ending by suffixing –us,-a, or –ensis is acceptable as valid Latin
name, e.g., japonica, indicus, chinensis. Use of Latin is also advantageous due to the fact that
most of the ancient scientific literature is written either in Latin or Greek and it would be easy
to refer to the old literature if names are given in Latin.
STABILITY: Zoological names would lose their utility if they were changed frequently and
arbitrarily. It would create confusion if we call an object spoon today and apple next
week. International Code of Zoological Nomenclature has been designed to bring about
stability. Taxonomists are bound to follow the rules given in the code before assigning names
to taxa. Most of the changes in names are due to taxonomists’ errors. Lot of name changing
has taken place during the last 200 years. International Code of Zoological Nomenclature
safeguards against frequent name changing.

4.4.2 ZOOLOGICAL NOMENCLATURE AND FORMATION OF

SCIENTIFIC NAMES OF VARIOUS TAXA

The format for writing scientific names of animals and plants is standardized and
internationally accepted. “Scientific nomenclature” refers to various names according to a
specific field of study. This article is the first in a series on scientific nomenclature within
specific kingdoms.

Usually, animals & plants are identified by common and scientific names.

Taxonomists have established several “codes” for scientific nomenclature. These codes are
universal and are periodically updated by consensus. The protocol for naming species was
invented in the 1700s by Swedish botanist Carl Linnaeus. Linnaeus created the system of
“binomial nomenclature,” which uses only two designations–genus and specific epithet as the
species name.
The levels from highest to lowest classification are as follows:

• Domain
• Kingdom
• Phylum
• Class
• Order
• Suborder
• Family
• Genus
• Species
• Subspecies
Using this system, the gray wolf, for example, would be identified as follows:

• Domain: Eukarya.
• Kingdom: Animalia.
• Phylum: Chordata.
• Class: Mammalia.
• Order: Carnivora.
• Suborder: Caniformia.
• Family: Canidae.
• Genus: Canis.
• Species: lupus.

WRITING SCIENTIFIC NAMES OF ANIMALS

When writing, we use both the scientific name and the “common” name on the first mention.
We then choose which to use throughout and make it consistent.

• Gray wolf (CANIS LUPUS) is native to North America and Eurasia.

In subsequent references, we can use either the common or scientific name. If we use the
scientific name, we need only to use the first letter of the genus followed by a period and the
specific epithet. For example:

• In North America, the gray wolf was nearly hunted to extinction.

• In North America, C. LUPUS was nearly hunted to extinction.

It is also common to refer to several species less than one genus when you want to point out
some similar characteristics within a genus. For example:

• All species of CANIS are known to be moderate to large and have large skulls.

You could also write this same information another way as follows:

• CANIS spp. is known to be moderate to large and have large skulls.

In this case, “spp.” is an abbreviation for “several species” (“sp” is the designation for one
species) in the genus. Either of the above is acceptable. If you are focusing on a few species
in particular, you would refer to the species name of each one.
 BLOCK II: EVOLUTION
UNIT 5: LAMARCK & DARWINISM

5.1 Objectives
5.2 Introduction
5.3 Concept & theories of Evolution
5.4 Hardy-Weinberg law of Genetic Equilibrium
5.5 Detailed account of Destabilizing Forces
5.5.1 Natural Selection
5.5.2 Mutation
5.5.3 Genetic Drift
5.5.4 Migration

5.1 OBJECTIVES
We will know about Concept & theories of Evolution & Hardy-Weinberg law of Genetic
Equilibrium, Natural Selection, Mutation and Genetic Drift.

5.2 INTRODUCTION
Evolution, theory in biology postulating that the various types of plants, animals, and other
living things on Earth have their origin in other preexisting types and that the distinguishable
differences are due to modifications in successive generations. The theory of evolution is one
of the fundamental keystones of modern biological theory.

The diversity of the living world is staggering. More than 2 million existing species of
organisms have been named and described; many more remain to be discovered—from 10
million to 30 million, according to some estimates. What is impressive is not just the numbers
but also the incredible heterogeneity in size, shape, and way of life—from lowly bacteria,
measuring less than a thousandth of a millimeter in diameter, to stately sequoias, rising 100
meters (300 feet) above the ground and weighing several thousand tons; from bacteria living
in hot springs at temperatures near the boiling point of water to fungi and algae thriving on
the ice masses of Antarctica and in saline pools at −23 °C (−9 °F); and from giant tube worms
discovered living near hydrothermal vents on the dark ocean floor to spiders and larkspur
plants existing on the slopes of Mount Everest more than 6,000 meters (19,700 feet) above
sea level.
The virtually infinite variations on life are the fruit of the evolutionary process. All living
creatures are related by descent from common ancestors. Humans and other mammals
descend from shrew like creatures that lived more than 150 million years ago; mammals,
birds, reptiles, amphibians, and fishes share as ancestors aquatic worms that lived 600 million
years ago; and all plants and animals derive from bacteria-like microorganisms that
originated more than 3 billion years ago. Biological evolution is a process of descent with
modification. Lineages of organisms change through generations; diversity arises because the
lineages that descend from common ancestors diverge through time.

The 19th-century English naturalist Charles Darwin argued that organisms come about by
evolution, and he provided a scientific explanation, essentially correct but incomplete, of how
evolution occurs and why it is that organisms have features—such as wings, eyes, and
kidneys—clearly structured to serve specific functions. Natural selection was the
fundamental concept in his explanation. Natural selection occurs because individuals having
more-useful traits, such as more-acute vision or swifter legs, survive better and produce more
progeny than individuals with less-favorable traits. Genetics, a science born in the 20th
century, reveals in detail how natural selection works and led to the development of the
modern theory of evolution. Beginning in the 1960s, a related scientific discipline, molecular
biology, enormously advanced knowledge of biological evolution and made it possible to
investigate detailed problems that had seemed completely out of reach only a short time
previously—for example, how similar the genes of humans and chimpanzees might be (they
differ in about 1–2 percent of the units that make up the genes).

The evidence for evolution

Darwin and other 19th-century biologists found compelling evidence for biological evolution
in the comparative study of living organisms, in their geographic distribution, and in the
fossil remains of extinct organisms. Since Darwin’s time, the evidence from these sources has
become considerably stronger and more comprehensive, while biological disciplines that
emerged more recently—genetics, biochemistry, physiology, ecology, animal behaviour
(ethology), and especially molecular biology—have supplied powerful additional evidence
and detailed confirmation. The amount of information about evolutionary history stored in
the DNA and proteins of living things is virtually unlimited; scientists can reconstruct any
detail of the evolutionary history of life by investing sufficient time and laboratory resources.
Evolutionists no longer are concerned with obtaining evidence to support the fact of
evolution but rather are concerned with what sorts of knowledge can be obtained from
different sources of evidence. The following sections identify the most productive of these
sources and illustrate the types of information they have provided.

Paleontologists have recovered and studied the fossil remains of many thousands of
organisms that lived in the past. This fossil record shows that many kinds of extinct
organisms were very different in form from any now living. It also shows successions of
organisms through time, manifesting their transition from one form to another.

When an organism dies, it is usually destroyed by other forms of life and by weathering
processes. On rare occasions some body parts—particularly hard ones such as shells, teeth, or
bones—are preserved by being buried in mud or protected in some other way from predators
and weather. Eventually, they may become petrified and preserved indefinitely with the rocks
in which they are embedded. Methods such as radiometric dating—measuring the amounts of
natural radioactive atoms that remain in certain minerals to determine the elapsed time since
they were constituted—make it possible to estimate the time period when the rocks, and the
fossils associated with them, were formed.

Radiometric dating indicates that Earth was formed about 4.5 billion years ago. The earliest
fossils resemble microorganisms such as bacteria and cyanobacteria (blue-green algae); the
oldest of these fossils appear in rocks 3.5 billion years old. The oldest known animal fossils,
about 700 million years old, come from the so-called Ediacara fauna, small wormlike
creatures with soft bodies. Numerous fossils belonging to many living phyla and exhibiting
mineralized skeletons appear in rocks about 540 million years old. These organisms are
different from organisms living now and from those living at intervening times. Some are so
radically different that paleontologists have created new phyla in order to classify them. The
first vertebrates, animals with backbones, appeared about 400 million years ago; the first
mammals, less than 200 million years ago. The history of life recorded by fossils presents
compelling evidence of evolution.

The fossil record is incomplete. Of the small proportion of organisms preserved as fossils,
only a tiny fraction have been recovered and studied by paleontologists. In some cases the
succession of forms over time has been reconstructed in detail. One example is the evolution
of the horse. The horse can be traced to an animal the size of a dog having several toes on
each foot and teeth appropriate for browsing; this animal, called the dawn horse (genus
Hyracotherium), lived more than 50 million years ago. The most recent form, the modern
horse (Equus), is much larger in size, is one-toed, and has teeth appropriate for grazing. The
transitional forms are well preserved as fossils, as are many other kinds of extinct horses that
evolved in different directions and left no living descendants.

Evolution of the horse over the past 55 million years. The present-day Przewalski's horse is
believed to be the only remaining example of a wild horse—i.e., the last remaining modern
horse to have evolved by natural selection. Numbered bones in the forefoot illustrations trace
the gradual transition from a four-toed to a one-toed animal.

Using recovered fossils, paleontologists have reconstructed examples of radical evolutionary

transitions in form and function. For example, the lower jaw of reptiles contains several
bones, but that of mammals only one. The other bones in the reptile jaw unmistakably
evolved into bones now found in the mammalian ear. At first, such a transition would seem
unlikely—it is hard to imagine what function such bones could have had during their
intermediate stages. Yet paleontologists discovered two transitional forms of mammal-like
reptiles, called therapsids, that had a double jaw joint (i.e., two hinge points side by side)—
one joint consisting of the bones that persist in the mammalian jaw and the other composed of
the quadrate and articular bones, which eventually became the hammer and anvil of the
mammalian ear.

For skeptical contemporaries of Darwin, the “missing link”—the absence of any known
transitional form between apes and humans—was a battle cry, as it remained for uninformed
people afterward. Not one but many creatures intermediate between living apes and humans
have since been found as fossils. The oldest known fossil hominins—i.e., primates belonging
to the human lineage after it separated from lineages going to the apes—are 6 million to 7
million years old, come from Africa, and are known as Sahelanthropus and Orrorin (or
Praeanthropus), which were predominantly bipedal when on the ground but which had very
small brains. Ardipithecus lived about 4.4 million years ago, also in Africa. Numerous fossil
remains from diverse African origins are known of Australopithecus, a hominin that appeared
between 3 million and 4 million years ago. Australopithecus had an upright human stance but
a cranial capacity of less than 500 cc (equivalent to a brain weight of about 500 grams),
comparable to that of a gorilla or a chimpanzee and about one-third that of humans. Its head
displayed a mixture of ape and human characteristics—a low forehead and a long, apelike
face but with teeth proportioned like those of humans. Other early hominins partly
contemporaneous with Australopithecus include Kenyanthropus and Paranthropus; both had
comparatively small brains, although some species of Paranthropus had larger bodies.
Paranthropus represents a side branch in the hominin lineage that became extinct. Along
with increased cranial capacity, other human characteristics have been found in Homo
habilis, which lived about 1.5 million to 2 million years ago in Africa and had a cranial
capacity of more than 600 cc (brain weight of 600 grams), and in H. erectus, which lived
between 0.5 million and more than 1.5 million years ago, apparently ranged widely over
Africa, Asia, and Europe, and had a cranial capacity of 800 to 1,100 cc (brain weight of 800
to 1,100 grams). The brain sizes of H. ergaster, H. antecessor, and H. heidelbergensis were
roughly that of the brain of H. erectus, some of which species were partly contemporaneous,
though they lived in different regions of the Eastern Hemisphere.

Five hominins—members of the human lineage after it separated at least seven million to six
million years ago from lineages going to the apes—are depicted in an artist's interpretation.
All but Homo sapiens, the species that comprises modern humans, are extinct and have been
reconstructed from fossil evidence.

5.3 CONCEPT & THEORIES OF EVOLUTION

(I) Lamarckism or Theory of Inheritance of Acquired characters.

(II) Darwinism or Theory of Natural Selection.

(III) Mutation theory of De - Vries.

(IV) Neo-Darwinism or Modern concept or Synthetic theory of evolution.

I. LAMARCKISM:

It is also called “Theory of inheritance of acquired characters” and was proposed by a great
French naturalist, Jean Baptiste de Lamarck (Fig. 7.34) in 1809 A.D. in his famous book
“Philosophic Zoologique”. This theory is based on the comparison between the contemporary
species of his time to fossil records.

His theory is based on the inheritance of acquired characters which are defined as the changes
(variations) developed in the body of an organism from normal characters, in response to the
changes in environment, or in the functioning (use and disuse) of organs, in their own life
time, to fulfill their new needs. Thus Lamarck stressed on adaptation as means of
evolutionary modification.
A. POSTULATES OF LAMARCKISM:

Lamarckism is based on following four postulates:

1. New needs:

Every living organism is found in some kind of environment. The changes in the
environmental factors like light, temperature, medium, food, air etc. or migration of animal
lead to the origin of new needs in the living organisms, especially animals. To fulfill these
new needs, the living organisms have to exert special efforts like the changes in habits or
behavior.

2. Use and disuse of organs:

The new habits involve the greater use of certain organs to meet new needs, and the disuse or
lesser use of certain other organs which are of no use in new conditions. This use and disuse
of organs greatly affect the form, structure and functioning of the organs. Continuous and
extra use of organs makes them more efficient while the continued disuse of some other
organs lead to their degeneration and ultimate disappearance. So, Lamarckism is also called
“Theory of use and disuse of organs.” So the organism acquires certain new characters due to
direct or indirect environmental effects during its own life span and are called Acquired or
adaptive characters.

3. Inheritance of acquired characters:

Lamarck believed that acquired characters are inheritable and are transmitted to the
offspring’s so that these are born fit to face the changed environmental conditions and the
chances of their survival are increased.

4. Speciation:

Lamarck believed that in every generation, new characters are acquired and transmitted to
next generation, so that new characters accumulate generation after generation. After a
number of generations, a new species is formed.

So according to Lamarck, an existing individual is the sum total of the characters acquired by
a number of previous generations and the speciation is a gradual process.

Summary of four postulates of Lamarckism:

1. Living organisms or their component parts tend to increase in size.

2. Production of new organ is resulted from a new need.

3. Continued use of an organ makes it more developed, while disuse of an organ results in
degeneration.

4. Acquired characters (or modifications) developed by individuals during their own lifetime
are inheritable and accumulate over a period of time resulting a new species.

B. EVIDENCES IN FAVOUR OF LAMARCKISM:

1. Phylogenetic studies of horse, elephant and other animals show that all these increase in
their evolution from simple to complex forms.

2. Giraffe

Development of present day long-necked and long fore-necked giraffe from deer-like
ancestor by the gradual elongation of neck and forelimbs in response to deficiency of food on
the barren ground in dry deserts of Africa. These body parts were elongated so as to eat the
leaves on the tree branches. This is an example of effect of extra use and elongation of certain
organs.

Stages in the evolution of present day Giraffe

3. Snakes:

Development of present day limbless snakes with long slender body from the limbed
ancestors due to continued disuse of limbs and stretching of their body to suit their creeping
mode of locomotion and fossorial mode of living out of fear of larger and more powerful
mammals. It is an example of disuse and degeneration of certain organs.

4. Aquatic birds:
Development of aquatic birds like ducks, geese etc. from their terrestrial ancestors by the
acquired characters like reduction of wings due to their continued disuse, development of
webs between their toes for wading purposes. These changes were induced due to deficiency
of food on land and severe competition. It is an example of both extra use (skin between the
toes) and disuse (wings) of organs.

5. Flightless birds:

Development of flightless birds like ostrich from flying ancestors due to continued disuse of
wings as these were found in well protected areas with plenty of food.

6. Horse:

The ancestors of modem horse (Equus caballus) used to live in the areas with soft ground and
were short legged with more number of functional digits (e.g. 4 functional fingers and 3
functional toes in Dawn horse-Eohippus). These gradually took to live in areas with dry
ground. This change in habit was accompanied by increase in length of legs and decrease in
functional digits for fast running over hard ground.

C. CRITICISM OF LAMARCKISM:

A hard blow to Lamarckism came from a German biologist, August Weismann who proposed
the “Theory of continuity of germplasm” in 1892 A.D. This theory states that environmental
factors do affect only somatic cells and not the germ cells.

As the link between the generations is only through the germ cells and the somatic cells are
not transmitted to the next generation so the acquired characters must be lost with the death
of an organism so these should have no role in evolution. He suggested that germplasm is
with special particles called “ids” which control the development of parental characters in
offsprings.

Weismann mutilated the tails of mice for about 22 generations and allowed them to breed, but
tailless mice were never born. Pavlov, a Russian physiologist, trained mice to come for food
on hearing a bell. He reported that this training is not inherited and was necessary in every
generation. Mendel’s laws of inheritance also object the postulate of inheritance of acquired
characters of Lamarckism.

Similarly, boring of pinna of external ear and nose in Indian women; tight waist, of European
ladies circumcising (removal of prepuce) in certain people; small sized feet of Chinese
women etc are not transmitted from one generation to another generator.
Eyes which are being used continuously and constantly develop defects instead of being
improved. Similarly, heart size does not increase generation after generation though it is used
continuously.

Presence of weak muscles in the son of a wrestler was also not explained by Lamarck.
Finally, there are a number of examples in which there is reduction in the size of organs e.g.
among Angiosperms, shrubs and herbs have evolved from the trees.

So, Lamarckism was rejected.

D. SIGNIFICANCE:

1. It was first comprehensive theory of biological evolution.

2. It stressed on adaptation to the environment as a primary product of evolution.

Neo-Lamarckism:

Long forgotten Lamarckism has been revived as Neo-Lamarckism, in the light of recent
findings in the field of genetics which confirm that environment does affect the form,
structure; colour, size etc. and these characters are inheritable.

Main scientists who contributed in the evolution of Neo-Lamarckism are: French Giard,
American Cope, T.H. Morgan, Spencer, Packard, Bonner, Tower, Naegali, Mc Dougal, etc.
Term neo-Lamarckism was coined by Alphaeus S. Packard.

Neo-Lamarckism states:

1. Germ cells may be formed from the somatic cells indicating similar nature of
chromosomes and gene make up in two cell lines e.g.

(a) Regeneration in earthworms.

(b) Vegetative propagation in plants like Bryophyllum (with foliar buds).

(c) A part of zygote (equipotential egg) of human female can develop into a complete baby
(Driesch).

2. Effect of environment on germ cells through the somatic cells e.g. Heslop Harrison found
that a pale variety of moth, Selenia bilunaria, when fed on manganese coated food, a true
breeding melanic variety of moth is produced.
3. Effect of environment directly on germ cells. Tower exposed the young ones of some
potato beetles to temperature fluctuation and found that though beetles remained unaffected
with no somatic change but next generation had marked changes in body colouration.
Muller confirmed the mutagenic role of X-rays on Drosophila while C. Auerbach et., al.
confirmed the chemical mutagens (mustard gas vapours) causing mutation in
Drosophila melanogaster, so neo-Lamarckism proved:

(a) Germ cells are not immune from the effect of environment.

(b) Germ cells can carry somatic changes to next progeny (Harrison’s experiment).

(c) Germ cells may be directly affected by the environmental factors (Tower’s experiment).

II. DARWINISM (THEORY OF NATURAL SELECTION):

A. INTRODUCTION:
Charles Darwin (1809- 1882 A.D.), an English naturalist, was the most dominant figure
among the biologists of the 19th century. He made an extensive study of nature for over 20
years, especially in 1831-1836 when he went on a voyage on the famous ship “H.M.S.
Beagle” (Fig. 7.37) and explored South America, the Galapagos Islands and other islands.

Charles Robert Darwin

 HMS beagle ship

He collected the observations on animal distribution and the relationship between living and
extinct animals. He found that existing living forms share similarities to varying degrees not
only among themselves but also with the life forms that existed millions of years ago, some
of which have become extinct.

He stated that every population has built in variations in their characters. From the analysis of
his data of collection and from Malthus’s Essay on Population, he got the idea of struggle for
existence within all the populations due to continued reproductive pressure and limited
resources and that all organisms, including humans, are modified descendants of previously
existing forms of life.

In 1858 A.D., Darwin was highly influenced by a short essay entitled “On the Tendency of
Varieties to Depart Indefinitely from the Original Type” written by another naturalist, Alfred
Russel Wallace (1812-1913) who studied biodiversity on Malayan archipelago and came to
similar conclusions.

Darwin and Wallace’s views about evolution were presented in the meeting of Linnaean
Society of London by Lyell and Hooker on July 1, 1858. Darwin’s and Wallace’s work was
jointly published in “Proceedings of Linnean Society of London” in 1859. So it is also called
Darwin-Wallace theory.

Darwin explained his theory of evolution in a book entitled “On the Origin of Species by
means of Natural Selection”. It was published on 24th Nov., 1859. In this theory, Charles
Darwin proposed the concept of natural selection as the mechanism of evolution.
B. Postulates of Darwinism:
Main postulates of Darwinism are:

1. Geometric increase.

2. Limited food and space.

3. Struggle for existence.

4. Variations.

5. Natural selection or Survival of the fittest.

6. Inheritance of useful variations.

7. Speciation.

1. Geometric increase:

According to Darwinism, the populations tend to multiply geometrically and the reproductive
powers of living organisms (biotic potential) are much more than required to maintain their
number e.g.,

Paramecium divides three times by binary fission in 24 hours during favorable conditions. At
this rate, a Paramecium can produce a clone of about 280 million Paramecia in just one
month and in five years, can produce Paramecia having mass equal to 10,000 times than the
size of the earth.

Other rapidly multiplying organisms are: Cod (one million eggs per year); Oyster (114
million eggs in one spawning); Ascaris (70, 00,000 eggs in 24 hours); housefly (120 eggs in
one laying and laying eggs six times in a summer season); a rabbit (produces 6 young ones in
a litter and four litters in a year and young ones start breeding at the age of six months).

Similarly, the plants also reproduce very rapidly e.g., a single evening primrose plant
produces about 1, 18,000 seeds and single fern plant produces a few million spores.

Even slow breeding organisms reproduce at a rate which is much higher than required e.g., an
elephant becomes sexually mature at 30 years of age and during its life span of 90 years,
produces only six offspring’s. At this rate, if all elephants survive then a single pair of
elephants can produce about 19 million elephants in 750 years.
These examples confirm that every species can increase manifold within a few generations
and occupy all the available space on the earth, provided all survive and repeat the process.
So the number of a species will be much more than can be supported on the earth.

2. Limited food and space:

Darwinism states that though a population tends to increase geometrically, the food increases
only arithmetically. So two main limiting factors on the tremendous increase of a population
are: limited food and space which together form the major part of carrying capacity of
environment. These do not allow a population to grow indefinitely which are nearly stable in
size except for seasonal fluctuation.

3. Struggle for existence:

Due to rapid multiplication of populations but limited food and space, there starts an
everlasting competition between individuals having similar requirements. In this competition,
every living organism desires to have an upper hand over others.

This competition between living organisms for the basic needs of life like food, space,
mate etc., is called struggle for existence which is of three types:

(a) Intraspecific:

Between the members of same species e.g. two dogs struggling for a piece of meat.

(b) Interspecific:

Between the members of different species e.g. between predator and prey.

(c) Environmental or Extra specific:

Between living organisms and adverse environmental factors like heat, cold, drought, flood,
earthquakes, light etc.

Out of these three forms of struggle, the intraspecific struggle is the strongest type of struggle
as the needs of the individuals of same species are most similar e.g., sexual selection in which
a cock with a more beautiful comb and plumage has better chances to win a hen than a cock
with less developed comb.

Similarly, cannabilism is another example of intraspecific competition as in this; individuals

eat upon the members of same species.
In this death and life struggle, the majority of individuals die before reaching the sexual
maturity and only a few individuals survive and reach the reproductive stage. So struggle for
existence acts as an effective check on an ever-increasing population of each species.

The nature appears saying, “They are weighed in the balance and are found wanting.” So the
number of offspring’s of each species remains nearly constant over long period of time.

4. Variations:

Variation is the law of nature. According to this law of nature, no two individuals except
identical (monozygotic) twins are identical. This everlasting competition among the
organisms has compelled them to change according to the conditions to utilize the natural
resources and can survive successfully.

Darwin stated that the variations are generally of two types—continuous variations or
fluctuations and discontinuous variations. On the basis of their effect on the survival chances
of living organisms, the variations may be neutral, harmful and useful.

Darwin proposed that living organisms tend to adapt to changing environment due to useful
continuous variations {e.g., increased speed in the prey; increased water conservation in
plants; etc.), as these will have a competitive advantage.

5. Natural selection or Survival of the fittest:

Darwin stated that as many selects the individuals with desired characters in artificial
selection; nature selects only those individuals out of the population which are with useful
continuous variations and are best adapted to the environment while the less fit or unfit
individuals are rejected by it.

Darwin stated that if the man can produce such a large number of new species/varieties with
limited resources and in short period of time by artificial selection, then natural selection
could account for this large biodiversity by considerable modifications of species with the
help of unlimited resources available over long span of time.

Darwin stated that discontinuous variations appear suddenly and will mostly be harmful, so
are not selected by nature. He called them “sports”. So the natural selection is an automatic
and self-going process and keeps a check on the animal population.
This sorting out of the individuals with useful variations from a heterogeneous population by
the nature was called Natural selection by Darwin and Survival of the fittest by Wallace. So
natural selection acts as a restrictive force and not a creative force.

6. Inheritance of useful variations:

Darwin believed that the selected individuals pass their useful continuous variations to their
offspring’s so that they are born fit to the changed environment.

7. Speciation:

According to Darwinism, useful variations appear in every generation and are inherited from
one generation to another. So the useful variations go on accumulating and after a number of
generations, the variations become so prominent that the individual turns into a new species.
So according to Darwinism, evolution is a gradual process and speciation occurs by gradual
changes in the existing species.

Thus the two key concepts of Darwinian Theory of Evolution are:

1. Branching Descent, and 2. Natural Selection.

C. EVIDENCES IN FAVOUR OF DARWINISM:

1. There is a close parallelism between natural selection and artificial selection.

2. The remarkable cases of resemblance e.g. mimicry and protective coloration can be
achieved only by gradual changes occurring simultaneously both in the model and the mimic.

3. Correlation between position of nectarines in the flowers and length of the proboscis of the
pollinating insect.

D. EVIDENCES AGAINST DARWINISM:

Darwinism is not able to explain:

1. The inheritance of small variations in those organs which can be of use only when fully
formed e.g. wing of a bird. Such organs will be of no use in incipient or underdeveloped
stage.

2. Inheritance of vestigial organs.

3. Inheritance of over-specialized organs e.g. antlers in deer and tusks in elephants.

4. Presence of neuter flowers and sterility of hybrids.

5. Did not differentiate between somatic and germinal variations.

6. He did not explain the causes of the variations and the mode of transmission of variations.

7. It was also refuted by Mendel’s laws of inheritance which state that inheritance is
particulate.

So this theory explains only the survival of the fittest but does not explain the arrival of the
fittest so Darwin himself confessed, “natural selection has been main but not the exclusive
means of modification.”

PRINCIPLE OF NATURAL SELECTION:

It was proposed by Ernst Mayer in 1982. It stems from five important observations and three
inferences. This principle demonstrates that natural selection is the differential success in
reproduction and enables the organisms to adapt them to their environment by development
of small and useful variations.

These favorable Variations accumulate over generation after generation and lead to
speciation. So natural selection operates through interactions between the environment and
inherent variability in the population.

III. Mutation Theory of Evolution:

The mutation theory of evolution was proposed by a Dutch botanist, Hugo de Vries (1848-
1935 A.D.) (Fig. 7.38) in 1901 A.D. in his book entitled “Species and Varieties, Their Origin
by Mutation”. He worked on evening primrose (Oenothera lamarckiana).

A. EXPERIMENT:

Hugo de Vries cultured O. lamarckiana in botanical gardens at Amsterdam. The plants were,
allowed to self-pollinate and next generation was obtained. The plants of next generation
were again subjected to self-pollination to obtain second generation. Process was repeated for
a number of generations.

B. OBSERVATIONS:

Majority of plants of first generation were found to be like the parental type and showed only
minor variations but 837 out of 54,343 members were found to be very different in characters
like flower size, shape and arrangement of buds, size of seeds etc. These markedly different
plants were called primary or elementary species.
A few plants of second generation were found to be still more different. Finally, a new type,
much longer than the original type. He also found the numerical chromosomal changes in the
variants (e.g. with chromosome numbers 16, 20, 22, 24, 28 and 30) up to 30 (Normal diploid
number is 14).

C. CONCLUSION:

1. The evolution is a discontinuous process and occurs by mutations (L. mutate = to change;
sudden and inheritable large differences from the normal and are not connected to normal by
intermediate forms). Individuals with mutations are called mutants.

2. Elementary species are produced in large number to increase chances of selection by

nature.

3. Mutations are recurring so that the same mutants appear again and again. This increases
the chances of their selection by nature.

4. Mutations occur in all directions so may cause gain or loss of any character.

5. Mutability is fundamentally different from fluctuations (small and directional changes).

So according to mutation theory, evolution is a discontinuous and jerky process in which

there is a jump from one species to another so that new species arises from pre-existing
species in a single generation (macro genesis or saltation) and not a gradual process as
proposed by Lamarck and Darwin.

D. EVIDENCES IN FAVOUR OF MUTATION THEORY:

1. Appearance of a short-legged sheep variety, Ancon sheep from long-legged parents in a

single generation in 1791 A.D. It was first noticed in a ram (male sheep) by an American
farmer, Seth Wright.

Appearance of short legged Ancon Sheep

2. Appearance of polled Hereford cattle from horned parents in a single generation in 1889.

3. De Vries observations have been experimentally confirmed by McDougal and Shull in

America and Gates in England.

4. Mutation theory can explain the origin of new varieties or species by a single gene
mutation e.g. Cicer gigas, Nuval orange. Red sunflower, hairless cats, double- toed cats, etc.

5. It can explain the inheritance of vestigial and over-specialized organs.

6. It can explain progressive as well as retrogressive evolution.

E. EVIDENCES AGAINST MUTATION THEORY:

1. It is not able to explain the phenomena of mimicry and protective colouration.

2. Rate of mutation is very low, i.e. one per million or one per several million genes.

3. Oenothera lamarckiana is a hybrid plant and contains anamolous type of chromosome

behaviour.

4. Chromosomal numerical changes as reported by de Vries are unstable.

5. Mutations are incapable of introducing new genes and alleles into a gene pool.

IV. NEO-DARWINISM OR MODERN CONCEPT OR SYNTHETIC THEORY OF

EVOLUTION:

The detailed studies of Lamarckism, Darwinism and Mutation theory of evolution showed
that no single theory is fully satisfactory. Neo-Darwinism is a modified version of theory of
Natural Selection and is a sort of reconciliation between Darwin’s and de Vries theories.

Modern or synthetic theory of evolution was designated by Huxley (1942). It emphasizes the
importance of populations as the units of evolution and the central role of natural selection as
the most important mechanism of evolution.

The scientists who contributed to the outcome of Neo-Darwinism were: J.S. Huxley, R.A.
Fischer and J.B.S. Haldane of England; and S. Wright, Ford, H.J. Muller and T. Dobzhansky
of America.

A. POSTULATES OF NEO-DARWINISM:

1. Genetic Variability:
Variability is an opposing force to heredity and is essential for evolution as the variations
form the raw material for evolution. The studies showed that the units of both heredity and
mutations are genes which are located in a linear manner on the chromosomes.

Various sources of genetic variability in a gene pool are:

(i) Mutations:

These are sudden, large and inheritable changes in the genetic material. On the basis of
amount of genetic material involved, mutations are of three types:

(a) Chromosomal aberrations:

These include the morphological changes in the chromosomes without affecting the number
of chromosomes. These result changes either in the number of genes (deletion and
duplication) or in the position of genes (inversion).

These are of four types:

1. Deletion (Deficiency) involves the loss of a gene block from the chromosome and may be
terminal or intercalary.

2. Duplication involves the presence of some genes more than once, called the repeat. It may
be tandem or reverse duplication.

3. Translocation involves transfer of a gene block from one chromosome to a non-

homologous chromosome and may be simple or reciprocal type.

4. Inversion involves the rotation of an intercalary gene block through 180° and may be Para
centric or pericentric.

(b) Numerical chromosomal mutations:

These include changes in the number of chromosomes. These may be euploidy (gain or loss
of one or more genomes) or aneuploidy (gain or loss of one or two chromosomes). Euploidy
may be haploidy or polyploidy.

Among polyploidy, tetraploidy is most common. Polyploidy provides greater genetic material
for mutations and variability. In haploids, recessive genes express in the same generation.

Aneuploidy may be hypoploidy or hyperploidyl Hypoploidy may be monosomy (loss of one

chromosome) or nullisomy (loss of two chromosomes). Hyperploidy may be trisomy (gain of
one chromosome) or tetrasomy (gain of two chromosomes).
(c) Gene mutations (Point mutations):

These are invisible changes in chemical nature (DNA) of a gene and are of three types:

1. Deletion involves loss of one or more nucleotide pairs.

2. Addition involves gain of one or more nucleotide pairs.

3. Substitution involves replacement of one or more nucleotide pairs by other base pairs.
These may be transition or trans version type.

These changes in DNA cause the changes in the sequence of amino acids so changing the
nature of proteins and the phenotype.

(ii) Recombination of genes:

Thousands of new combinations of genes are produced due to crossing over, chance
arrangement of bivalents at the equator during metaphase – I and chance fusion of gametes
during fertilization.

(iii) Hybridization:

It involves the interbreeding of two genetically different individuals to produce ‘hybrids’.

(iv) Physical mutagens (e.g. radiations, temperature etc.) and chemical mutagens (e.g. nitrous
acid, colchicine, nitrogen mustard etc.).

(v) Genetic drift:

It is the elimination of the genes of some original characteristics of a species by extreme

reduction in a population due to epidemics or migration or Sewell Wright effect.

The chances of variations are also increased by non-random mating.

2. Natural Selection:

Natural selection of Neo- Darwinism differs from that of Darwinism that it does not operate
through “survival of the fittest” but operates through differential reproduction and
comparative reproductive success.

Differential reproduction states that those members, which are best adapted to the
environment, reproduce at a higher rate and produce more offsprings than those which are
less adapted. So these contribute proportionately greater percentage of genes to the gene pool
of next generation while less adapted individuals produce fewer offsprings.
If the differential reproduction continues for a number of generations, then the genes of those
individuals which produce more offspring’s will become predominant in the gene pool of the
population.

Spread of Genetic variability by differential reproduction

Due to sexual communication, there is free flow of genes so that the genetic variability which
appears in certain individuals, gradually spreads from one deme to another deme, from deme
to population and then on neighboring sister populations and finally on most of the members
of a species. So natural selection causes progressive changes in gene frequencies, ‘i.e. the
frequency of some genes increases while the frequency of some other genes decreases.

Which individuals produce more offspring’s?

(i) Mostly those individuals who are best adapted to the environment.

(ii) Whose sum of the positive selection pressure due to useful genetic variability is more
than the sum of negative selection pressure due to harmful genetic variability?

(iii) Which have better chances of sexual selection due to development of some bright
coloured spots on their body e.g. in many male birds and fish.

(iv) Those who are able to overcome the physical and biological environmental factors to
successfully reach the sexual maturity.

So natural selection of Neo-Darwinism acts as a creative force and operates through

comparative reproductive success. Accumulation of a number of such variations leads to the
origin of a new species.

3. Reproductive isolation:

Any factor which reduces the chances of interbreeding between the related groups of living
organisms is called an isolating mechanism. Reproductive isolation is must so as to allow the
accumulation of variations leading to speciation by preventing hybridization.
In the absence of reproductive isolation, these variants freely interbreed which lead to
intermixing of their genotypes, dilution of their peculiarities and disappearance of differences
between them. So, reproductive isolation helps in evolutionary divergence.

5.4 HARDY-WEINBERG LAW OF GENETIC EQUILIBRIUM

This fundamental idea in population genetics was offered by the Englishman G.H. Hardy (a
mathematician) and the German W. Weinberg simultaneously in the year 1908. It is known as
the Hardy-Weinberg law.

Mendelian genetics were rediscovered in 1900. However, it remained somewhat controversial

for several years as it was not then known how it could cause continuous characteristics.
Udny Yule (1902) argued against Mendelism because he thought that dominant alleles would
increase in the population. The AmericanWilliam E. Castle (1903) showed that without
selection, the genotype frequencies would remain stable. Karl Pearson (1903) found one
equilibrium position with values of p = q = 0.5. Reginald Punnett, unable to counter Yule's
point, introduced the problem to G. H. Hardy, a Britishmathematician, with whom he played
cricket. Hardy was a pure mathematician and held applied mathematics in some contempt; his
view of biologists' use of mathematics comes across in his 1908 paper where he describes this
as "very simple".

To the Editor of Science: I am reluctant to intrude in a discussion concerning matters of

which I have no expert knowledge, and I should have expected the very simple point which I
wish to make to have been familiar to biologists. However, some remarks of Mr. Udny Yule,
to which Mr. R. C. Punnett has called my attention, suggest that it may still be worth
making...

Suppose that Aa is a pair of Mendelian characters, A being dominant, and that in any given
generation the number of pure dominants (AA), heterozygotes (Aa), and pure recessives (aa)
are asp:2q:r. Finally, suppose that the numbers are fairly large, so that mating may be
regarded as random, that the sexes are evenly distributed among the three varieties, and that
all are equally fertile. A little mathematics of the multiplication-table type is enough to show
that in the next generation the numbers will be as (p + q)2: 2 (p + q)(q + r):(q + r)2, or as
p1:2q1:r1, say.
The interesting question is: in what circumstances will this distribution be the same as that in
the generation before? It is easy to see that the condition for this isq2 = pr. And since
q12 = p1r1, whatever the values ofp, q, andrmay be, the distribution will in any case continue
unchanged after the second generation

The principle was thus known as Hardy's law in the English-speaking world until 1943, when
Curt Stern pointed out that it had first been formulated independently in 1908 by the German
physician Wilhelm Weinberg. William Castle in 1903 also derived the ratios for the special
case of equal allele frequencies, and it is sometimes (but rarely) called the Hardy–Weinberg–
Castle Law.

The law forms the foundation of population genetics and of modern evolutionary theory. The
law states that: both gene (allelic) frequencies and genotype frequencies will remain constant
from generation to generation in an infinitely large interbreeding population in which mating
is at random and no selection, migration or mutation occurs. Should a population initially be
in disequilibrium, one generation of random mating is sufficient to bring it into genetic
equilibrium and thereafter the population will remain in equilibrium (unchanged in gametic
and zygotic frequencies) as long as Hardy-Weinberg condition persists.

Hardy-Weinberg law depends on the following kinds of genetic equilibrium for its
full attainment.

1. The population is infinitely large and mate at random.

2. No selection is operative.

3. No mutation is operative in alleles.

4. The-population is closed, i.e., no immigration or emigration occurs.

5. Meiosis is normal so that chance is the only factor operative in gametogenesis.

The law describes a theoretical situation in which a population is undergoing no evolutionary

change. It explains that if evolutionary forces are absent; the population is large; its
individuals have random mating, each parent produces roughly equal number of gametes and
the gametes produced by the mating parents combine at random and the gene frequency
remains constant; then the genetic equilibrium of the genes in question is maintained and the
variability present in the population is preserved. Suppose there is a panmictic population
with gene (allele) A and a on one locus, then the frequency of gametes with gene A will be
the same as the frequency of gene A and similarly the frequency of gametes with a will be
equal to the frequency of gene a. Let us presume that the numerical proportion of different
gene in this population is as follows:

AA- 36%

Aa- 48%

aa -16%

Since AA individuals make up 36% of the total population they will contribute approximately
36% of all the gametes formed in the population. These gametes will possess gene A.
Similarly, aa individuals will produce 16% of all the gametes. But the gametes from Aa
individuals will be of two types i.e., with gene A and gene a roughly in equal proportion.
Since these constitute together 48% of the total population, they will contribute 48% gametes
but out of them 24% will possess gene A and the other 24% will have gene a. Hence the
overall output of the gametes ‘will be as follows:

If frequency of gene A is represented by p and frequency of gene a is represented by q and

there is a random mating of the gametes with allele A arid a at the equilibrium state, the
population will contain the following frequencies of the genes A and a, generation after
generation.

AA + 2Aa + aa genotype

p2 + 2pq + q2 gene (allele) frequency

The above results could be explained by relying on the theory of probability. In a population
of large size, the probability of receiving the gene A from both parents will be p x p = p2,
similarly, for gene a it will be q x q = q2 and the probability of being heterozygous will be pq
+ pq = 2pq. The relationship between gene (allele) frequency and genotype frequency can be
expressed as

p2+2pq + q2 = 1 or (p + q)2 = 1

This is known as Hardy-Weinberg formula or binomial expression. If the frequency of one of

the alleles (e.g., p) is known then the frequency of the other allele (q = 1-p) is known, and the
frequencies of the homozygous genotypes (p2 and q2) as well as those of the heterozygous
genotype (2pq) can be calculated. Or, if the frequency of homozygous recessive individuals
in the population (a/a or q2) is known, then the frequencies of the allele (q) and the A allele (p
or 1-q) can be calculated. It is then possible to predict genotypic frequencies in the present
and further generations. From this binomial expression, proposed by Hardy and Weinberg, it
is clear that in a large random mating population not only gene frequencies but also the
genotype frequencies will remain constant.

SALIENT FEATURES OF HARDY-WEINBERG LAW:

1. The gene and genotype frequencies of each gene or allele in a population remain at an
equilibrium generation after generation.

2. In a population, the mating is a completely random phenomenon.

3. The equilibrium in the gene and genotype frequencies occurs only in large sized
populations. In a small population gene frequencies may be unpredictable.

4. All the genotypes in a population reproduce equally successfully.

5. Particular alleles will neither be differentially added to nor differentially subtracted from a
population.

SIGNIFICANCE OF HARDY-WEINBERG LAW:

The law is important primarily because it describes the situation in which there is no
evolution, and thus it provides a theoretical baseline for measuring evolutionary change. The
equilibrium tendency serves to conserve gains which have been made in the past and also to
avoid too rapid changes; in other words, giving a genetic stability to the population.

The Hardy-Weinberg equation describes conditions that are not found in natural population.
The function of the Hardy-Weinberg principle, and its equation, is as an experimental
control— a prediction of what the allelic and genotypic frequencies should be if nothing acts
to alter the gene pool. Thus, if q is known to be 0.40 then q2 in the next generation should be
0.16.

If instead it is 0.02, then we know that a change has occurred in the gene pool, the magnitude
of that change, and that it was caused by: mutations, genetic drift, gene flow, assertive
mating, or natural selection. We can then design experiments to test which of the five agents
of change contributed most to the change in allelic and genotypic frequencies.

Deviations from Hardy–Weinberg equilibrium

The seven assumptions underlying Hardy–Weinberg equilibrium are as follows:[3]

• organisms are diploid

• only sexual reproduction occurs

• generations are nonoverlapping

• mating is random

• population size is infinitely large

• allele frequencies are equal in the sexes

• there is no migration, gene flow, admixture, mutation or selection

Violations of the Hardy–Weinberg assumptions can cause deviations from expectation. How
this affects the population depends on the assumptions that are violated.

• Random mating. The HWP states the population will have the given genotypic
frequencies (called Hardy–Weinberg proportions) after a single generation of random
mating within the population. When the random mating assumption is violated, the
population will not have Hardy–Weinberg proportions. A common cause of non-
random mating is inbreeding, which causes an increase in homozygosis for all genes.

If a population violates one of the following four assumptions, the population may continue
to have Hardy–Weinberg proportions each generation, but the allele frequencies will change
over time.

• Selection, in general, causes allele frequencies to change, often quite rapidly. While
directional selection eventually leads to the loss of all alleles except the favored one
(unless one allele is dominant, in which case recessive alleles can survive at low
 frequencies), some forms of selection, such as balancing selection, lead to equilibrium
without loss of alleles.

• Mutation will have a very subtle effect on allele frequencies. Mutation rates are of the
order 10−4 to 10−8, and the change in allele frequency will be, at most, the same order.
Recurrent mutation will maintain alleles in the population, even if there is strong
selection against them.

• Migration genetically links two or more populations together. In general, allele

frequencies will become more homogeneous among the populations. Some models for
migration inherently include nonrandom mating (Wahlund effect, for example). For
those models, the Hardy–Weinberg proportions will normally not be valid.

• Small population size can cause a random change in allele frequencies. This is due to
a sampling effect, and is called genetic drift. Sampling effects are most important
when the allele is present in a small number of copies.

In real world genotype data, deviations from Hardy-Weinberg Equilibrium may be a sign of
genotyping error.

5.5 DETAILED ACCOUNT OF DESTABILIZING FORCES

It’s hard for us, with our typical human life spans of less than 100 years, to imagine all the
way back, 3.8 billion years ago, to the origins of life. Scientists still study and debate how life
came into being and whether it originated on Earth or in some other region of the universe
(including some scientists who believe that studying evolution can reveal the complex
processes that were set in motion by God or a higher power). What we do know is that a
living single-celled organism was present on Earth during the early stages of our planet’s
existence. This organism had the potential to reproduce by making copies of itself, just like
bacteria, many amoebae, and our own living cells today. In fact, with today’s genetic and
genomic technologies, we can now trace genetic lineages, or phylogenies, and determine the
relationships between all of today’s living organisms—eukaryotes (animals, plants, fungi,
etc.), archaea, and bacteria—on the branches of the phylogenetic tree of life. Looking at the
common sequences in modern genomes, we can even make educated guesses about what the
genetic sequence of the first organism, or universal ancestor of all living things, would likely
have been. Through a wondrous series of mechanisms and events, that first single-celled
organism gave rise to the rich diversity of species that fill the lands, seas, and skies of our
planet. This chapter explores the mechanisms by which that amazing transformation occurred
and considers some of the crucial scientific experiments that shaped our current
understanding of the evolutionary process.

5.5.1 NATURAL SELECTION

(i) Definition:The process by which comparatively better adapted individuals out of a
heterogeneous population are favoured by the Nature over the less adapted individuals is
called natural selection.

(ii) Mechanism:The process of natural selection operates through differential reproduction. It

means that those individuals, which are best adapted to the environment, survive longer and
reproduce at a higher rate and produce more offspring’s than those which are less adapted. So
the formers contribute proportionately greater percentage of genes to the gene pool of next
generation while less adapted individuals produce fewer offspring’s. If differential
reproduction continues for a number of generations, then the genes of those individuals which
produce more offspring’s will become predominant in the gene pool of the population:

Due to sexual communication, there is free flow of genes so that the genetic variability which
appears in certain individuals, gradually spreads from one deme to another deme, from deme
to population and then on neighboring sister populations and finally on most of the members
of a species. So natural selection causes progressive changes in gene frequencies, i.e. the
frequency of adaptive genes increases while the frequency of less adaptive genes decreases.
So natural selection of Neo-Darwinism acts as a creative force and operates through
comparative reproductive success. Accumulation of such variations leads to the origin of a
new species.

(iii) Typesof Natural selection:The three different types of natural selections observed are:

1. Stabilizing or balancing selection:It leads to the elimination of organisms having

overspecialized characters and maintains homogenous population which is genetically
constant. It favours the average or normal phenotypes, while eliminates the individuals with
extreme expressions. In this, more individuals acquire mean character value. It reduces
variation but does not change the mean value. It results very slow rateof evolution. If we
draw a graphical curve of population, it is bell-shaped. The bell-shaped curve narrows due to
elimination of extreme variants.

Example:Sickle-cell anaemia in human beings.

2. Directional or Progressive selection: In this selection, the populationchanges towards one
particular direction along with change in environment. As environment is undergoing a
continuous change, the organisms having acquired new characters survive and others are
eliminated gradually. In this, individuals at one extreme (less adapted) are eliminated while
individuals at other extreme (more adapted) are favoured. This produces more andmore
adapted individuals in the population when such a selection operates for many generations. In
this type of selection, more individuals acquire value other than mean character value.

Examples: Industrial melanism: In this, number of the light coloured moths {Biston betularia)
decreased gradually while that of the melanic moths (B. carbonaria) increased showing
directional selection. DDT-resistant mosquitoes:In this, sensitive mosquitoeswere eliminated
and resistant ones increased in number. So the population of resistant mosquitoes increased
showing directional selection.

3. Disruptive selection: It is a type of natural selection which favours extreme expressions of

certain traits to increase variance in a population. It breaks a homogeneous population into
many adaptive forms. It results in balanced polymorphism. In this type of selection, more
individuals acquire peripheral character value at both ends of the distribution curve. This kind
of selection is rare and eliminates most of the members with mean expression so producing
two peaks in the distribution of a trait

Example: In sea, the three types of snails i.e. white coloured; brown coloured and black
coloured are present. The white coloured snails are invisible when covered by barnacles. The
black coloured snails are invisible when rock is bare. But brown coloured snails are eaten by
predators in both the conditions. So these are eliminated gradually

5.5.2 MUTATION
These are characterized by:

(i) These are sudden, large and inheritable changes in the genetic material.
(ii) Mutations are random (indiscriminate) and occur in all directions.
(iii) Most mutations are harmful or neutral. It is estimated that only one out of
1,000 mutations is useful.
(iv) Rate of mutation is very low, i.e. one per million or one per several million
genie loci. But rate of mutation is sufficient to produce considerable
genetic variability.
(v) Certain mutations are preadaptive and appear even without exposure to a
specific environment. These express and become advantageous only when
after exposure to new environment which only selects the preadaptive
mutations that occurred earlier. Existence of preadaptive mutations in
Escherichia coli was experimentally demonstrated by Esther Lederberg
(1952) in replica plating experiment (Explained in Neo-Darwinism).
(vi) Onthe basis of amount of genetic material involved, mutations are of three
types
(vii) On the basis of their origin, mutations are of two types
Differences between Spontaneous and Induced mutations.

Spontaneous Induced
Characters
mutations mutations
By natural By man
Caused by
agents, so also
called natural
mutations or
background
mutations.
Very low (about Faster
Frequency of mutations
one per million
genes or even
more)
Not certain, Certain physical
Causes
many cellular {e.g. radiations
products e.g. temperature,
formaldehyde, etc.) and
nitrous acid, chemical agents
peroxides, etc. called mutagens
act as mutagens
 5.5.3 GENETIC DRIFT

Genetic Drift: It is the random change in the frequency of alleles occurring by chance
fluctuations. It is characterized by:

(viii) It is a binomial sampling error of the gene pool, i.e. that alleles which form
the gene pool of the next generation are a sample of the alleles of present
population.
(ix) Genetic drift always influences frequencies of alleles and is inversely
proportional to the size of population. So genetic drift is most important in
very small populations in which there are increased chances of inbreeding
which increases the frequency of individuals homozygous for recessive
alleles, many of which maybe deleterious.
(x) Genetic drift occurs when a small group separates from a larger population
and may not have all the alleles or may differ from the parental population
in the frequencies of certain genes. This explains for the difference
between island populations and mainland population.
(xi) In a small population, a chance event (e.g. snow storm) may increase the
frequency of a character having little adaptive value.
(xii) Genetic drift can also operate through founder effect. In this, genetic drift
can cause dramatic changes in the allele frequencies in a population
derived from small groups of colonizers, called founders, to a new habitat.
These founders do not have all of the alleles found in their source
population. These founders become quickly different from the parental
population and may form a new species, e.g. evolution of Darwin finches
on Galapagos Islands which were probably derived from a few initial
founders.
(xiii) Population bottleneck: It is reduction in allele frequencies caused by
drastic reduction in population size called population crash e.g. decrease in
cheetah population in Africa due to over-hunting. As the given gene pool
is limited, population bottleneck often prevents the species to reestablish
its former richness so new population has a much restricted gene pool than
the larger parent population.
5.5.4 MIGRATION
Most populations are only partially isolated from other populations of same species. Usually
some migration-emigration (moving out of some individuals out of a population) or
immigration (entry of some members of a population into another population of same
species) occurs between the populations. Immigration results in the addition of new alleles
into the existing gene pool and changes the allele frequencies. Degree of changes in allele
frequencies depends upon the differences between the genotypes of immigrants and native
population. If there is no much genetic differences, then entry of a small number of migrants
will not change the allele frequencies much. However, if the populations are genetically quite
different, a small amount of immigration can result in large changes in allele frequencies. If
the migrating individuals interbreed with the members of local population, called
hybridization, these may bring many new alleles into the local gene pool of the host
population. This is called gene migration. If the inter specific hybrids are fertile, then these
may initiate a new trend in evolution which lead to formation of new species.

This addition or removal of alleles when individuals enter or leave a population from another
locality is called gene flow. Unrestricted gene flow decreases the differences between the
gene pools and reduces the distinctiveness between different populations.
 UNIT 6: QUANTIFYING GENETIC VARIABILITY

6.1 Objectives
6.2 Introduction
6.3 Genetic structure of Natural Populations
6.4 Phenotypic Variations
6.4.1 Phenotype & Phenotypic Variation

6.1 OBJECTIVES

We study about Genetic structure of Natural Populations Phenotypic Variations in this topic.

6.2 INTRODUCTION

Population genetics began as a reconciliation of Mendelian inheritance and biostatistics

models. Natural selection will only cause evolution if there is enough genetic variation in a
population. Before the discovery of Mendelian genetics, one common hypothesis was
blending inheritance. But with blending inheritance, genetic variance would be rapidly lost,
making evolution by natural or sexual selection implausible. The Hardy–Weinberg principle
provides the solution to how variation is maintained in a population with Mendelian
inheritance. According to this principle, the frequencies of alleles (variations in a gene) will
remain constant in the absence of selection, mutation, migration and genetic drift. The next
key step was the work of the British biologist and statistician Ronald Fisher. In a series of
papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural
Selection, Fisher showed that the continuous variation measured by the biometricians could
be produced by the combined action of many discrete genes, and that natural selection could
change allele frequencies in a population, resulting in evolution. In a series of papers
beginning in 1924, another British geneticist, J. B. S. Haldane, worked out the mathematics
of allele frequency change at a single gene locus under a broad range of conditions. Haldane
also applied statistical analysis to real-world examples of natural selection, such as peppered
moth evolution and industrial melanism, and showed that selection coefficients could be
larger than Fisher assumed, leading to more rapid adaptive evolution as a camouflage strategy
following increased pollution.

6.3 GENETIC STRUCTURE OF NATURAL POPULATIONS

Population genetics is a subfield of genetics that deals with genetic differences within and
between populations, and is a part of evolutionary biology. Studies in this branch of biology
examine such phenomena as adaptation, speciation, and population structure.

Population genetics was a vital ingredient in the emergence of the modern evolutionary
synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who
also laid the foundations for the related discipline of quantitative genetics. Traditionally a
highly mathematical discipline, modern population genetics encompasses theoretical,
laboratory, and field work. Population genetic models are used both for statistical inference
from DNA sequence data and for proof/disproof of concept.

What sets population genetics apart from newer, more phenotypic approaches to modelling
evolution, such as evolutionary game theory and adaptive dynamics, is its emphasis on such
genetic phenomena as dominance, epistasis, the degree to which genetic recombination
breaks linkage disequilibrium, and the random phenomena of mutation and genetic drift. This
makes it appropriate for comparison to population genomics data.

MODERN SYNTHESIS

The mathematics of population genetics were originally developed as the beginning of the
modern synthesis. Authors such as Beatty have asserted that population genetics defines the
core of the modern synthesis. For the first few decades of the 20th century, most field
naturalists continued to believe that Lamarckism and orthogenesis provided the best
explanation for the complexity they observed in the living world. During the modern
synthesis, these ideas were purged, and only evolutionary causes that could be expressed in
the mathematical framework of population genetics were retained. Consensus was reached as
to which evolutionary factors might influence evolution, but not as to the relative importance
of the various factors.

Theodosius Dobzhansky, a postdoctoral worker in T. H. Morgan's lab, had been influenced

by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. He
helped to bridge the divide between the foundations of microevolution developed by the
population geneticists and the patterns of macroevolution observed by field biologists, with
his 1937 book Genetics and the Origin of Species. Dobzhansky examined the genetic
diversity of wild populations and showed that, contrary to the assumptions of the population
geneticists, these populations had large amounts of genetic diversity, with marked differences
between sub-populations. The book also took the highly mathematical work of the population
geneticists and put it into a more accessible form. Many more biologists were influenced by
population genetics via Dobzhansky than were able to read the highly mathematical works in
the original. In Great Britain E. B. Ford, the pioneer of ecological genetics, continued
throughout the 1930s and 1940s to empirically demonstrate the power of selection due to
ecological factors including the ability to maintain genetic diversity through genetic
polymorphisms such as human blood types. Ford's work, in collaboration with Fisher,
contributed to a shift in emphasis during the modern synthesis towards natural selection as
the dominant force.

NEUTRAL THEORY AND ORIGIN-FIXATION DYNAMICS

The original, modern synthesis view of population genetics assumes that mutations provide
ample raw material, and focuses only on the change in frequency of alleles within
populations. The main processes influencing allele frequencies are natural selection, genetic
drift, gene flow and recurrent mutation. Fisher and Wright had some fundamental
disagreements about the relative roles of selection and drift. The availability of molecular
data on all genetic differences led to the neutral theory of molecular evolution. In this view,
many mutations are deleterious and so never observed, and most of the remainder are neutral,
i.e. are not under selection. With the fate of each neutral mutation left to chance (genetic
drift), the direction of evolutionary change is driven by which mutations occur, and so cannot
be captured by models of change in the frequency of (existing) alleles alone. The origin-
fixation view of population genetics generalizes this approach beyond strictly neutral
mutations, and sees the rate at which a particular change happens as the product of the
mutation rate and the fixation probability.

FOUR PROCESSES

SELECTION

Natural selection, which includes sexual selection, is the fact that some traits make it more
likely for an organism to survive and reproduce. Population genetics describes natural
selection by defining fitness as a propensity or probability of survival and reproduction in a
particular environment. The fitness is normally given by the symbol w=1-s where s is the
selection coefficient. Natural selection acts on phenotypes, so population genetic models
assume relatively simple relationships to predict the phenotype and hence fitness from the
allele at one or a small number of loci. In this way, natural selection converts differences in
the fitness of individuals with different phenotypes into changes in allele frequency in a
population over successive generations.

Before the advent of population genetics, many biologists doubted that small differences in
fitness were sufficient to make a large difference to evolution. Population geneticists
addressed this concern in part by comparing selection to genetic drift. Selection can
overcome genetic drift when s is greater than 1 divided by the effective population size.
When this criterion is met, the probability that a new advantageous mutant becomes fixed is
approximately equal to 2s.The time until fixation of such an allele depends little on genetic
drift, and is approximately proportional to log(sN)/s.

DOMINANCE

Dominance means that the phenotypic and/or fitness effect of one allele at a locus depends on
which allele is present in the second copy for that locus. Consider three genotypes at one
locus, with the following fitness values

Genotype: A1A1 A1A2 A2A2

Relative fitness: 1 1-hs 1-s

s is the selection coefficient and h is the dominance coefficient. The value of h yields the
following information:

h=0 A1 dominant, A2 recessive

h=1 A2 dominant, A1 recessive

0<h<1 incomplete dominance

h<0 overdominance

h>1 Underdominance
EPISTASIS

The logarithm of fitness as a function of the number of deleterious mutations. Synergistic

epistasis is represented by the red line - each subsequent deleterious mutation has a larger
proportionate
ionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line
shows the non-epistatic
epistatic case, where fitness is the product of the contributions
butions from each of its
loci. Epistasis means that the phenotypic and/or fitness effect of an allele at one locus
depends on which alleles are present at other loci. Selection does not act
act on a single locus,
but on a phenotype that arises through development from a complete genotype. However,
many population genetics models of sexual species are "single locus" models, where the
fitness of an individual is calculated as the product of the contributions from each of its
loci—effectively
effectively assuming no epistasis.

In fact, the genotype to fitness

ess landscape is more complex. Population genetics must either
model this complexity in detail, or capture it by some simpler average rule. Empirically,
beneficial mutations tend to have a smaller fitness benefit when added to a genetic
background that already
eady has high fitness: this is known as diminishing returns epistasis.When
deleterious mutations also have a smaller fitness effect on high fitness backgrounds, this is
known as "synergistic epistasis". However, the effect of deleterious mutations tends on
average to be very close to multiplicative, or can even show the opposite pattern, known as
"antagonistic epistasis". Synergistic epistasis is central to some theories of the purging of
mutation load and to the evolution of sexual reproduction
reproduction.

MUTATION

Mutation is the ultimate source of genetic variation in the form of new alleles. In addition,
mutation may influence the direction of evolution when there is mutation bias,
bias, i.e. different
probabilities for different mutations to occur. For example, recurrent mutation that tends to be
in the opposite direction to selection can lead to mutation–selection balance.. At the molecular
level, if mutation from G to A happens more often than mutation from A to G, then
genotypes with A will tend to evolve. Different insertion vs. deletion mutation biases in
different taxa can lead to the evolution of different genome sizes. Developmental or
mutational biases have also been observed in morphological evolution. For example,
according to the phenotype-first theory of evolution, mutations can eventually cause the
genetic assimilation of traits that were previously induced by the environment. Mutation bias
effects are superimposed on other processes. If selection would favor either one out of two
mutations, but there is no extra advantage to having both, then the mutation that occurs the
most frequently is the one that is most likely to become fixed in a population.

Drosophila melanogaster

Mutation can have no effect, alter the product of a gene, or prevent the gene from
functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a
protein produced by a gene, this will probably be harmful, with about 70 percent of these
mutations having damaging effects, and the remainder being either neutral or weakly
beneficial. Most loss of function mutations are selected against. But when selection is weak,
mutation bias towards loss of function can affect evolution. For example, pigments are no
longer useful when animals live in the darkness of caves, and tend to be lost. This kind of loss
of function can occur because of mutation bias, and/or because the function had a cost, and
once the benefit of the function disappeared, natural selection leads to the loss. Loss of
sporulation ability in a bacterium during laboratory evolution appears to have been caused by
mutation bias, rather than natural selection against the cost of maintaining sporulation ability.
When there is no selection for loss of function, the speed at which loss evolves depends more
on the mutation rate than it does on the effective population size, indicating that it is driven
more by mutation bias than by genetic drift. Mutations can involve large sections of DNA
becoming duplicated, usually through genetic recombination. This leads to copy-number
variation within a population. Duplications are a major source of raw material for evolving
new genes. Other types of mutation occasionally create new genes from previously
noncoding DNA.

GENETIC DRIFT

Genetic drift is a change in allele frequencies caused by random sampling. That is, the alleles
in the offspring are a random sample of those in the parents. Genetic drift may cause gene
variants to disappear completely, and thereby reduce genetic variability. In contrast to natural
selection, which makes gene variants more common or less common depending on their
reproductive success, the changes due to genetic drift are not driven by environmental or
adaptive pressures, and are equally likely to make an allele more common as less common.
The effect of genetic drift is larger for alleles present in few copies than when an allele is
present in many copies. The population genetics of genetic drift are described using either
branching processes or a diffusion equation describing changes in allele frequency. These
approaches are usually applied to the Wright-Fisher and Moran models of population
genetics. Assuming genetic drift is the only evolutionary force acting on an allele, after t
generations in many replicated populations, starting with allele frequencies of p and q, the
variance in allele frequency across those populations is

Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and
this remained the dominant view for several decades. No population genetics perspective has
ever given genetic drift a central role by itself, but some have made genetic drift important in
combination with another non-selective force. The shifting balance theory of Sewall Wright
held that the combination of population structure and genetic drift was important. Motoo
Kimura's neutral theory of molecular evolution claims that most genetic differences within
and between populations are caused by the combination of neutral mutations and genetic
drift. The role of genetic drift by means of sampling error in evolution has been criticized by
John H Gillespie and Will Provine, who argue that selection on linked sites is a more
important stochastic force, doing the work traditionally ascribed to genetic drift by means of
sampling error. The mathematical properties of genetic draft are different from those of
genetic drift. The direction of the random change in allele frequency is autocorrelated across
generations.
GENE FLOW

Gene flow is the transfer of alleles from one population to another population through
immigration of individuals. In this
th example, one of the birds from population A immigrates to
population B, which has fewer of the dominant alleles, and through mating incorporates its
alleles into the other. Because of physical barriers to migration, along with the limited
tendency for individuals to move or spread ((vagility),
), and tendency to remain or come back
to natal place (philopatry),
), natural populations rarely all interbreed as may be assumed in
theoretical random models (panmixy
panmixy). There is usually a geographic
graphic range within which
individuals are more closely related to one another than those randomly selected from the
general population. This is describe
describedd as the extent to which a population is genetically
structured. Genetic structuring can be caused by migration due to historical climate cha
change,
species range expansion or current availability of habitat.. Gene flow is hindered by mountain
ranges, oceans
ans and deserts or even man
man-made structures such as the Great Wall of China
China,
which has hindered the flow of plant genes. Gene flow is the exchange of genes between
populations or species, breaking down the structure. Examples of gene flow within a species
include the migration and then breeding of organisms, or the exchange of pollen. Gene
transfer between species includes the formation of hybrid organisms and horizontal gene
transfer.. Population genetic models can be used to identify which populations show
significant genetic isolation from one another, and to reconstruct
reconstruct their history. Subjecting a
population to isolation leads to inbreeding depression.. Migration into a population can
introduce new genetic variants, potentially
potentia contributing to evolutionary rescue
rescue. If a
significant proportion of individuals or gametes migrate, it can also change allele frequencies,
e.g. giving rise to migration load
load. In the presence of gene flow, other barriers to hybrid
hybridization
between two diverging populations of an outcrossing species are required for the populations
to become new species.
HORIZONTAL GENE TRANSFER

Current tree of life showing vertical and horizontal gene transfers.

Horizontal gene transfer is the transfer of genetic material from one organism to another
organism that is not its offspring; this is most common among prokaryotes.. In medicine, this
contributes to the spread of antibiotic resistance,
resistance as when one bacterium acquires resistance
genes it can rapidly transfer them to other speci
species.
es. Horizontal transfer of genes from bacteria
to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle
Callosobruchus chinensis may also have occurred. An example of larger-scale
larger scale transfers are
the eukaryotic bdelloid
d rotifers,
rotifers, which appear to have received a range of genes from
bacteria, fungi, and plants. Viruses can also carry DNA between organisms, allowing transfer
of genes even across biological domains.
domains Large-scale
scale gene transfer has also occurred between
the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and
mitochondria.

LINKAGE

If all genes are in linkage equilibrium,

equilibrium, the effect of an allele at one locus can be averaged
across the gene pool at other loci. In reality,
reality, one allele is frequently found in linkage
disequilibrium with genes at other loci, especially with genes located nearby on the same
chromosome. Recombination breaks up this linkage disequilibrium too slowly to avoid
genetic hitchhiking,, where an allele at one locus rises to high frequency because it is linked to
an allele under selection at a nearby locus. Linkage also slows down the rate of adaptation,
even in sexual populations. The effect of linkage disequilibrium in slowing down the rate of
adaptive evolution arises from a combination of the Hill–Robertson effect (delays in bringing
beneficial mutations together) and background selection (delays in separating beneficial
mutations from deleterious hitchhikers). Linkage is a problem for population genetic models
that treat one gene locus at a time. It can, however, be exploited as a method for detecting the
action of natural selection via selective sweeps. In the extreme case of an asexual population,
linkage is complete, and population genetic equations can be derived and solved in terms of a
travelling wave of genotype frequencies along a simple fitness landscape. Most microbes,
such as bacteria, are asexual. The population genetics of their adaptation have two contrasting
regimes. When the product of the beneficial mutation rate and population size is small,
asexual populations follow a "successional regime" of origin-fixation dynamics, with
adaptation rate strongly dependent on this product. When the product is much larger, asexual
populations follow a "concurrent mutations" regime with adaptation rate less dependent on
the product, characterized by clonal interference and the appearance of a new beneficial
mutation before the last one has fixed.

APPLICATIONS

EXPLAINING LEVELS OF GENETIC VARIATION

Neutral theory predicts that the level of nucleotide diversity in a population will be
proportional to the product of the population size and the neutral mutation rate. The fact that
levels of genetic diversity vary much less than population sizes do is known as the "paradox
of variation". While high levels of genetic diversity were one of the original arguments in
favor of neutral theory, the paradox of variation has been one of the strongest arguments
against neutral theory.

It is clear that levels of genetic diversity vary greatly within a species as a function of local
recombination rate, due to both genetic hitchhiking and background selection. Most current
solutions to the paradox of variation invoke some level of selection at linked sites. For
example, one analysis suggests that larger populations have more selective sweeps, which
remove more neutral genetic diversity. A negative correlation between mutation rate and
population size may also contribute. Life history affects genetic diversity more than
population history does, e.g. r-strategists have more genetic diversity.

DETECTING SELECTION

Population genetics models are used to infer which genes are undergoing selection. One
common approach is to look for regions of high linkage disequilibrium and low genetic
variance along the chromosome, to detect recent selective sweeps. A second common
approach is the McDonald–Kreitman test. The McDonald–Kreitman test compares the
amount of variation within a species (polymorphism) to the divergence between species
(substitutions) at two types of sites, one assumed to be neutral. Typically, synonymous sites
are assumed to be neutral. Genes undergoing positive selection have an excess of divergent
sites relative to polymorphic sites. The test can also be used to obtain a genome-wide
estimate of the proportion of substitutions that are fixed by positive selection, α. According to
the neutral theory of molecular evolution, this number should be near zero. High numbers
have therefore been interpreted as a genome-wide falsification of neutral theory.

DEMOGRAPHIC INFERENCE

The simplest test for population structure in a sexually reproducing, diploid species, is to see
whether genotype frequencies follow Hardy-Weinberg proportions as a function of allele
frequencies. For example, in the simplest case of a single locus with two alleles denoted A
and a at frequencies p and q, random mating predicts freq(AA) = p2 for the AAhomozygotes,
freq(aa) = q2 for the aa homozygotes, and freq(Aa) = 2pq for the heterozygotes. In the
absence of population structure, Hardy-Weinberg proportions are reached within 1-2
generations of random mating. More typically, there is an excess of homozygotes, indicative
of population structure. The extent of this excess can be quantified as the inbreeding
coefficient, F. Individuals can be clustered into K subpopulations. The degree of population
structure can then be calculated using FST, which is a measure of the proportion of genetic
variance that can be explained by population structure. Genetic population structure can then
be related to geographic structure, and genetic admixture can be detected.

Coalescent theory relates genetic diversity in a sample to demographic history of the

population from which it was taken. It normally assumes neutrality, and so sequences from
more neutrally-evolving portions of genomes are therefore selected for such analyses. It can
be used to infer the relationships between species (phylogenetics), as well as the population
structure, demographic history (e.g. population bottlenecks, population growth), biological
dispersal, source–sink dynamics and introgression within a species.

EVOLUTION OF GENETIC SYSTEMS

By assuming that there are loci that control the genetic system itself, population genetic
models are created to describe the evolution of dominance and other forms of robustness, the
evolution of sexual reproduction and recombination rates, the evolution of mutation rates, the
evolution of evolutionary capacitors, the evolution of costly signalling traits, the evolution of
ageing, and the evolution of co-operation. For example, most mutations are deleterious, so
the optimal mutation rate for a species may be a trade-off between the damage from a high
deleterious mutation rate and the metabolic costs of maintaining systems to reduce the
mutation rate, such as DNA repair enzymes.

One important aspect of such models is that selection is only strong enough to purge
deleterious mutations and hence overpower mutational bias towards degradation if the
selection coefficient s is greater than the inverse of the effective population size. This is
known as the drift barrier and is related to the nearly neutral theory of molecular evolution.
Drift barrier theory predicts that species with large effective population sizes will have highly
streamlined, efficient genetic systems, while those with small population sizes will have
bloated and complex genomes containing for example introns and transposable elements.
However, somewhat paradoxically, species with large population sizes might be so tolerant to
the consequences of certain types of errors that they evolve higher error rates, e.g. in
transcription and translation, than small populations.

6.4 PHENOTYPIC VARIATIONS

Phenotypes are traits or characteristics of an organism that we can observe, such as size,
color, shape, capabilities, behaviors, etc. Not all phenotypes can actually be seen. For
example, blood types are phenotypes that we can only observe using laboratory techniques.
Phenotypes can be caused by genes, environmental factors, or a combination of both.

Phenotypic variation, then, is the variability in phenotypes that exists in a population. For
example, people come in all shapes and sizes: height, weight, and body shape are phenotypes
that vary. Hair, eye color, and the ability to roll your tongue are variable phenotypes, too.
What about other organisms? All organisms can have phenotypic variation. In plants, flower
color and leaf shape are examples of variable phenotypes. In bacteria, resistance to antibiotics
is a variable phenotype: some bacteria are resistant and survive antibiotic treatment, while
others are susceptible and die when antibiotics are given.

In genetics, the phenotype (from Greek φαινο- (faino-) 'showing', and τύπος (túpos) 'type') is
the set of observable characteristics or traits of an organism.The term covers the organism's
morphology or physical form and structure, its developmental processes, its biochemical and
physiological properties, its behavior, and the products of behavior. An organism's phenotype
results from two basic factors: the expression of an organism's genetic code, or its genotype,
and the influence of environmental factors. Both factors may interact, further affecting
phenotype. When two or more clearly different phenotypes exist in the same population of a
species, the species is called polymorphic. A well-documented example of polymorphism is
Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in
the environment as yellow, black, and brown. Richard Dawkins in 1978 and then again in his
1982 book The Extended Phenotype suggested that one can regard bird nests and other built
structures such as caddis-fly larvae cases and beaver dams as "extended phenotypes".
Wilhelm Johannsen proposed the genotype-phenotype distinction in 1911 to make clear the
difference between an organism's heredity and what that heredity produces. The distinction
resembles that proposed by August Weismann (1834–1914), who distinguished between
germ plasm (heredity) and somatic cells (the body). The genotype-phenotype distinction
should not be confused with Francis Crick's central dogma of molecular biology, a statement
about the directionality of molecular sequential information flowing from DNA to protein,
and not the reverse.

6.4.1 PHENOTYPE AND PHENOTYPIC VARIATION

The word phenotype refers to the observable characters or attributes of individual organisms,
including their morphology, physiology, behavior, and other traits. The phenotype of an
organism is limited by the boundaries of its specific genetic complement (genotype), but is
also influenced by environmental factors that impact the expression of genetic potential.

All organisms have unique genetic information, which is embodied in the particular
nucleotide sequences of their DNA (deoxyribonucleic acid), the genetic biochemical of
almost all organisms, except for viruses and bacteria that utilize RNA as their genetic
material. The genotype is fixed within an individual organism but is subject to change
(mutations) from one generation to the next due to low rates of natural or spontaneous
mutation. However, there is a certain degree of developmental flexibility in the phenotype,
which is the actual or outward expression of the genetic information in terms of anatomy,
behavior, and biochemistry. This flexibility can occur because the expression of genetic
potential is affected by environmental conditions and other circumstances.

Consider, for example, genetically identical bacterial cells, with a fixed complement of
genetic each plated on different gels. If one bacterium is colonized under ideal conditions, it
can grow and colonize its full genetic potential. However, if a genetically identical bacterium
is exposed to improper nutrients or is otherwise grown under adverse conditions, colony
formation may be stunted. Such varying growth patterns of the same genotype are referred to
as phenotypic plasticity. Some traits of organisms, however, are fixed genetically, and their
expression is not affected by environmental conditions. Moreover, the ability of species to
exhibit phenotypically plastic responses to environmental variations is itself, to a substantial
degree, genetically determined. Therefore, phenotypic plasticity reflects both genetic
capability and varying expression of that capability, depending on circumstances.

Phenotypic variation is essential for evolution. Without a discernable difference among

individuals in a population there are no genetic selection pressures acting to alter the variety
and types of alleles (forms of genes) present in a population. Accordingly, genetic mutations
that do not result in phenotypic change are essentially masked from evolutionary
mechanisms. Phenetic similarity results when phenotypic differences among individuals are
slight. In such cases, it may take a significant alteration in environmental conditions to
produce significant selection pressure that results in more dramatic phenotypic differences.
Phenotypic differences lead to differences in fitness and affect adaptation.

Phenotypes are traits or characteristics of an organism that we can observe, such as size,
color, shape, capabilities, behaviors, etc. Not all phenotypes can actually be seen. For
example, blood types are phenotypes that we can only observe using laboratory techniques.
Phenotypes can be caused by genes, environmental factors, or a combination of both.
Phenotypic variation, then, is the variability in phenotypes that exists in a population. For
example, people come in all shapes and sizes: height, weight, and body shape are phenotypes
that vary. Hair, eye color, and the ability to roll your tongue are variable phenotypes, too.
What about other organisms? All organisms can have phenotypic variation. In plants, flower
color and leaf shape are examples of variable phenotypes. In bacteria, resistance to antibiotics
is a variable phenotype: some bacteria are resistant and survive antibiotic treatment, while
others are susceptible and die when antibiotics are given.

Phenotypic variation is an important adaptive mechanism in rotifers, but has posed difficult
problems for systematists. This variation arises by several mechanisms including
cyclomorphosis, dietary- and predatorinduced polymorphisms, polymorphisms in hatchlings
from resting eggs, and dwarfism. Cyclomorphosis is the seasonal phenotypic change in body
size, spine length, pigmentation, or ornamentation found in successive generations of
zooplankton. These changes are phenotypic alterations in a single population that are related
to physical, chemical, or biologic features of the environment. Each different morphological
form is called a morphotype. Specifically excluded from cyclomorphotic change are seasonal
succession of sibling species and clonal replacements of genotypes, both of which are genetic
changes in populations.

A striking phenotypic change in morphology that is associated with a dietary polymorphism

was described for three Asplanchna species (brightwelli, intermedia, sieboldi) by Gilbert
(1980a). Diets that include the plant product a-tocopherol (vitamin E) induce saccate females,
the smallest morphotype, to produce cruciform daughters. Cruciforms have lateral outgrowths
of the body wall that protect them from cannibalism by conspecifics by making them larger
and, thus, more difficult to ingest if captured. In the presence of a-tocopherol and certain prey
types, cruciforms can produce a third morphotype called campanulates (more prevalent in A.
sieboldi and A. intermedia). Campanulates are very large females (>2000 µm), which heavily
cannibalize saccate females. Female polymorphism is much less pronounced in A. brightwelli
where there is a 50–60% increase in body size, but no campanulates are produced and body
wall outgrowths are slight. Dietary polymorphism in Asplanchna (gigantism) may have
evolved originally as a generalized growth response to larger prey typical of eutrophic waters
(Gilbert, 1980a; Gilbert and Stemberger, 1985c). The tocopherol response probably is
adaptive, because it signals the availability of nutritious rotifer and microcrustacean prey.

Another source of phenotypic variation is predator-induced polymorphisms. Spined and

unspined forms had been recognized in several rotifer species for many years, but the
cause(s) and significance(s) of these variations remained an enigma (Fig. 12). However,
Gilbert (1966, 1967) was the first to show that spine production could be induced in the
offspring of female B. calyciflorus if adults were exposed to culture medium which had
previously held the predatory species Asplanchna. Gilbert (1967) also demonstrated that such
spines were strong deterrents to predation by Asplanchna (see Section III.C.4). However,
Stemberger (1990) has shown that food concentration can dramatically modify the
development of spines in B. calyciflorus.

Two additional sources of phenotypic variation are polymorphisms called “aptera

generations” in the hatchlings of resting eggs and dwarfism, both of which have been
reported in rotifers of some tropical crater lakes (Green, 1977). Aptera morphotypes were
initially thought to be different species of Polyarthra, but later were shown to be forms
lacking the paddles that are characteristic of this genus. Only the generation hatching from
resting eggs lacks paddles; their parthenogenetic offspring develop into typical morphotypes.
Similar polymorphisms between resting egg hatchlings and parthenogenetic generations were
described for Keratella quadrata and are suspected for Notholca acuminata (Amrén, 1964).
Dwarfism in Brachionus caudatus in Cameroon crater lakes was described by Green (1977)
and is characterized by reduced body size and spination as compared to normal morphotypes.
Green speculated that high temperature combined with reduced food supply may cause this
condition.

DIFFICULTIES IN DEFINITION

Despite its seemingly straightforward definition, the concept of the phenotype has hidden
subtleties. It may seem that anything dependent on the genotype is a phenotype, including
molecules such as RNA and proteins. Most molecules and structures coded by the genetic
material are not visible in the appearance of an organism, yet they are observable (for
example by Western blotting) and are thus part of the phenotype; human blood groups are an
example. It may seem that this goes beyond the original intentions of the concept with its
focus on the (living) organism in itself. Either way, the term phenotype includes inherent
traits or characteristics that are observable or traits that can be made visible by some technical
procedure. A notable extension to this idea is the presence of "organic molecules" or
metabolites that are generated by organisms from chemical reactions of enzymes. The term
"phenotype" has sometimes been incorrectly used as a shorthand for phenotypic difference
from wild type, yielding the statement that a "mutation has no phenotype". Another extension
adds behavior to the phenotype, since behaviors are observable characteristics. Behavioral
phenotypes include cognitive, personality, and behavioral patterns. Some behavioral
phenotypes may characterize psychiatric disorders or syndromes.

PHENOTYPIC VARIATION

Phenotypic variation (due to underlying heritable genetic variation) is a fundamental

prerequisite for evolution by natural selection. It is the living organism as a whole that
contributes (or not) to the next generation, so natural selection affects the genetic structure of
a population indirectly via the contribution of phenotypes. Without phenotypic variation,
there would be no evolution by natural selection.

The interaction between genotype and phenotype has often been conceptualized by the
following relationship:

genotype (G) + environment (E) → phenotype (P)

A more nuanced version of the relationship is:

genotype (G) + environment (E) + genotype & environment interactions (GE) →

phenotype (P)

Genotypes often have much flexibility in the modification and expression of phenotypes; in
many organisms these phenotypes are very different under varying environmental conditions
(see ecophenotypic variation). The plant Hieracium umbellatum is found growing in two
different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy
with broad leaves and expanded inflorescences; the other is among sand dunes where the
plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate
along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in,
determine the phenotype that grows. An example of random variation in Drosophila flies is
the number of ommatidia, which may vary (randomly) between left and right eyes in a single
individual as much as they do between different genotypes overall, or between clones raised
in different environments.

The concept of phenotype can be extended to variations below the level of the gene that
affect an organism's fitness. For example, silent mutations that do not change the
corresponding amino acid sequence of a gene may change the frequency of guanine-cytosine
base pairs (GC content). These base pairs have a higher thermal stability (melting point) than
adenine-thymine, a property that might convey, among organisms living in high-temperature
environments, a selective advantage on variants enriched in GC content.

THE EXTENDED PHENOTYPE

Richard Dawkins described a phenotype that included all effects that a gene has on its
surroundings, including other organisms, as an extended phenotype, arguing that "An
animal's behavior tends to maximize the survival of the genes 'for' that behavior, whether or
not those genes happen to be in the body of the particular animal performing it." For instance,
an organism such as a beaver modifies its environment by building a beaver dam; this can be
considered an expression of its genes, just as its incisor teeth are—which it uses to modify its
environment. Similarly, when a bird feeds a brood parasite such as a cuckoo, it is unwittingly
extending its phenotype; and when genes in an orchid affect orchid bee behavior to increase
pollination, or when genes in a peacock affect the copulatory decisions of peahens, again, the
phenotype is being extended. Genes are, in Dawkins's view, selected by their phenotypic
effects. Other biologists broadly agree that the extended phenotype concept is relevant, but
consider that its role is largely explanatory, rather than assisting in the design of experimental
tests.

PHENOME AND PHENOMICS

Although a phenotype is the ensemble of observable characteristics displayed by an

organism, the word phenome is sometimes used to refer to a collection of traits, while the
simultaneous study of such a collection is referred to as phenomics. Phenomics is an
important field of study because it can be used to figure out which genomic variants affect
phenotypes which then can be used to explain things like health, disease, and evolutionary
fitness. Phenomics has widespread applications in the agricultural industry. With an
exponentially growing population and inconsistent weather patterns due to global warming, it
has become increasingly difficult to cultivate enough crops to support the world's population.
Advantageous genomic variations, such as drought and heat resistance, can be identified
through phenomics to create more durable GMOs. Phenomics may be a stepping stone
towards personalized medicine, particularly drug therapy. Once the phenomic database has
acquired more data, a person's phonemic information can be used to select specific drugs tail

The RNA world is the hypothesized pre-cellular stage in the evolutionary history of life on
earth, in which self-replicating RNA molecules proliferated prior to the evolution of DNA
and proteins. The folded three-dimensional physical structure of the first RNA molecule that
possessed ribozyme activity promoting replication while avoiding destruction would have
been the first phenotype, and the nucleotide sequence of the first self-replicating RNA
molecule would have been the original genotype.
 UNIT 7: GENETICS OF SPECIATION

7.1 OBJECTIVES

• Study of Species
• Study of Speciation
• How do we study speciation?
• Study of Phylogenetic, Biological and other Concepts of Species

7.2 INTRODUCTION

Speciation has occurred, is occurring and will occur. These are undeniable facts. The problem
is: How do we study speciation? There is no single approach since there is no single
mechanism by which species spectate. Some approaches used in the past:
Study patterns of morphological change in the fossil record in a well-defined lineage of
organisms. Success depends on many unknowns: stratigraphic resolution (will you "see" the
speciation event); distinguishing geographic variants from true species (all you have is
morphology.
Comparisons of closely related species. These have speciated recently (assuming closely
related ~ short time since speciation) so careful studies of their biology may identify
important features that contribute to reproductive isolation.
Study intraspecific variation. Look for evidence of incipient barriers to gene exchange.
Perform crosses between individuals from different regions; look for differences in genital
morphology, secondary sexual characteristics. These may show some bimodal distribution
suggestive of early steps in evolution. Must ask: what might we expect to find? This depends
entirely on the model of speciation that might apply to the organism under study. Looking
within a large species range for signs of variation may be fruitless if the speciation mode is
peripatric with genetic revolutions?
Laboratory populations might serve as model systems. One can establish the conditions of
the specific model under question and ask if the predicted divergence is observed.
Mathematical models can address specific predictions about modes of speciation. Both of
these "artificial" methods are important since they can identify what is possible. Knowing
what's possible might spur one on to looking for it in unexpected contexts in natural
populations.
With the use of molecular tools the comparisons of intraspecific and interspecific genetic
variation has been studied in some detail. Aim is to identify genetic changes during
speciation. These data show us that genetic change is associated with speciation. We want to
be able to describe the genetics of speciation and the genetics of species differences. To do
so we need to distinguish genetic changes that cause speciation from those that accompany
speciation. These will differ a lot from one group of organisms to the next and will depend
on the genetic architecture of speciation. Best data on both of these issues have come from
the many species of Drosophila
Coyne and Orr (1989, Evolution vol. 43, pg. 362-381) take Ayala's approach one step further
and attempt to correlate genetic distance (Nei's D) with amounts of prezygotic and
postzygotic isolation. In the literature there are many reports of the amount of genetic
distance between closely related species of Drosophila and the amount of reproductive
isolation between many of the species for which genetic distance has been measured
(premating or prezygotic isolation is measured as [1-(proportion of heterotypic
matings/proportion of homotypic matings)] which ranges from - infinity for all heterotypic
(between species) matings to 0 for random mating to +1 for all homotypic matings. Rarely do
two species prefer to mate with the wrong type so the index effectively ranges from 0 to 1).
Post zygotic or postmating isolation can be measured as in the following example. Consider
two species, A and B. These can be crossed two ways (reciprocally) to produce hybrid
offspring. We can also examine the viability or fertility of the two sexes of these hybrid
offspring, hence four contexts are examined to score post zygotic isolation:
Case Female Male parent Offspring In viable or
Parent sterile?

1. Species A Species B Male No = 0 Yes = 1

2. Species A Species B Male No = 0 No = 0

3. Species B Species A Female No = 0 No = 0

4. Species B Species A Female No = 0 No = 0

I=0 I = 0.25

In any particular case one could choose to score isolation in terms of the presence or absence
of either isolation or sterility. Normally hybrid sterility evolves before hybrid in viability
(mules are sterile but viable). Hence an index based on sterility would have higher values
than an index based only on evidence for in viable hybrid offspring.
Coyne and Orr extracted these two types of data from the literature and tested some important
ideas about the genetics of speciation. The general idea is that genetic distance (D) is
positively related to time (the molecular clock hypothesis) and thus species pairs showing
different degrees of genetic distance should be at different degrees of completion of the
speciation process (be aware that many organisms are in the process of spectating as you read
these notes). Coyne and Orr show that there is a significant relationship between genetic
Distance and both premating and post mating isolation two interesting additional points:
sympatric species show greater prezygotic isolation than allopatric species pairs. This
pattern is consistent with the reinforcement hypothesis and suggests that reinforcement can
act. A second observation: less genetic distance between species pairs that produce sterile
or inviable males than between species pairs that produce sterile or inviable females (D (A-
B)sterile males< D(A-B)sterile females).
This observation confirmed a well-documented pattern known as Haldane's Rule stating that
when hybrid crosses produce sterile or in viable offspring, the sex that exhibits this is most
likely the heterogametic sex (the sex with two different sex chromosomes, e.g. X and Y in
male humans and Drosophila; in birds and butterflies the female is heterogametic with Z and
W). Another "rule" of speciation is that genes affecting reproductive isolation are typically
found on the X chromosome (where X is the "female" chromosome; see another paper by
Coyne and Orr: "Two Rules of Speciation", in Speciation and its Consequences, 1989, D.
Otte & J. Endler, editors, Sinauer Associates).
The current belief about the large "X effect" is that advantageous mutations are more likely to
accumulate on the X since it is homozygous in males, so half of the time recessive
advantageous mutations will be expressed. Similar mutations occurring on autosomes will be
less likely to be expressed because autosomes are always paired and an advantageous
mutation would have to be dominant to be "visible" to selection. Thus diverging populations
(incipient species) will tend to accumulate different mutations on their respective X
chromosomes. When individuals are crossed between these divergent populations, there will
deleterious pleiotropic interaction effects between these new alleles on the X and other genes
throughout the genome. The new mutations certainly were not deleterious when they arose
within each separated population, but when paired with autosomes from a diverged
population these mutations do not function properly, thus one would only see the effect in a
hybrid cross.
Attempts to identify genes that keep species isolated go back to Dobzhansky in the 1930's:
crosses between D. pseudoobscura and D. persimilis produce sterile males and fertile females
as F1 hybrids. These F1 females can be backcrossed to males of either species, so the
backcrossed offspring can have all combinations of chromosomes. With four chromosome
pairs in each species, the F1 hybrid will have four heterokaryotypicpairs of chromosomes.
The two possible backcrosses (one in each direction) can result in 16 possible combinations
of chromosomes. Frequently find that the offspring with nonmotile sperm (= sterile) are the
ones with sex chromosomes from each species. Deleterious interactions between sex
chromosomes and/or between sex chromosomes and autosomes are implied, but the details
are the topic of a lot of current research. These types of experiments, coupled with molecular
biology may someday allow us to identify the genes and the types of changes that can lead to
speciation. Again, we would like to know the genetic architecture of speciation: how many
genes involved? what sorts of mutations at each gene? What sorts of interactions among
genes? Etc.
7.3 PHYLOGENETIC, BIOLOGICAL AND OTHER CONCEPTS OF
SPECIES

The concept of a species as an irreducible group whose members are descended from a
common ancestor and who all possess a combination of certain defining, or derived traits.
Hence, this concept defines a species as a group having a shared and unique evolutionary
history. It is less restrictive than the biological species concept, in that breeding between
members of different species does not pose a problem. Also, it permits successive species to
be defined even if they have evolved in an unbroken line of descent, with continuity of sexual
fertility. However, because slight differences can be found among virtually any group of
organisms, the concept tends to encourage extreme division of species into ever-smaller
groups.

A new population that results from a speciation event is called a species. But although species
result from a simple process, recognizing species in nature can be complicated. Biologists
cannot travel in time to observe the speciation’s that resulted in today's diversity of life, so
they must observe the reproduction of living organisms to determine the makeup of species.
Paleontologists can find the fossil evidence of the ancestors of today's species, but they
cannot observe whether those fossil organisms could reproduce with each other. Because
scientists have different kinds of evidence about organisms, they use different concepts of
species when testing hypotheses about their evolution.

BIOLOGICAL SPECIES
The most obvious property that helps to define species is reproductive isolation. Biologists
studying living animals often use the biological species concept, which envisions a species as
a "group of actually or potentially interbreeding natural populations which are reproductively
isolated from other such groups" (Mayr 1942). It is the biological species concept that
primatologists use to grapple with whether chimpanzees and bonobos are different species,
for example, by observing the differences in their reproductive behaviors and the strength of
geographic isolation between their populations.
The biological species concept has some important limitations for paleontology. Making use
of the concept depends on observing the mating behavior and interbreeding patterns of
animals in their natural environments, which is not possible with fossils of organisms that
lived in the past. Other kinds of observations that paleontologists might gather, such as
morphological differences between fossils, have no necessary value under this concept.
Another limitation is that the biological species concept does not incorporate any idea of how
species may change over time. Paleontologists study fossils that may be separated by
hundreds of thousands of years of time. It is difficult to imagine such widely separated
individuals as part of the same reproductive community, even if they were very similar to
each other. Over such time periods, evolution can transform populations substantially. The
biological species concept recognizes the genetic continuity within a species caused by gene
flow, but it does not incorporate a view of species existing over evolutionary time. For these
reasons, paleontology requires a different kind of species concept.

PHYLOGENETIC SPECIES CONCEPT

The phylogenetic species concept is an attempt to define species by their relationships to
other species. Instead of trying to determine the reproductive boundaries of populations,
scientists using the phylogenetic species concept attempt to uncover their genealogical
relationships. A group of individuals that includes all the descendants of one common
ancestor, leaving no descendants out, is called a monophyletic group.
Paleontologists Niles Eldredge and Joel Cracraft devised a species concept called the
"Phylogenetic Species Concept," intended to apply to circumstances in which reproduction or
isolation among organisms could not be observed. Under this concept, a species is "a
diagnosable cluster of individuals within which there is a parental pattern of ancestry and
escent, beyond which there is not, and which exhibits a pattern of phylogenetic ancestry and
descent among units of like kind" (Eldredge and Cracraft 1980:92).
Key to the phylogenetic species concept is the idea that species must be "diagnosable." In
other words, members of the species should share a combination of characteristics that other
species lack. To look for the unique features that define a phylogenetic species,
paleontologists must perform systematic comparisons with other related fossils or living
species. These aspects of the concept make it widely applicable in paleontology.
But the phylogenetic species concept is not without its problems. Because the concept defines
species based on morphology, without explicitly referring to populations or reproductive
boundaries, it does not apply well to cases where morphologically different populations are
connected by gene flow. Morphological variation among populations is not uncommon
within living species. Humans today are a species with substantial morphological variation
from continent to continent. Humans on different continents are not reproductively isolated,
and their variation is largely distributed as clines over large geographic distances. Yet a
paleontologist who had only a few fragmentary specimens from each continent would not
necessarily know the pattern of variation and many features of his specimens would appear to
be unique. What would the paleontologist make of the high nose of a European specimen, the
forward-facing cheeks of an Asian fossil, or the strong brow ridge above the eye orbits of an
Australian, each taken randomly from their variable populations? By applying the
phylogenetic species concept, a paleontologist would probably conclude that the different
continents were homes to different human species.
Thus, because the phylogenetic species concept does not identify species based on the
reproductive boundaries between them, it may have the effect of identifying populations
connected by gene flow as different species. For this reason, a phylogenetic species as
defined by a paleontologist may not correspond to a real prehistoric population that was the
product of a speciation. Some paleontologists do not view this potential conflict as a problem,
because identifying species based on unique characteristics will create as full as possible a
systematization of the evolution of new features. Assuming that the number of ancient
species was very large, and the number of fossils representing each of them is very small,
then paleontologists can hardly hope to identify every speciation event in the past. The
phylogenetic species concept may therefore provide a better approximation of the number
and diversity of species that existed than other alternatives.
On the other hand, identifying populations connected by gene flow as different species can be
a significant problem for paleontologists who take a greater interest in the processes of
evolution than in the diversity of species in the past. Gene flow is a significant force shaping
evolutionary change within populations. Moreover, evolution may cause a single species to
change over time, possibly acquiring new unique features without any division of a species
into separate reproductively isolated populations. Some paleontologists approach these
difficulties by altering their view of the evolutionary process. If speciation’s can happen as a
transformation of a single population in addition to the appearance of reproductive
boundaries between populations, then a single evolving population may over time comprise
several phylogenetic species. Or if most evolutionary change happened at the time of
speciation, as asserted by the concept of punctuated equilibrium, then the phylogenetic
species concept might more closely approximate the actual pattern of speciation’s in the past.
But without such assumptions, the phylogenetic species concept's problems sometimes create
a stumbling block for some paleontologists in attempting to understand the evolutionary
process.

EVOLUTIONARY SPECIES
The evolutionary species concept combines the genealogical basis of the phylogenetic species
concept with the genetic basis of the biological species concept. An evolutionary species is a
lineage of interbreeding organisms, reproductively isolated from other lineages that have a
beginning, an end, and a distinct evolutionary trajectory (Wiley 1978). The beginning of a
species' existence is a speciation, as a population becomes reproductively isolated from a
parent population. The end of a species occurs either with extinction or with the branching of
the species into one or more descendants.
Central to the evolutionary species concept is the idea of an evolutionary trajectory. The
trajectory of a species is the evolutionary pattern of its characteristics over time. For example,
one of the earliest species in the story of human evolution, Australopithecus afarensis, is
represented by dozens of fossil teeth and mandibles, as well as other remains. Paleontologists
hypothesize that these fossils, from several sites in East Africa, are members of a single
species because of their many morphological resemblances. No very similar fossils have ever
been found before 3.6 million or after 3 million years ago, dates that appear to indicate the
beginning and the end of the species.
Nevertheless, the fossils do show some differences that appear over time. Although the molar
teeth of the fossils do not change over time, the mandibles are thicker and more massive in
more recent fossils than in the most ancient ones. As far as paleontologists can test, the
mandibles form a single series evolving over time toward greater size and thickness. The
evolutionary species concept infers that the fossils represent a species, beginning 3.6 million
years ago and ending 3 million years ago, with an evolutionary trajectory that includes the
evolution of greater mandibular thickness, without apparent changes in molar sizes.
The strength of the evolutionary species concept is that it allows paleontologists to focus on
the causes of evolutionary change, whether they occur during speciation’s or at other times.
Regarding A. afarensis, the observation that mandibles increased in size during the existence
of the species may be explained by different evolutionary forces and conditions than if all the
change occurred with the reproductive isolation of a new population. Although the greater
mandibular thickness of later mandibles might be a unique feature, attempting to establish a
new phylogenetic species for the later fossils might detract from an explanation of the overall
evolutionary pattern.
Phylogenetic species vs. evolutionary species concepts
But the evolutionary species concept also has its problems. Because it uses several different
criteria, much more information may be necessary to define an evolutionary species. Some
scientists do not view this as a drawback, since even if a scientific view of the species that
once existed and their boundaries and relationships proves a challenge, it may nevertheless
add to our understanding of the evolutionary process.
Yet for many paleontologists, the need to amass great numbers of fossils from different times
makes the evolutionary species concept nearly impossible to implement. At the same time, if
scientists always hold out the possibility that two different fossils were actually connected by
gene flow, it may impede an understanding of evolutionary changes that accompany the
appearance of new reproductively isolated species. If we want to have a scientific, meaning
falsificationist, view of the species that have existed and their boundaries and relationships to
each other, we must accept that the process will in many cases be difficult. Simply making up
many species hypotheses cannot add to our knowledge and in many cases it may detract.
What is important is that we realize that our record of past species is incomplete, and our
failure to substantiate the existence of many species in the past does not constitute evidence
that they did not exist.
TESTING SPECIES HYPOTHESES
However species are defined, whenever scientists identify a species, they actually are stating
a hypothesis about the relationships among individual organisms. Such a hypothesis may be
tested using morphological, genetic, or behavioral evidence. Discovering real species that
existed in the past involves predicting the morphological variability of populations, including
variation that occurs among populations connected by gene flow. In the relatively small fossil
samples available to paleontologists, determining the number of species in a sample is a
significant problem. Researchers use a number of techniques to test species hypotheses with
limited morphological samples.
Two fossil hominids: different species or not?
1. What is the level of morphological difference between two or more specimens? Using
a living species for comparison, scientists can determine the likelihood of sampling
similar variability as the fossil sample (Miller 2000).
2. What are the relative frequencies of characteristics in two samples of fossils?
Statistical comparison with the differences between different populations within a
living species can determine whether the differences in frequencies observed in the
 fossils would be likely to occur within the comparison species. Such comparisons can
be extended to the differences between the sexes of a living species to test whether
sexual dimorphism accounts for differences between fossils (Lee 1999).
3. If one fossil sample has a high incidence of several features that are absent or at low
frequency in another sample, this supports the hypothesis that the two samples
represent different species. With samples of sufficient size, say, 10 individuals or
more, paleontologists can even estimate the maximum level of gene flow consistent
with the morphological differences, and thereby frame a test of the hypothesis of
different species in solid evolutionary terms (Hawks and Wolpoff 2001).
4. Do samples represent change over time? Sometimes paleontologists can use different
populations from living species to evaluate likelihood that certain kinds of changes
might occur over time. The best comparisons are with large samples of fossils that
represent long spans of time, however. Although the evolutionary process is in ways
unique for each species, analyses of the rate and level of changes in other species
provide the most powerful tests of species hypotheses available in studying the past.

7.4 ISOLATION

The reproductive characteristics which prevent species from fusing. Isolating mechanisms are
particularly important in the biological species concept, in which species of sexual organisms
are defined by reproductive isolation, i.e. a lack of gene mixture. Two broad kinds of
isolating mechanisms between species are typically distinguished, together with a number of
sub-types (modified from Mayr 1970):
1) Pre-mating isolating mechanisms. Factors which cause species to mate with their own kind
(assortative mating).
a) Temporal isolation. Individuals of different species do not mate because they are active at
different times of day or in different seasons.
b) Ecological isolation. Individuals mate in their preferred habitat, and therefore do not meet
individuals of other species with different ecological preferences.
c) Behavioral isolation. Potential mates meet, but choose members of their own species.
d) Mechanical isolation. Copulation is attempted, but transfer of sperm does not take place.
2) Post-mating isolating mechanisms. Genomic incompatibility, hybrid inviability or sterility.
a) Gametic incompatibility. Sperm transfer takes place, but egg is not fertilized.
b) Zygotic mortality. Egg is fertilized, but zygote does not develop.
c) Hybrid inviability. Hybrid embryo forms, but of reduced viability.
d) Hybrid sterility. Hybrid is viable, but resulting adult is sterile.
e) Hybrid breakdown. First generation (F1) hybrids are viable and fertile, but further hybrid
generations (F2 and backcrosses) may be inviable or sterile.
An alternative classification of isolating mechanisms contrasts pre-zygotic isolation (items 1+
2a above) with post-zygoticisolation (items 2b-e above). As an example of the application of
isolating mechanisms, the apple-feeding host race of the tephritid fruit fly (Rhagoletis
pomonella) differs from the hawthorn-feeding race in that the apple race emerges earlier in
the year (1a), and each host race preferentially chooses to rest, lay eggs and mate on its own
host plant (1b). On the other hand, laboratory experiments show that there is little behavioral,
mechanical, or post-mating isolation (1c,d; 2a-e).
The term isolating mechanisms was introduced by T. Dobzhansky in the 1930s, and has been
popularized in a number of books by E Mayr. Both authors originally proposed that isolating
mechanisms were group traits beneficial at the level of the species; today, this is generally
disbelieved. Recent authors have pointed out that the word "mechanism" is particularly
misleading as pre-mating and post-mating isolation are likely to evolve as a by-product of
natural selection or genetic drift within species, rather than as a direct result of their utility as
barriers to fertilization and gene mixing between species (a process known as reinforcement).
A leading critic of the biological species concept and of the term isolating mechanisms is
HEH Paterson, who argues that species are cohesive wholes as a result of pre-zygotic sexual
signalling within species, rather than due to isolating mechanisms between species. Paterson
therefore introduced a competing idea of species, the recognition concept of species, in which
isolating mechanisms were replaced by specific mate recognition systems as an alternative.
Unfortunately, the word "system" has as many group-benefit connotations as "mechanism",
and the recognition concept of species has not gained universal acceptance.
There is also the terminological problem that reproductive isolation combines traits that
reduce gene flow, such as mate choice or fertilization barriers, with traits that select against
genes that have flowed, such as hybrid incompatibility. Lumping these two antagonistic
features is confusing, since they are unrelated and evolve in very different ways. For instance,
whereas it is conceivable that reinforcement might evolve to reduce an individual's tendency
to mate with another species and produce inviable offspring, it is almost impossible to
imagine that hybrid in viability itself would evolve as an adaptation. This reproductive
isolation terminology leads also to a muddled use of the term gene flow as the opposite of
reproductive isolation; in other words, gene flow comes to include not only the flow of genes,
but also the effects of any natural selection on the frequency of such genes within each
population.
Perhaps the most fundamental problem with isolating mechanisms (and specific mate
recognition systems) is that species are implied to be qualitatively different from subspecies,
races, or forms by their possession of these traits. Races cannot, in theory, differ in either type
of trait because only species are defined by their possession. Arguably, by making species
seem qualitatively different from races, these terms have spawned a number of special
models of speciation where geographic isolation, also known as allopatry, or sudden bursts
of evolution in small founder populations (founder events or punctuated equilibria) play
important roles. Only such unusual conditions were thought to be able to give rise to new
species that differ in isolating mechanisms (or specific mate recognition systems). In reality,
there is little to distinguish mate choice and disruptive natural selection commonly observed
within species from pre-mating and post-mating isolation between species; and, indeed, it is
hard to distinguish species from races in many actual organisms. There are five types of
isolation that biologically prevent species that might otherwise interbreed to produce hybrid
offspring. These are ecological, temporal, behavioral, mechanical/chemical and geographical.
ECOLOGICAL ISOLATION
Ecological, or habitat, isolation occurs when two species that could interbreed do not because
the species live in different areas. For example, in India both the lion and tiger exist and are
capable of interbreeding; however, the lion lives in the grasslands and the tiger lives in the
forest. The two species live in different habitats and will not encounter one another: each is
isolated from the other species.
TEMPORAL ISOLATION
Temporal isolation is when species that could interbreed do not because the different species
breed at different times. This temporal difference could occur at difference times of day,
different times of the year, or anything in between. For example, the field crickets Gryllus
pennsylvanicus and G. veleti become sexually mature at different seasons, one in the spring
and the other in the autumn.
BEHAVIORAL ISOLATION
Behavioral isolation refers to the fact that many species perform different mating rituals. This
is a common barrier between animals. For example, certain species of crickets will only mate
with males that produce a particular mating song. Other species rituals may include a mating
dance or emitting a scent. These clues are ignored by species not accustomed to the ritual.
MECHANICAL OR CHEMICAL ISOLATION
Mechanical isolation is caused by structures or chemical barriers that keep species isolated
from one another. For example, in flowering plants, the shape of the flower will tend to
match up with a natural pollinator. Plants that do not have the correct shape for the pollinator
will not receive a pollen transfer. Likewise, certain chemical barriers prevent gametes from
forming. These chemical barriers will only allow sperm from the correct species to fertilize
the egg.

GEOGRAPHICAL ISOLATION
Geographical isolation refers to the physical barriers that exist that keep two species from
mating. For example, a species of monkey that is located on an island cannot breed with
another species of monkey on the mainland. The water and distance between the two species
keep them isolated from one another and make it impossible for them to breed.

7.5 PATTERNS AND MECHANISMS OF REPRODUCTIVE

ISOLATION

The mechanisms of reproductive isolation are a collection of evolutionary mechanisms,

behaviors and physiological processes critical for speciation. They prevent members of
different species from producing offspring, or ensure that any offspring are sterile. These
barriers maintain the integrity of a species by reducing gene flow between related species.
The mechanisms of reproductive isolation have been classified in a number of ways.
Zoologist Ernst Mayr classified the mechanisms of reproductive isolation in two broad
categories: pre-zygotic for those that act before fertilization (or before mating in the case of
animals) and post-zygotic for those that act after it. The mechanisms are genetically
controlled and can appear in species whose geographic distributions overlap (sympatric
speciation) or are separate (allopatric speciation).
PRE-ZYGOTIC ISOLATION
Pre-zygotic isolation mechanisms are the most economic in terms of the natural selection of a
population, as resources are not wasted on the production of a descendant that is weak, non-
viable or sterile. These mechanisms include physiological or systemic barriers to fertilization.
Temporal or habitat isolation
Any of the factors that prevent potentially fertile individuals from meeting will
reproductively isolate the members of distinct species. The types of barriers that can cause
this isolation include: different habitats, physical barriers, and a difference in the time of
sexual maturity or flowering. An example of the ecological or habitat differences that impede
the meeting of potential pairs occurs in two fish species of the family Gasterosteidae
(sticklebacks). One species lives all year round in fresh water, mainly in small streams. The
other species lives in the sea during winter, but in spring and summer individuals migrate to
river estuaries to reproduce. The members of the two populations are reproductively isolated
due to their adaptations to distinct salt concentrations. An example of reproductive isolation
due to differences in the mating season is found in the toad species Bufo americanus and Bufo
fowleri. The members of these species can be successfully crossed in the laboratory
producing healthy, fertile hybrids. However, mating does not occur in the wild even though
the geographical distribution of the two species overlaps. The reason for the absence of inter-
species mating is that B. americanus mates in early summer and B. fowleri in late summer.
Certain plant species, such as Tradescantia canaliculata and T. subaspera, are sympatric
throughout their geographic distribution, yet they are reproductively isolated as they flower at
different times of the year. In addition, one species grows in sunny areas and the other in
deeply shaded areas.
Behavioral isolation
The different mating rituals of animal species creates extremely powerful reproductive
barriers, termed sexual or behavior isolation that isolates apparently similar species in the
majority of the groups of the animal kingdom. In dioeciously species, males and females have
to search for a partner, be in proximity to each other, carry out the complex mating rituals and
finally copulate or release their gametes into the environment in order to breed. Mating
dances, the songs of males to attract females or the mutual grooming of pairs, are all
examples of typical courtship behavior that allows both recognition and reproductive
isolation. This is because each of the stages of courtship depends on the behavior of the
partner. The male will only move onto the second stage of the exhibition if the female shows
certain responses in her behavior. He will only pass onto the third stage when she displays a
second key behavior. The behaviors of both interlink, are synchronized in time and lead
finally to copulation or the liberation of gametes into the environment. No animal that is not
physiologically suitable for fertilization can complete this demanding chain of behavior. In
fact, the smallest difference in the courting patterns of two species is enough to prevent
mating (for example, a specific song pattern acts as an isolation mechanism in distinct species
of grasshopper of the genus Chorthippus). Even where there are minimal morphological
differences between species, differences in behavior can be enough to prevent mating. For
example, Drosophila melanogaster and D. simulans which are considered twin species due to
their morphological similarity do not mate even if they are kept together in a
laboratory.Drosophila ananassae and D. pallidosa are twin species from Melanesia. In the
wild they rarely produce hybrids, although in the laboratory it is possible to produce fertile
offspring. Studies of their sexual behavior show that the males court the females of both
species but the females show a marked preference for mating with males of their own species.
A different regulator region has been found on Chromosome II of both species that affects the
selection behavior of the females. Pheromones play an important role in the sexual isolation
of insect species. These compounds serve to identify individuals of the same species and of
the same or different sex. Evaporated molecules of volatile pheromones can serve as a wide-
reaching chemical signal. In other cases, pheromones may be detected only at a short distance
or by contact.
In species of the melanogaster group of Drosophila, the pheromones of the females are
mixtures of different compounds; there is a clear dimorphism in the type and/or quantity of
compounds present for each sex. In addition, there are differences in the quantity and quality
of constituent compounds between related species; it is assumed that the pheromones serve to
distinguish between individuals of each species. An example of the role of pheromones in
sexual isolation is found in 'corn borers' in the genus Ostrinia. There are two twin species in
Europe that occasionally cross. The females of both species produce pheromones that contain
a volatile compound which has two isomers, E and Z; 99% of the compound produced by the
females of one species is in the E isomer form, while the females of the other produce 99%
isomer Z. The production of the compound is controlled by just one locus and the
interspecific hybrid produces an equal mix of the two isomers. The males, for their part,
almost exclusively detect the isomer emitted by the females of their species, such that the
hybridization although possible is scarce. The perception of the males is controlled by one
gene, distinct from the one for the production of isomers; the heterozygous males show a
moderate response to the odour of either type. In this case, just 2 'loci' produce the effect of
ethological isolation between species that are genetically very similar. Sexual isolation
between two species can be asymmetrical. This can happen when the mating that produces
descendants only allows one of the two species to function as the female progenitor and the
other as the male, while the reciprocal cross does not occur. For instance, half of the wolves
tested in the Great Lakes area of America show mitochondrial DNA sequences of coyotes,
while mitochondrial DNA from wolves is never found in coyote populations. This probably
reflects an asymmetry in inter-species mating due to the difference in size of the two species
as male wolves take advantage of their greater size in order to mate with female coyotes,
while female wolves and male coyotes do not mate.

Mechanical isolation
Mating pairs may not be able to couple successfully if their genitals are not compatible. The
relationship between the reproductive isolation of species and the form of their genital organs
was signaled for the first time in 1844 by the French entomologistLéon Dufour. Insects' rigid
carapaces act in a manner analogous to a lock and key, as they will only allow mating
between individuals with complementary structures, that is, males and females of the same
species (termed co-specifics). Evolution has led to the development of genital organs with
increasingly complex and divergent characteristics, which will cause mechanical isolation
between species. Certain characteristics of the genital organs will often have converted them
into mechanisms of isolation. However, numerous studies show that organs that are
anatomically very different can be functionally compatible, indicating that other factors also
determine the form of these complicated structures. Mechanical isolation also occurs in plants
and this is related to the adaptation and coevolution of each species in the attraction of a
certain type of pollinator (where pollination is zoophilic) through a collection of
morphophysiological characteristics of the flowers (called floral syndromes), in such a way
that the transport of pollen to other species does not occur.

GAMETIC ISOLATION
The synchronous spawning of many species of coral in marine reefs means that inter-species
hybridization can take place as the gametes of hundreds of individuals of tens of species are
liberated into the same water at the same time. Approximately a third of all the possible
crosses between species are compatible, in the sense that the gametes will fuse and lead to
individual hybrids. This hybridization apparently plays a fundamental role in the evolution of
coral species. However, the other two-thirds of possible crosses are incompatible. It has been
observed that in sea urchins of the genus Strongylocentrotus the concentration of
spermatocytes that allow 100% fertilization of the ovules of the same species is only able to
fertilize 1.5% of the ovules of other species. This inability to produce hybrid offspring,
despite the fact that the gametes are found at the same time and in the same place, is due to a
phenomenon known as gamete incompatibility, which is often found between marine
invertebrates, and whose physiological causes are not fully understood. In some Drosophila
crosses, the swelling of the female's vagina has been noted following insemination. This has
the effect of consequently preventing the fertilization of the ovule by sperm of a different
species.
In plants the pollen grains of a species can germinate in the stigma and grow in the style of
other species. However, the growth of the pollen tubes may be detained at some point
between the stigma and the ovules, in such a way that fertilization does not take place. This
mechanism of reproductive isolation is common in the angiosperms and is called cross-
incompatibility or incongruence. A relationship exists between self-incompatibility and the
phenomenon of cross-incompatibility. In general crosses between individuals of a self-
compatible species (SC) with individuals of a self-incompatible (SI) species give hybrid
offspring. On the other hand, a reciprocal cross (SI x SC) will not produce offspring, because
the pollen tubes will not reach the ovules. This is known as unilateral incompatibility, which
also occurs when two SC or two SI species are crossed.

POST-ZYGOTIC ISOLATION
Zygote mortality and non-viability of hybrids
A type of incompatibility that is found as often in plants as in animals occurs when the egg or
ovule is fertilized but the zygote does not develop, or it develops and the resulting individual
has a reduced viability. This is the case for crosses between species of the frog genus, where
widely differing results are observed depending upon the species involved. In some crosses
there is no segmentation of the zygote (or it may be that the hybrid is extremely non-viable
and changes occur from the first mitosis). In others, normal segmentation occurs in the
blastula but gastrulation fails. Finally, in other crosses, the initial stages are normal but errors
occur in the final phases of embryo development. This indicates differentiation of the embryo
development genes (or gene complexes) in these species and these differences determine the
non-viability of the hybrids. Similar results are observed in mosquitoes of the genus Culex,
but the differences are seen between reciprocal crosses, from which it is concluded that the
same effect occurs in the interaction between the genes of the cell nucleus (inherited from
both parents) as occurs in the genes of the cytoplasmic organelles which are inherited solely
from the female progenitor through the cytoplasm of the ovule.In Angiosperms, the
successful development of the embryo depends on the normal functioning of its endosperm.
The failure of endosperm development and its subsequent abortion has been observed in
many interploidal crosses (that is, those between populations with a particular degree of intra
or interspecific ploidy), and in certain crosses in species with the same level of ploidy. The
collapse of the endosperm, and the subsequent abortion of the hybrid embryo is one of the
most common post-fertilization reproductive isolation mechanism found in angiosperms.
HYBRID STERILITY
A hybrid may have normal viability but is typically deficient in terms of reproduction or is
sterile. This is demonstrated by the mule and in many other well-known hybrids. In all of
these cases sterility is due to the interaction between the genes of the two species involved; to
chromosomal imbalances due to the different number of chromosomes in the parent species;
or to nucleus-cytoplasmic interactions such as in the case of Culex described above.
Hinnies and mules are hybrids resulting from a cross between a horse and a donkey or
between a mare and a donkey, respectively. These animals are nearly always sterile due to the
difference in the number of chromosomes between the two parent species. Both horses and
donkeys belong to the genus Equus, but Equus caballus has 64 chromosomes, while Equus
asinus only has 62. A cross will produce offspring (mule or hinny) with 63 chromosomes that
will not form pairs which means that they do not divide in a balanced manner during meiosis.
In the wild, the horses and donkeys ignore each other and do not cross. In order to obtain
mules or hinnies it is necessary to train the progenitors to accept copulation between the
species or create them through artificial insemination.
The sterility of many interspecific hybrids in angiosperms has been widely recognised and
studied. Interspecific sterility of hybrids in plants has multiple possible causes. These may be
genetic, related to the genomes, or the interaction between nuclear and cytoplasmic factors, as
will be discussed in the corresponding section. Nevertheless, it is important to note that in
plants, hybridization is a stimulus for the creation of new species – the contrary to the
situation in animals. Although the hybrid may be sterile, it can continue to multiply in the
wild by asexual reproduction, whether vegetative propagation or apomixis or the production
of seeds. Indeed, interspecific hybridization can be associated with polyploidia and, in this
way, the origin of new species that are called allopolyploids. Rosa canina, for example, is the
result of multiple hybridizations. or there is a type of wheat that is an allohexaploid that
contains the genomes of three different species.

MULTIPLE MECHANISMS
In general, the barriers that separate species do not consist of just one mechanism. The twin
species of Drosophila, D. pseudoobscura and D. persimilis, are isolated from each other by
habitat (persimilis generally lives in colder regions at higher altitudes), by the timing of the
mating season (persimilis is generally more active in the morning and pseuoobscura at night)
and by behavior during mating (the females of both species prefer the males of their
respective species). In this way, although the distribution of these species overlaps in wide
areas of the west of the United States of America, these isolation mechanisms are sufficient to
keep the species separated. Such that, only a few fertile females have been found amongst the
other species among the thousands that have been analyzed. However, when hybrids are
produced between both species, the gene flow between the two will continue to be impeded
as the hybrid males are sterile. Also, and in contrast with the great vigor shown by the sterile
males, the descendants of the backcrosses of the hybrid females with the parent species are
weak and notoriously non-viable. This last mechanism restricts even more the genetic
interchange between the two species of fly in the wild.

HYBRID SEX: HALDANE'S RULE

Haldane's rule states that when one of the two sexes is absent in interspecific hybrids between
two specific species, and then the sex that is not produced, is rare or is sterile is the
heterozygous (or heterogametic) sex. In mammals, at least, there is growing evidence to
suggest that this is due to high rates of mutation of the genes determining masculinity in the
Y chromosome.
It has been suggested that Haldane's rule simply reflects the fact that the male sex is more
sensitive than the female when the sex-determining genes are included in a hybrid genome.
But there are also organisms in which the heterozygous sex is the female: birds and
butterflies and the law is followed in these organisms. Therefore, it is not a problem related to
sexual development, nor with the sex chromosomes. Haldane proposed that the stability of
hybrid individual development requires the full gene complement of each parent species, so
that the hybrid of the heterozygous sex is unbalanced (i.e. missing at least one chromosome
from each of the parental species). For example, the hybrid male obtained by crossing D.
melanogaster females with D. simulans males, which is non-viable, lacks the X chromosome
of D. simulans.

GENETICS
Pre-copulatory mechanisms in animals
The genetics of ethological isolation barriers will be discussed first. Pre-copulatory isolation
occurs when the genes necessary for the sexual reproduction of one species differ from the
equivalent genes of another species, such that if a male of species A and a female of species
B are placed together they are unable to copulate. Study of the genetics involved in this
reproductive barrier tries to identify the genes that govern distinct sexual behaviors in the two
species. The males of Drosophila melanogaster and those of D. simulans conduct an
elaborate courtship with their respective females, which are different for each species, but the
differences between the species are more quantitative than qualitative. In fact the simulans
males are able to hybridize with the melanogaster females. Although there are lines of the
latter species that can easily cross there are others that are hardly able to. Using this
difference, it is possible to assess the minimum number of genes involved in pre-copulatory
isolation between the melanogaster and simulans species and their chromosomal location.
In experiments, flies of the D. melanogaster line, which hybridizes readily with simulans,
were crossed with another line that it does not hybridize with, or rarely. The females of the
segregated populations obtained by this cross were placed next to simulans males and the
percentage of hybridization was recorded, which is a measure of the degree of reproductive
isolation. It was concluded from this experiment that 3 of the 8 chromosomes of the haploid
complement of D. melanogaster carry at least one gene that affects isolation, such that
substituting one chromosome from a line of low isolation with another of high isolation
reduces the hybridization frequency. In addition, interactions between chromosomes are
detected so that certain combinations of the chromosomes have a multiplying effect. Cross
incompatibility or incongruence in plants is also determined by major genes that are not
associated at the self-incompatibilityS locus.
Post-copulation or fertilization mechanisms in animals
Reproductive isolation between species appears, in certain cases, a long time after
fertilization and the formation of the zygote, as happens – for example – in the twin species
Drosophila pavani and D. gaucha. The hybrids between both species are not sterile, in the
sense that they produce viable gametes, ovules and spermatozoa. However, they cannot
produce offspring as the sperm of the hybrid male do not survive in the semen receptors of
the females, be they hybrids or from the parent lines. In the same way, the sperm of the males
of the two parent species do not survive in the reproductive tract of the hybrid female. This
type of post-copulatory isolation appears as the most efficient system for maintaining
reproductive isolation in many species.
The development of a zygote into an adult is a complex and delicate process of interactions
between genes and the environment that must be carried out precisely, and if there is any
alteration in the usual process, caused by the absence of a necessary gene or the presence of a
different one, it can arrest the normal development causing the non-viability of the hybrid or
its sterility. It should be borne in mind that half of the chromosomes and genes of a hybrid are
from one species and the other half come from the other. If the two species are genetically
different, there is little possibility that the genes from both will act harmoniously in the
hybrid. From this perspective, only a few genes would be required in order to bring about
post copulatory isolation, as opposed to the situation described previously for pre-copulatory
isolation.
In many species where pre-copulatory reproductive isolation does not exist, hybrids are
produced but they are of only one sex. This is the case for the hybridization between females
of Drosophila simulans and Drosophila melanogaster males: the hybridized females die early
in their development so that only males are seen among the offspring. However, populations
of D. simulans have been recorded with genes that permit the development of adult hybrid
females, that is, the viability of the females is "rescued". It is assumed that the normal activity
of these speciation genes is to "inhibit" the expression of the genes that allow the growth of
the hybrid. There will also be regulator genes.
A number of these genes have been found in the melanogaster species group. The first to be
discovered was "Lhr" (Lethal hybrid rescue) located in Chromosome II of D. simulans. This
dominant allele allows the development of hybrid females from the cross between simulans
females and melanogaster males. A different gene, also located on Chromosome II of D.
simulans is "Shfr" that also allows the development of female hybrids, its activity being
dependent on the temperature at which development occurs. Other similar genes have been
located in distinct populations of species of this group. In short, only a few genes are needed
for an effective post copulatory isolation barrier mediated through the non-viability of the
hybrids.
As important as identifying an isolation gene is knowing its function. The Hmr gene, linked
to the X chromosome and implicated in the viability of male hybrids between D.
melanogaster and D. simulans, is a gene from the proto-oncogene family myb, that codes for
a transcriptional regulator. Two variants of this gene function perfectly well in each separate
species, but in the hybrid they do not function correctly, possibly due to the different genetic
background of each species. Examination of the allele sequence of the two species shows that
change of direction substitutions are more abundant than synonymous substitutions,
suggesting that this gene has been subject to intense natural selection.
The Dobzhansky–Muller model proposes that reproductive incompatibilities between species
are caused by the interaction of the genes of the respective species. It has been demonstrated
recently that Lhr has functionally diverged in D. simulans and will interact with Hmr which,
in turn, has functionally diverged in D. melanogaster to cause the lethality of the male
hybrids. Lhr is located in a heterochromatic region of the genome and its sequence has
diverged between these two species in a manner consistent with the mechanisms of positive
selection. An important unanswered question is whether the genes detected correspond to old
genes that initiated the speciation favoring hybrid non-viability, or are modern genes that
have appeared post-speciation by mutation, that are not shared by the different populations
and that suppress the effect of the primitive non-viability genes. The OdsH (abbreviation of
Odysseus) gene causes partial sterility in the hybrid between Drosophila simulans and a
related species, D. mauritiana, which is only encountered on Mauritius, and is of recent
origin. This gene shows monophyly in both species and also has been subject to natural
selection. It is thought that it is a gene that intervenes in the initial stages of speciation, while
other genes that differentiate the two species show polyphyly. Odsh originated by duplication
in the genome of Drosophila and has evolved at very high rates in D. mauritania, while its
paralogue, unc-4, is nearly identical between the species of the group melanogaster.
Seemingly, all these cases illustrate the manner in which speciation mechanisms originated in
nature, therefore they are collectively known as "speciation genes", or possibly, gene
sequences with a normal function within the populations of a species that diverge rapidly in
response to positive selection thereby forming reproductive isolation barriers with other
species. In general, all these genes have functions in the transcriptional regulation of other
genes.
The Nup96 gene is another example of the evolution of the genes implicated in post-
copulatory isolation. It regulates the production of one of the approximately 30 proteins
required to form a nuclear pore. In each of the simulans groups of Drosophila the protein
from this gene interacts with the protein from another, as yet undiscovered, gene on the X
chromosome in order to form a functioning pore. However, in a hybrid the pore that is
formed is defective and causes sterility. The differences in the sequences of Nup96 have been
subject to adaptive selection, similar to the other examples of speciation genes described
above.
Post-copulatory isolation can also arise between chromosomally differentiated populations
due to chromosomal translocations and inversions. If, for example, a reciprocal translocation
is fixed in a population, the hybrid produced between this population and one that does not
carry the translocation will not have a complete meiosis. This will result in the production of
unequal gametes containing unequal numbers of chromosomes with a reduced fertility. In
certain cases, complete translocations exist that involve more than two chromosomes, so that
the meiosis of the hybrids is irregular and their fertility is zero or nearly zero. Inversions can
also give rise to abnormal gametes in heterozygous individuals but this effect has little
importance compared to translocations. An example of chromosomal changes causing
sterility in hybrids comes from the study of Drosophila nasuta and D. albomicans which are
twin species from the Indo-Pacific region. There is no sexual isolation between them and the
F1 hybrid is fertile. However, the F2 hybrids are relatively infertile and leave few
descendants which have a skewed ratio of the sexes. The reason is that the X chromosome of
albomicans is translocated and linked to an autosome which causes abnormal meiosis in
hybrids. Robertsonian translocations are variations in the numbers of chromosomes that arise
from either: the fusion of two acrocentric chromosomes into a single chromosome with two
arms, causing a reduction in the haploid number, or conversely; or the fission of one
chromosome into two acrocentric chromosomes, in this case increasing the haploid number.
The hybrids of two populations with differing numbers of chromosomes can experience a
certain loss of fertility, and therefore a poor adaptation, because of irregular meiosis.
7.6 MODELS OF SPECIATION

Speciation is a fundamental issue in evolutionary biology, but it is both fascinating and

frustrating: we know it does happen but it it’s an historical phenomenon so it is difficult to
observe. The two camps of evolutionary biologists best equipped to deal with speciation (in
terms of mechanism, population geneticists; in terms of time-frames, paleontologists) are
both incapable of "seeing" speciation except in very special situations. We must rely on
strong inference to properly understand speciation. This inference is in many cases very
rigorous and scientific although it is historical, i.e., requires an interpretation of what has
gone on in the past.
Defining speciation depends on one's species concept. (Recall species concepts: typological,
evolutionary, biological, recognition). In its simplest form speciation is lineage splitting; the
resulting lineages are genetically isolated and ecologically distinct. This implies that
something intrinsic about the new lineages (an aspect of its biology, e.g., genetics)
makes/keeps them distinct. Speciation then must involve the evolution of intrinsic barriers
to gene exchange. Intrinsic barriers can related in many ways to extrinsic barriers to gene
exchange (abiotic factors limiting gene flow: rivers, isolated islands, glaciers). A variant of a
species could be adapted to live in a particular environment that is spatially distinct from
other types of environmental conditions; here an intrinsic component contributes to an
extrinsic barrier. The notion of the evolution of barriers to gene exchange applies to virtually
all species concepts since unlimited gene exchange between two populations/species would
prevent the evolution of the defining principles of a given species concept: 1) true typological
differences must have a genetic basis, 2) evolutionary lineages would not have their own
"evolutionary tendencies" with homogenization due to gene exchange, 3) reproductive
isolation (either pre- or postmating) would not be maintained with unlimited gene flow, and
4) mate recognition systems could not be maintained as distinct with unlimited gene
exchange.
Without the evolution of some intrinsic barrier to gene exchange, fusion of the two incipient
species would be one likely outcome (populations would blend back into one), or extinction
of one or the other lineages (one population out competed [at the individual level!] the
diverged sister population leaving only one population).
MODELS OF SPECIATION
There are many models which have been proposed that enable barriers to gene exchange to
evolve; as argued by Ernst Mayr, geographic isolation provides the most effective barrier. We
thus consider the allopatric model:
1. Continuous distribution split into two (or more) sub populations
2. Differentiation in allopatric (different selection regimes; not necessarily selection for
speciation)
3. if populations come into secondary contact, no gene flow (= speciation complete)

If no gene flow after secondary contact, speciation was completed in allopatric. Speciation
would then be viewed as a byproduct of divergence in allopatry. What happens after
secondary contact is a matter of great debate: If the two differentiated forms mix or
hybridize this may provide the context for selection for assortative mating also called
reinforcement of premating isolation (reinforcement hypothesis). In this case speciation
was not completed in allopatry and fate of the two populations depends on the outcome of the
interaction upon secondary contact.
Patterns predicted from the action of reinforcement:

Selection in zone of overlap for increased premating isolation. See artificial demonstration
with a selection experiment.
Reinforcement model assumes that hybrids are less fit (=means by which selection for
further isolation can operate). This assumes that post mating barriers arise first and that
premating barriers arise as a result of selection in sympatry; these assumptions may not
hold in all cases. However, if premating barriers evolved first, there might be little
hybridization (speciation complete?); if there was no postmating barrier, even with small
amounts of hybridization the two forms would fuse back together because there would be no
selection against hybrids!
Reinforcement is actually a special case of character displacement which is the
accentuation of differences between species (or forms) by selection against the individuals of
similar phenotype (reinforcement = reproductive character displacement and is achieved by
selection against hybrids). If reinforcement is true, we should expect to see displacement of
characters associated with pre-mating barriers to gene exchange in areas of secondary
contact. Some cases we do: calling songs of anurans; frequently such reproductive character
displacement is not observed. When "reinforcement-like" patterns are observed, one has to
be sure that the phenotypic shift is actually an evolutionary response to the presence of the
other incipient species and not to some other clinal variation (e.g., ecological factors that
generate parallel clines).
Problems with reinforcement: other possible outcomes: fusion of the two populations
because differentiation was sufficiently slight that selection against hybrids is weak relative
to the gene flow between forms. Extinction of one or the other of the two forms. Quite
likely when there is selection against heterozygotes. In population genetic terms, equivalent
to heterozygote disadvantage AA, Aa, aa with fitnesses 1,1-s,1, a metastable equilibrium

Selection against hybrids within the zone of secondary contact only favors displacement in
sympatry; gene flow in from allopatry will swamp the effect. One could view such hybrid
zones as genetic canyons of lost alleles. Another important question: if selection against
hybrids is the driving force for reproductive character displacement, how will the genes for
the different components of isolation/recognition sweep through the allopatric regions of the
two species ranges where there is no hybridization, hence no selection?
Another allopatric model is the Peripatric model referring to populations surrounding the
main part of the current species range.
1. Small isolated populations
2. Genetic drift via population bottleneck or founder event => new allele frequencies
3. new "genetic environment" => different response to selection than in main population
4. effect is a major genetic change = "genetic revolution"

One consequence is that speciation may not be dichotomous. Important consequence: rapid
divergence, unlikely to leave fossil intermediates (these possibilities will come in to play
when we discuss "punctuated equilibrium" later).
A variant on this theme proposed by Hampton Carson an influential evolutionary biologist
from the University of Hawaii is Founder-Flush speciation:
1. population initiated with small number of individuals (founders)
2. flush in population size; relaxed selection during this phase; low fitness recombinants
survive
3. crash in population size; selection and drift determine which genotypes survive.

Carson's view: two "parts" to the genome: the "open variability system" and the "closed
variability system" Open system has much variability, responds rapidly to selection (loci
encoding allozyme polymorphisms such as enzymes in glycolysis and Krebs cycle, etc.);
closed system is resistant to selection; less variable) loci encoding courtship song,
developmental patterns, etc.) In Carson's view the closed system is reorganized during the
flush-crash cycles, leads to a genetic change that contributes to reproductive isolation/mate
recognition.
Questions about the founder flush speciation: how small is population after crash?, how long
does population stay at reduced population size? Could retain a large portion of the genetic
variation after one crash; extended bottle necks will be more effective in reducing variation.
These questions also could apply to Mayr's peripatric speciation model
Parapatric Model of speciation. Ranges of two differentiated forms are contiguous and non-
overlapping. Patterns of discontinuities between differentiated forms/populations may be due
to secondary contact after a period in allopatry, or the discontinuity could be due to primary
differentiation in situ. One cause of this might be a steep environmental gradient or habitat
boundary. With selection on loci that affect reproductive isolation/mate recognition,
populations can become differentiated. Will be apparent in the formation of a cline. Can lead
to sufficient divergence of reproductive/mating characteristics that barrier to gene flow is
established (e.g., plants growing on mine tailings have diverged in flowering time).

Studies of parapatric distributions are frequently concerned with the concordance of clines.
Selection acting on one locus/trait can impose a cline on another character if the two
characters/loci are linked. Are clines superimposed, shifted, different slopes. Slatkin (1973)

has shown that the width of a cline is: See fig. 16.9, page 439; text uses different
letters for equation). Different loci may have different cline shapes due to different strengths
of selection acting on them.
The text is a bit misleading about Parapatric speciation. It might lead one to believe that when
a hybrid zone is observed, parapatric speciation is involved. This is not true since the hybrid
zone may be the result of secondary contact after allopatry, rather than primary differentiation
at the hybrid zone interface. Here again we need to determine the relative importance of the
allopatric phase and the parapatric interaction in determining the outcome of speciation (or
fusion). The cricket hybrid zone is in fact the result of allopatry followed by secondary
contact (my personal knowledge), but Ridley does not let you know this.
Non-allopatric models of speciation are controversial but not impossible. Sympatric
speciation can be modeled with a two locus polymorphism, one locus (A) affecting fitness
(in this case by affecting fitness in terms of survival on one of two alternative hosts/patches),
and another locus (B) affecting mate choice which is crucial in the evolution of assortative
mating, a barrier to gene exchange (proposed by John Maynard-Smith in 1966)
These selective regimes maintain polymorphism at the A locus as in a multiple niche
polymorphism considered in the population genetics section. These sets of fitness/mating
values will result in the evolution of associations (e.g., linkage disequilibria) between the A
and the B locus (e.g., AABB individuals and aabb individuals will be found in the
populations with few intermediates.

These have high fitness these have low fitness

The green lacewings (Genus Chrysoperla; formerly Chrysopa) seem to exhibit patterns of
host preference and mate choice similar to that presented above (studied by the Taubers,
Cornell University). One form is adapted to one host/habitat and a second to another; this
habitat preference appears to be controlled by a single locus with other modifying loci (some
evolutionists have not accepted the lacewing data as conclusive).
See the other sympatric speciation model that involves variation in a resource base. This
model still requires the evolution of associations (e.g., linkage disequilibrium) between
fitness genes and behavior genes.
But, if sympatric speciation is, if not common, at least possible, is the model really
sympatric?: is it just microallopatric speciation (some argue NO if adults come up off their
hosts into a mating swarm, but then proceed to mate). Another crucial issue is: what is the
rate of recombination between these two types of loci since crossing over will break up
favorable associations. A model of host preference and assortative mating invoking many
genes (polygenic model) make it more difficult to maintain nonrandom associations. A
general issue with all of these models is how much gene flow is tolerated. Evolution of
barriers to gene exchange is the issue, gene flow = gene exchange; how much gene flow
can take place and still evolve barriers to the gene flow?? The answer depends on the
genetic architecture of speciation (how many genes, how much divergence, etc.; next
lecture on genetics of speciation).
Saltatory speciation: Richard Goldschmitt in the Material Basis of Evolution proposed the
idea that Macromutations (mutations with big effects) would result in major developmental
and phenotypic changes in their carriers producing the so-called hopeful monster. Ridiculed
at the time; recently gained a new readership due to the molecular characterization of genes
that cause major phenotypic effects (more later on evolution of development). Big problem
remains: who is the hopeful monster going to mate with?
Chromosomal speciation: Consider a diploid with 2N = 4 chromosomes. If two such
individuals failed to undergo the reduction division of meiosis their gametes would be 2N=4.
If these gametes were used in fertilization of one another, a new chromosomal number
would be established: 4N = 8. If this became stabilized as a new chromosomal type (and this
is common in plants), this new type can be reproductively isolated from the original 2N = 4
species. The reproductive isolation would be due to an imbalance of chromosome sets in the
new zygote: N = 2 gamete crossed to an N = 4 gamete results chromosomal type of 3N = 6.
There can be two consequences with this imbalance: i) inviability due to failure during
development or ii) instability during chromosome segregation could result in gametes with an
incomplete set of chromosomes (aneuploidy). These consequences could have the effect of a
reproductive barrier between the original 2N = 4 and the polyploid 4N = 8 type. Speciation
can be nearly instantaneous when such chromosomal events are involved (multiples of even
numbered ploidy levels: can produce gametes with some exceptions; multiples of odd
numbered ploidy levels: usually cannot produce gametes due to imbalance of haploid
complements) => speciation. Thus polyploid hybrids are frequency genetically isolated
from their progenitors.
The simple inversion model illustrates another way that chromosomal factors might play a
role in speciation.
How should we think about speciation events? What are the models of divergence: is
speciation like a peak shift in an adaptive landscape, or is speciation a gradual divergence
process on a flat adaptive landscape? Main issue is whether the peak itself shifts and hence
the population shifts with it, or whether the two alternative peaks already exist and the
problem is shifting between the two alternatives.
Some fundamental issues in thinking about speciation:
1) does speciation require allopatry or can speciation occur in non-allopatric contexts
(sympatric, parapatric) ?;
2) does speciation require changes in many genes or can changes in a few specific genes lead
to speciation?;
3) is speciation itself adaptive or does speciation occur as a byproduct of adaptive responses
to other pressures?;
4) what determines the rates of speciation? (some lineages speciate at very different rates).
 7.6.1 ALLOPATRIC

Allopatric speciation (from Ancient Greek ἄλλος, allos, meaning "other", and πατρίς, patris,
"fatherland"), also referred to as geographic speciation, vicariant speciation, or its earlier
name, the dumbbell model, is a mode of speciation that occurs when biological populations
become geographically isolated from each other to an extent that prevents or interferes with
gene flow.
Various geographic changes can arise such as the movement of continents, and the formation
of mountains, islands, bodies of water, or glaciers. Human activity such as agriculture or
developments can also change the distribution of species populations. These factors can
substantially alter a region's geography, resulting in the separation of a species population
into isolated subpopulations. The vicariant populations then undergo genetic changes as they
become subjected to different selective pressures, experience genetic drift, and accumulate
different mutations in the separated populations gene pools. The barriers prevent the
exchange of genetic information between the two populations leading to reproductive
isolation. If the two populations come into contact they will be unable to reproduce—
effectively speciating. Other isolating factors such as population dispersal leading to
emigration can cause speciation (for instance, the dispersal and isolation of a species on an
oceanic island) and is considered a special case of allopatric speciation called peripatric
speciation.
Allopatric speciation is typically subdivided into two major models: vicariance and peripatric.
Both models differ from one another by virtue of their population sizes and geographic
isolating mechanisms. The terms allopatry and vicariance are often used in biogeography to
describe the relationship between organisms whose ranges do not significantly overlap but
are immediately adjacent to each other—they do not occur together or only occur within a
narrow zone of contact. Historically, the language used to refer to modes of speciation
directly reflected biogeographical distributions. As such, allopatry is a geographical
distribution opposed to sympatry (speciation within the same area). Furthermore, the terms
allopatric, vicariant, and geographical speciation are often used interchangeably in the
scientific literature. This article will follow a similar theme, with the exception of special
cases such as peripatric, centrifugal, among others.
Observation of nature creates difficulties in witnessing allopatric speciation from "start-to-
finish" as it operates as a dynamic process. From this arises a host of various issues in
defining species, defining isolating barriers, measuring reproductive isolation, among others.
Nevertheless, verbal and mathematical models, laboratory experiments, and empirical
evidence overwhelmingly supports the occurrence of allopatric speciation in nature.
Mathematical modeling of the genetic basis of reproductive isolation supports the plausibility
of allopatric speciation; whereas laboratory experiments of Drosophila and other animal and
plant species have confirmed that reproductive isolation evolves as a byproduct of natural
selection.
A population becomes separated by a geographic barrier; reproductive isolation develops,
resulting in two separate species.
The notion of vicariant evolution was first developed by Leon Croizat in the mid-twentieth
century. The Vicariance theory, which showed coherence along with the acceptance of plate
tectonics in the 1960s, was developed in the early 1950s by this Venezuelan botanist, who
had found an explanation to the existence of American and Africa similar plants, by deducing
that they had originally been a single population before the two continents drifted apart.
Currently, speciation by vicariance is widely regarded as the most common form of
speciation; and is the primary model of allopatric speciation. Vicariance is a process by
which the geographical range of an individual taxon, or a whole biota, is split into
discontinuous populations (disjunct distributions) by the formation of an extrinsic barrier to
the exchange of genes: that is, a barrier arising externally to a species. These extrinsic
barriers often arise from various geologic-caused, topographic changes such as: the formation
of mountains (orogeny); the formation of rivers or bodies of water; glaciation; the formation
or elimination of land bridges; the movement of continents over time (by tectonic plates); or
island formation, including sky islands. Vicariant barriers can change the distribution of
species populations. Suitable or unsuitable habitat may be come into existence, expand,
contract, or disappear as a result of global climate change or even large scale human activities
(for example, agricultural, civil engineering developments, and habitat fragmentation). Such
factors can alter a region's geography in substantial ways, resulting in the separation of a
species population into isolated subpopulations. The vicariant populations may then undergo
genotypic or phenotypic divergence as: (a) different mutations arise in the gene pools of the
populations, (b) they become subjected to different selective pressures, and/or (c) they
independently undergo genetic drift. The extrinsic barriers prevent the exchange of genetic
information between the two populations, potentially leading to differentiation due to the
ecologically different habitats they experience; selective pressure then invariably leads to
complete reproductive isolation. Furthermore, a species' proclivity to remain in its ecological
niche through changing environmental conditions may also play a role in isolating
populations from one another, driving the evolution of new lineages.
Allopatric speciation can be represented as the extreme on a gene flow continuum. As such,
the level of gene flow between populations in allopatry would be, where equals the rate of
gene exchange. In sympatry (panmixis), while in parapatric speciation, represents the entire
continuum, although some scientists argue that a classification scheme based solely on
geographic mode does not necessarily reflect the complexity of speciation. Allopatry is often
regarded as the default or "null" model of speciation. but this too is debates.

Reproductive isolation
Reproductive isolation acts as the primary mechanism driving genetic divergence in allopatry
and can be amplified by divergent selection. Pre-zygotic and post-zygotic isolation are often
the most cited mechanisms for allopatric speciation, and as such, it is difficult to determine
which form evolved first in an allopatric speciation event. Pre-zygotic simply implies the
presence of a barrier prior to any act of fertilization (such as an environmental barrier
dividing two populations), while post-zygotic implies the prevention of successful inter-
population crossing after fertilization (such as the production of an infertile hybrid). Since
species pairs who diverged in allopatry often exhibit pre- and post-zygotic isolation
mechanisms, investigation of the earliest stages in the life cycle of the species can indicate
whether or not divergence occurred due to a pre-zygotic or post-zygotic factor. However,
establishing the specific mechanism may not be accurate, as a species pair continually
diverges over time. For example, if a plant experiences a chromosome duplication event,
reproduction will occur, but sterile hybrids will result—functioning as a form of post-zygotic
isolation. Subsequently, the newly formed species pair may experience pre-zygotic barriers to
reproduction as selection, acting on each species independently, will ultimately lead to
genetic changes making hybrids impossible. From the researcher's perspective, the current
isolating mechanism may not reflect the past isolating mechanism.

Reinforcement
In allopatric speciation, a species population becomes separated by a geographic barrier,
whereby reproductive isolation evolves producing two separate species. From this, if a
recently separated population comes in contact again, low fitness hybrids may form, but
reinforcement acts to complete the speciation process.
Reinforcement has been a contentious factor in speciation. It is more often invoked in
sympatric speciation studies, as it requires gene flow between two populations. However,
reinforcement may also play a role in allopatric speciation, whereby the reproductive barrier
is removed, reuniting the two previously isolated populations. Upon secondary contact,
individuals reproduce, creating low-fitness hybrids. Traits of the hybrids drive individuals to
discriminate in mate choice, by which pre-zygotic isolation increases between the
populations. Some arguments have been put forth that suggest the hybrids themselves can
possibly become their own species. known as hybrid speciation. Reinforcement can play a
role in all geographic modes (and other non-geographic modes) of speciation as long as gene
flow is present and viable hybrids can be formed. The production of inviable hybrids is a
form of reproductive character displacement, under which most definitions is the completion
of a speciation event.
Research has well established the fact that interspecific mate discrimination occurs to a
greater extent between sympatric populations than it does in purely allopatric populations;
however, other factors have been proposed to account for the observed patterns.
Reinforcement in allopatry has been shown to occur in nature (evidence for speciation by
reinforcement), albeit with less frequency than a classic allopatric speciation event. A major
difficulty arises when interpreting reinforcement's role in allopatric speciation, as current
phylogenetic patterns may suggest past gene flow. This masks possible initial divergence in
allopatry and can indicate a "mixed-mode" speciation event—exhibiting both allopatric and
sympatric speciation processes.
Mathematical models
Developed in the context of the genetic basis of reproductive isolation, mathematical
scenarios model both prezygotic and postzygotic isolation with respect to the effects of
genetic drift, selection, sexual selection, or various combinations of the three. Masatoshi Nei
and colleagues were the first to develop a neutral, stochastic model of speciation by genetic
drift alone. Both selection and drift can lead to postzygotic isolation, supporting the fact that
two geographically separated populations can evolve reproductive isolation—sometimes
occurring rapidly. Fisherian sexual selection can also lead to reproductive isolation if there
are minor variations in selective pressures (such as predation risks or habitat differences)
among each population. Mathematical models concerning reproductive isolation-by distance
have shown that populations can experience increasing reproductive isolation that correlates
directly with physical, geographical distance. This has been exemplified in models of ring
species. however, it has been argued that ring species are a special case, representing
reproductive isolation-by distance, and demonstrate parapatric speciation instead—as
parapatric speciation represents speciation occurring along a cline.

Other models
Various alternative models have been developed concerning allopatric speciation. Special
cases of vicariant speciation have been studied in great detail, one of which is peripatric
speciation, whereby a small subset of a species population becomes isolated geographically;
and centrifugal speciation, an alternative model of peripatric speciation concerning expansion
and contraction of a species' range. Other minor allopatric models have also been developed
are discussed below.

Peripatric
In peripatric speciation, a small, isolated population on the periphery of a central population
evolves reproductive isolation due to the reduction or elimination of gene flow between the
two.
Peripatric speciation is a mode of speciation in which a new species is formed from an
isolated peripheral population. If a small population of a species becomes isolated (e.g. a
population of birds on an oceanic island), selection can act on the population independent of
the parent population. Given both geographic separation and enough time, speciation can
result as a byproduct. It can be distinguished from allopatric speciation by three important
features: 1) the size of the isolated population, 2) the strong selection imposed by the
dispersal and colonization into novel environments, and 3) the potential effects of genetic
drift on small populations. However, it can often be difficult for researchers to determine if
peripatric speciation occurred as vicariant explanations can be invoked due to the fact that
both models posit the absence of gene flow between the populations. The size of the isolated
population is important because individuals colonizing a new habitat likely contain only a
small sample of the genetic variation of the original population. This promotes divergence
due to strong selective pressures, leading to the rapid fixation of an allele within the
descendant population. This gives rise to the potential for genetic incompatibilities to evolve.
These incompatibilities cause reproductive isolation, giving rise to rapid speciation events.
Models of peripatry are supported mostly by species distribution patterns in nature. Oceanic
islands and archipelagos provide the strongest empirical evidence that peripatric speciation
occurs.
Centrifugal
Centrifugal speciation is a variant, alternative model of peripatric speciation. This model
contrasts with peripatric speciation by virtue of the origin of the genetic novelty that leads to
reproductive isolation. When a population of a species experiences a period of geographic
range expansion and contraction, it may leave small, fragmented, peripherally isolated
populations behind. These isolated populations will contain samples of the genetic variation
from the larger parent population. This variation leads to a higher likelihood of ecological
niche specialization and the evolution of reproductive isolation. Centrifugal speciation has
been largely ignored in the scientific literature. Nevertheless, a wealth of evidence has been
put forth by researchers in support of the model, much of which has not yet been refuted. One
example is the possible center of origin in the Indo-West Pacific.

Microallopatric
Microallopatry refers to allopatric speciation occurring on a small geographic scale.
Examples of microallopatric speciation in nature have been described. Rico and Turner found
intralacustrine allopatric divergence of Pseudotropheus callainos (Maylandia callainos)
within Lake Malawi separated only by 35 meters. Gustave Paulay found evidence that species
in the subfamily Cryptorhynchinae have microallopatrically speciated on Rapa and its
surrounding islets. A sympatrically distributed triplet of diving beetle (Paroster) species
living in aquifers of Australia's Yilgarn region have likely speciated microallopatrically
within a 3.5 km2 area. The term was originally proposed by Hobart M. Smith to describe a
level of geographic resolution. A sympatric population may exist in low resolution, whereas
viewed with a higher resolution (i.e. on a small, localized scale within the population) it is
"microallopatric". Ben Fitzpatrick and colleagues contend that this original definition, "is
misleading because it confuses geographical and ecological concepts".

Modes with secondary contact

Ecological speciation can occur allopatrically, sympatrically, or parapatrically; the only
requirement being that it occurs as a result of adaptation to different ecological or micro-
ecological conditions. Ecological allopatry is a reverse-ordered form of allopatric speciation
in conjunction with reinforcement. First, divergent selection separates a non-allopatric
population emerging from pre-zygotic barriers, from which genetic differences evolve due to
the obstruction of complete gene flow. The terms allo-parapatric and allo-sympatric have
been used to describe speciation scenarios where divergence occurs in allopatry but
speciation occurs only upon secondary contact. These are effectively models of reinforcement
or "mixed-mode" speciation events.

Observational evidence
As allopatric speciation is widely accepted as a common mode of speciation, the scientific
literature is abundant with studies documenting its existence. The biologist Ernst Mayr was
the first to summarize the contemporary literature of the time in 1942 and 1963. Many of the
examples he set forth remain conclusive; however, modern research supports geographic
speciation with molecular phylogenetics—adding a level of robustness unavailable to early
researchers. The most recent thorough treatment of allopatric speciation (and speciation
research in general) is Jerry Coyne and H. Allen Orr's 2004 publication Speciation. They list
six mainstream arguments that lend support to the concept of vicariant speciation:
• Closely related species pairs, more often than not, reside in geographic ranges
adjacent to one another, separated by a geographic or climatic barrier.
• Young species pairs (or sister species) often occur in allopatry, even without a known
barrier.
• In occurrences where several pairs of related species share a range, they are
distributed in abutting patterns, with borders exhibiting zones of hybridization.
• In regions where geographic isolation is doubtful, species do not exhibit sister pairs.
• Correlation of genetic differences between an array of distantly related species that
correspond to known current or historical geographic barriers.
• Measures of reproductive isolation increase with the greater geographic distance of
separation between two species pairs.

Endemism
Allopatric speciation has resulted in many of the biogeographic and biodiversity patterns
found on Earth: on islands, continents, and even among mountains.
Islands are often home to species endemics—existing only on an island and nowhere else in
the world—with nearly all taxa residing on isolated islands sharing common ancestry with a
species on the nearest continent. Not without challenge, there is typically a correlation
between island endemics and diversity; that is, that the greater the diversity (species richness)
of an island, the greater the increase in endemism. Increased diversity effectively drives
speciation. Furthermore, the number of endemics on an island is directly correlated with the
relative isolation of the island and its area. In some cases, speciation on islands has occurred
rapidly.
Islands are not the only geographic locations that have endemic species. South America has
been studied extensively with its areas of endemism representing assemblages of
allopatrically distributed species groups. Charis butterflies are a primary example, confined
to specific regions corresponding to phylogenies of other species of butterflies, amphibians,
birds, marsupials, primates, reptiles, and rodents. The pattern indicates repeated vicariant
speciation events among these groups. It is thought that rivers may play a role as the
geographic barriers to Charis, not unlike the river barrier hypothesis used to explain the high
rates of diversity in the Amazon basin—though this hypothesis has been disputed. Dispersal-
mediated allopatric speciation is also thought to be a significant driver of diversification
throughout the Neotropics.
Allopatric speciation can result from mountain topography. Climatic changes can drive
species into altitudinal zones—either valleys or peaks. Colored regions indicate distributions.
As distributions are modified due to the change in suitable habitats, reproductive isolation can
drive the formation of a new species.
Patterns of increased endemism at higher elevations on both islands and continents have been
documented on a global level. As topographical elevation increases, species become isolated
from one another; often constricted to graded zones. This isolation on "mountain top islands"
creates barriers to gene flow, encouraging allopatric speciation, and generating the formation
of endemic species. Mountain building (orogeny) is directly correlated with—and directly
affects biodiversity. The formation of the Himalayan mountains and the Qinghai–Tibetan
Plateau for example have driven the speciation and diversification of numerous plants and
animals such as Lepisorus ferns; glyptosternoid fishes (Sisoridae); and the Rana chensinensis
species complex. Uplift has also driven vicariant speciation in Macowania daisies in South
Africa's Drakensberg mountains, along with Dendrocincla woodcreepers in the South
American Andes. The Laramide orogeny during the Late Cretaceous even caused vicariant
speciation and radiations of dinosaurs in North America. Adaptive radiation, like the
Galapagos finches observed by Charles Darwin, is often a consequence of rapid allopatric
speciation among populations. However, in the case of the finches of the Galapagos, among
other island radiations such as the honeycreepers of Hawaii represent cases of limited
geographic separation and were likely driven by ecological speciation.
Isthmus of Panama
A conceptual representation of species populations becoming isolated (blue and green) by the
closure of the Isthmus of Panama (red circle). With the closure, North and South America
became connected, allowing the exchange of species (purple). Grey arrows indicate the
gradual movement of tectonic plates that resulted in the closure.
Geological evidence supports the final closure of the isthmus of Panama approximately 2.7 to
3.5 mya, with some evidence suggesting an earlier transient bridge existing between 13 and
15 mya. Recent evidence increasingly points towards an older and more complex emergence
of the Isthmus, with fossil and extant species dispersal (part of the American biotic
interchange) occurring in three major pulses, to and from North and South America. Further,
the changes in terrestrial biotic distributions of both continents such as with Eciton army ants
supports an earlier bridge or a series of bridges. Regardless of the exact timing of the isthmus
closer, biologists can study the species on the Pacific and Caribbean sides in what has been
called, "one of the greatest natural experiments in evolution". Additionally, as with most
geologic events, the closure was unlikely to have occurred rapidly, but instead dynamically—
a gradual shallowing of sea water over millions of years.
Studies of snapping shrimp in the genus Alpheus have provided direct evidence of an
allopatric speciation event, as phylogenetic reconstructions support the relationships of 15
pairs of sister species of Alpheus, each pair divided across the isthmus and molecular clock
dating supports their separation between 3 and 15 million years ago. Recently diverged
species live in shallow mangrove waters while older diverged species live in deeper water,
correlating with a gradual closure of the isthmus. Support for an allopatric divergence also
comes from laboratory experiments on the species pairs showing nearly complete
reproductive isolation. Similar patterns of relatedness and distribution across the Pacific and
Atlantic sides have been found in other species pairs such as:
• Diadema antillarum and Diadema mexicanum
• Echinometra lucunter and Echinometra vanbrunti
• Echinometra viridis and E. vanbrunti
• Bathygobius soporator and Bathygobius ramosus
• B. soporator and Bathygobius andrei
• Excirolana braziliensis and variant morphs
•
Refugia
Ice ages have played important roles in facilitating speciation among vertebrate species. This
concept of refugia has been applied to numerous groups of species and their biogeographic
distributions.
Glaciation and subsequent retreat caused speciation in many boreal forest birds, such as with
North American sapsuckers (Yellow-bellied, Red-naped, and Red-breasted); the warblers in
the genus Setophaga (S. townsendii, S. occidentalis, and S. virens), Oreothlypis (O. virginiae,
O. ridgwayi, and O. ruficapilla), and Oporornis (O. tolmiei and O. philadelphia now
classified in the genus Geothlypis); Fox sparrows (sub species P. (i.) unalaschensis, P. (i.)
megarhyncha, and P. (i.) schistacea); Vireo (V. plumbeus, V. cassinii, and V. solitarius);
tyrant flycatchers (E. occidentalis and E. difficilis); chickadees (P. rufescens and P.
hudsonicus); and thrushes (C. bicknelli and C. minimus).
As a special case of allopatric speciation, peripatric speciation is often invoked for instances
of isolation in glaciation refugia as small populations become isolated due to habitat
fragmentation such as with North American red (Picea rubens) and black (Picea mariana)
spruce or the prairie dogs Cynomys mexicanus and C. ludovicianus.

Super species
The red shading indicates the range of the bonobo (Pan paniscus). The blue shading indicates
the range of the Common chimpanzee (Pan troglodytes). This is an example of allopatric
speciation because they are divided by a natural barrier (the Congo River) and have no
habitat in common. Other Pan subspecies are shown as well.
Numerous species pairs or species groups show abutting distribution patterns, that is, reside
in geographically distinct regions next to each other. They often share borders, many of
which contain hybrid zones. Some examples of abutting species and superspecies (an
informal rank referring to a complex of closely related allopatrically distributed species, also
called allospecies) include:
• Western and Eastern meadowlarks in North America reside in dry western and wet
eastern geographic regions with rare occurrences of hybridization, most of which
results in infertile offspring.
• Monarch flycatchers endemic to the Solomon Islands; a complex of several species
and subspecies (Bougainville, white-capped, and chestnut-bellied monarchs and their
related subspecies).
 • North American sapsuckers and members of the genus Setophaga (the hermit warbler,
black-throated green warbler, and Townsend's warbler).
• Sixty-six subspecies in the genus Pachycephala residing on the Melanesian islands.
• Bonobos and chimpanzees.
• Climacteris tree creeper birds in Australia.
• Birds-of-paradise in the mountains of New Guinea (genus Astrapia).
• Red-shafted and yellow-shafted flickers; black-headed grosbeaks and rose-breasted
grosbeaks; Baltimore orioles and Bullock's orioles; and the lazuli and indigo buntings.
• All of these species pairs connect at zones of hybridization that correspond with major
geographic barriers.
• Dugesia flatworms in Europe, Asia, and the Mediterranean regions.
In birds, some areas are prone to high rates of superspecies formation such as the 105
superspecies in Melanesia, comprising 66 percent of all bird species in the region. Patagonia
is home to 17 superspecies of forest birds, while North America has 127 superspecies of both
land and freshwater birds. Sub-Saharan Africa has 486 passerine birds grouped into 169
superspecies. Australia has numerous bird superspecies as well, with 34 percent of all bird
species grouped into superspecies.

7.6.2 SYMPATRIC

SYMPATRIC
Sympatric speciation is speciation that occurs when two groups of the same species live in
the same geographic location, but they evolve differently until they can no longer interbreed
and are considered different species. It is different from other types of speciation, which
involve the formation of a new species when a population is split into groups via a
geographic barrier or migration. Sympatric speciation can be seen in many different types of
organisms including bacteria, cichlid fish, and the apple maggot fly, but it can be difficult to
tell when sympatric speciation is occurring or has occurred in nature.
To understand sympatric speciation, one must first understand the other types of speciation.
There are four types of speciation: sympatric, allopatric, parapatric, and peripatric. The other
three types of speciation involve the physical separation of two populations of the same
species, while sympatric speciation does not.
 • In allopatric speciation, two different species can form when one species is separated
into different groups due to population dispersal or a natural geologic event such as a
mountain formation. Like all forms of speciation, the process is usually very gradual.
• Parapatric speciation is when speciation occurs in subpopulations of the same species
that are mostly isolated from each other, but have a narrow area where their ranges
overlap.
• Peripatric speciation occurs when members of a population on the border of that
population’s habitat separate off from the main group and evolve over many
generations to become a different species.
Sympatric speciation is unique because it takes place while two subpopulations of the same
species are occupying the same range or in a range that highly overlaps. Even though the
territory that the organisms live in is the same, they are able to split into two different groups
that eventually become so genetically different from one another that they can no longer
breed with each other. When one group can no longer breed with another, it is a separate
species.
It can be difficult to tell whether speciation that has taken place is sympatric, another type, or
even a mix of both during the speciation process. This has led to much discussion among
evolutionary biology researchers as to what species have truly evolved sympatrically. For
example, it was originally thought that two closely related stickleback species evolved via
sympatric speciation, but further research suggests that the two different species actually
colonized the lake independently. The first colonization led to the rise of one species of
stickleback, while the other species evolved from the second colonization.
Jerry Coyne and H. Allen Orr have developed four criteria for inferring whether species have
arisen sympatrically:
1. The species’ ranges must overlap significantly.
2. There must be complete speciation (i.e., the two species cannot interbreed).
3. The species must be sister species (most closely related to each other) or part of a
monophyletic group, which includes an ancestor and all its descendants; in other
words, all the descendant species have to be included if there are more than two, not
just some of them.
 4. The history of the species’ geographic range and evolution must make allopatry seem
very unlikely, as allopatric speciation is much more common than sympatric
speciation.
EXAMPLES
In Bacteria
True examples of sympatric speciation have rarely been observed in nature. Sympatric
speciation is thought to occur more often in bacteria, because bacteria can exchange genes
with other individuals that aren’t parent and offspring in a process known as horizontal gene
transfer. Sympatric speciation has been observed in BACILLUS and SYNECHOCOCCUS
species of bacteria, and in the bacterioplankton VIBRIO SPLENDIDUS, among others.
Subgroups of species that are undergoing sympatric speciation will show few differences
since they have been diverging for a relatively recent time on the slow timescale at which
evolution takes place. It is thought that one important factor in cases of sympatric speciation
is adaptation to environmental conditions; if some members are specialized for living in a
certain environment, that subgroup may go on to occupy a different environmental niche and
eventually evolve into a new species over time.

In Cichlids
Another example of sympatric speciation is found in two species of Midas cichlid fish
(AMPHILOPHUS species), which live in Lake Apoyo, a volcanic crater lake in Nicaragua.
Researchers analyzed the DNA, appearance, and ecology of these two closely related species.
The two species, though overall very similar, do have slight differences in appearance, and
they cannot interbreed. All available evidence suggests that one species evolved from the
other, which is the species of Midas cichlids that originally colonized the lake. The newer
species evolved relatively recently, but in evolutionary terms, this means that it is thought to
have evolved less than 10,000 years ago.
In Apple Maggot Flies
An extremely recent example of sympatric speciation may be occurring in the apple maggot
fly, RHAGOLETIS POMONELLA. Apple maggot flies used to lay their eggs only on the fruit of
hawthorn trees, but less than 200 years ago, some apple maggot flies began to lay their eggs
on apples instead. Now there are two groups of apple maggot flies: one that lays eggs on
hawthorns and one that lays eggs on apples. Males look for mates on the same type of fruit
that they grew on, and females lay their eggs on the same type of fruit that they grew up on.
Therefore, flies that grew up on hawthorns will raise offspring on hawthorns, and flies that
grew up on apples will raise offspring on apples. There are already genetic differences
between the two groups, and over a long period of time, they could become separate species.
This shows how speciation can occur even when different subgroups of the same species
have the same geographic range.

7.6.3 PARAPATRIC

In parapatric speciation, two subpopulations of a species evolve reproductive isolation from

one another while continuing to exchange genes. This mode of speciation has three
distinguishing characteristics:
1) Mating occurs non-randomly,
2) Gene flow occurs unequally, and
3) Populations exist in either continuous or discontinuous geographic ranges.
This distribution pattern may be the result of unequal dispersal, incomplete geographical
barriers, or divergent expressions of behavior, among other things. Parapatric speciation
predicts that hybrid zones will often exist at the junction between the two populations.
In biogeography, the terms parapatric and parapatry are often used to describe the
relationship between organisms whose ranges do not significantly overlap but are
immediately adjacent to each other; they do not occur together except in a narrow contact
zone. Parapatry is a geographical distribution opposed to sympatry (same area) and allopatry
or peripatry (two similar cases of distinct areas). Various "forms" of parapatry have been
proposed and are discussed below. Coyne and Orr in Speciation categorise these forms into
three groups: clinal (environmental gradients), "stepping-stone" (discrete populations), and
stasipatric speciation in concordance with most of the parapatric speciation literature.
Henceforth, the models are subdivided following a similar format. Charles Darwin was the
first to propose this mode of speciation. It was not until 1930 when Ronald Fisher published
The Genetical Theory of Natural Selection where he outlined a verbal theoretical model of
clinal speciation. In 1981, Joseph Felsenstein proposed an alternative, "discrete population"
model (the "stepping-stone model). Since Darwin, a great deal of research has been
conducted on parapatric speciation—concluding that its mechanisms are theoretically
plausible, "and has most certainly occurred in nature".
MODELS
Mathematical models, laboratory studies, and observational evidence supports the existence
of parapatric speciation's occurrence in nature. The qualities of parapatry imply a partial
extrinsic barrier during divergence; thus leading to a difficulty in determining whether this
mode of speciation actually occurred, or if an alternative mode (notably, allopatric speciation)
can explain the data. This problem poses the unanswered question as to its overall frequency
in nature.
Parapatric speciation can be understood as a level of gene flow between populations wherein
allopatry (and peripatry), in sympatry, and midway between the two in parapatry.Intrinsic to
this, parapatry covers the entire continuum. Some biologists reject this delineation,
advocating the disuse of the term "parapatric" outright, "because many different spatial
distributions can result in intermediate levels of gene flow". Others champion this position
and suggest the abandonment of geographic classification schemes (geographic modes of
speciation) altogether.
Natural selection has been shown to be the primary driver in parapatric speciation (among
other modes), and the strength of selection during divergence is often an important factor.
Parapatric speciation may also result from reproductive isolation caused by social selection:
individuals interacting altruistically.
Environmental gradients
Due to the continuous nature of a parapatric population distribution, population niches will
often overlap, producing a continuum in the species’ ecological role across an environmental
gradient. Whereas in allopatric or peripatric speciation—in which geographically isolated
populations may evolve reproductive isolation without gene flow—the reduced gene flow of
parapatric speciation will often produce a cline in which a variation in evolutionary pressures
causes a change to occur in allele frequencies within the gene pool between populations. This
environmental gradient ultimately results in genetically distinct sister species.
Fisher's original conception of clinal speciation relied on (unlike most modern speciation
research) the morphological species concept. With this interpretation, his verbal, theoretical
model can effectively produce a new species; of which was subsequently confirmed
mathematically. Further mathematical models have been developed to demonstrate the
possibility of clinal speciation with most relying on, what Coyne and Orr assert are,
"assumptions that are either restrictive or biologically unrealistic".
A mathematical model for clinal speciation was developed by Caisse and Antonovics that
found evidence that, "both genetic divergence and reproductive isolation may therefore occur
between populations connected by gene flow". This research supports clinal isolation
comparable to a ring species (discussed below), except that the terminal geographic ends do
not meet to form a ring.
Doebeli and Dieckmann developed a mathematical model that suggested that ecological
contact is an important factor in parapatric speciation and that, despite gene flow acting as a
barrier to divergence in the local population, disruptive selection drives assortative mating;
eventually leading to a complete reduction in gene flow. This model resembles reinforcement
with the exception that there is never a secondary contact event. The authors conclude that,
"spatially localized interactions along environmental gradients can facilitate speciation
through frequency-dependent selection and result in patterns of geographical segregation
between the emerging species." However, one study by Polechová and Barton disputes these
conclusions.
Ring species

In a ring species, individuals are able to successfully reproduce (exchange genes) with
members of their own species in adjacent populations occupying a suitable habitat around a
geographic barrier. Individuals at the ends of the cline are unable to reproduce when they
come into contact.
The concept of a ring species is associated with allopatric speciation as a special case;
however, Coyne and Orr argue that Mayr's original conception of a ring species does not
describe allopatric speciation, "but speciation occurring through the attenuation of gene flow
with distance". They contend that ring species provide evidence of parapatric speciation in a
non-conventional sense. They go on to conclude that:
Nevertheless, ring species are more convincing than cases of clinal isolation for showing that
gene flow hampers the evolution of reproductive isolation. In clinal isolation, one can argue
that reproductive isolation was caused by environmental differences that increase with
distance between populations. One cannot make a similar argument for ring species because
the most reproductively isolated populations occur in the same habitat.
Discrete populations
Referred to as a "stepping-stone" model by Coyne and Orr, it differs by virtue of the species
population distribution pattern. Populations in discrete groups undoubtedly speciate more
easily than those in a cline due to more limited gene flow. This allows for a population to
evolve reproductive isolation as either selection or drift overpower gene flow between the
populations. The smaller the discrete population, the species will likely undergo a higher rate
of parapatric speciation.
Several mathematical models have been developed to test whether this form of parapatric
speciation can occur, providing theoretical possibility and supporting biological plausibility
(dependent on the models parameters and their concordance with nature). Joseph Felsenstein
was the first to develop a working model. Later, Sergey Gavrilets and colleagues developed
numerous analytical and dynamical models of parapatric speciation that have contributed
significantly to the quantitative study of speciation.
Para-allopatric speciation

Further concepts developed by Barton and Hewitt in studying 170 hybrid zones, suggested
that parapatric speciation can result from the same components that cause allopatric
speciation. Called para-allopatric speciation, populations begin diverging parapatrically, fully
speciating only after allopatry.
Stasipatric models
One variation of parapatric speciation involves species chromosomal differences. Michael J.
D. White developed the stasipatric speciation model when studying Australian morabine
grasshoppers (Vandiemenella). The chromosomal structure of sub-populations of a
widespread species become underdominate; leading to fixation. Subsequently, the sub-
populations expand within the species larger range, hybridizing (with sterility of the
offspring) in narrow hybrid zones. Futuyama and Mayer contend that this form of parapatric
speciation is untenable and that chromosomal rearrangements are unlikely to cause
speciation. Nevertheless, data does support that chromosomal rearrangements can possibly
lead to reproductive isolation, but it does not mean speciation results as a consequence.

7.7 CO-EVOLUTION AND SEXUAL SELECTION, ALTRUISM

Coevolution, the process of reciprocal evolutionary change that occurs between pairs of
species or among groups of species as they interact with one another. The activity of each
species that participates in the interaction applies selection pressure on the others. In a
predator-prey interaction, for example, the emergence of faster prey may select against
individuals in the predatory species who are unable to keep pace. Thus, only fast individuals
or those with adaptations allowing them to capture prey using other means will pass their
genes to the next generation. Coevolution is one of the primary methods by which biological
communities are organized. It can lead to very specialized relationships between species,
such as those between pollinator and plant, between predator and prey, and between parasite
and host. It may also foster the evolution of new species in cases where individual
populations of interacting species separate themselves from their greater met populations for
long periods of time.
How an interaction coevolves between species depends not only on the current genetic
makeup of the species involved but also on new mutations that arise, the population
characteristics of each species, and the communitycontext in which the interaction takes
place. Under some ecological conditions (such as in some predator-prey interactions or
between competitors for a resource), an antagonistic interaction between two species can
coevolve to enhance the antagonism; the species “build up” methods of defense and attack,
much like an evolutionary arms race. Under other ecological conditions (such as in certain
parasite-host interactions), however, the antagonism may be lessened.
Coevolution does not necessarily require the presence of antagonism. The interactions or
characteristics within groups of unrelated species may converge to allow individual species to
exploit valuable resources or enjoy increased protection. Once an interaction evolves between
two species, other species within the community may develop traits akin to those integral to
the interaction, whereby new species enter into the interaction. This type of convergence of
species has occurred commonly in the evolution of mutualistic interactions, including those
between pollinators (such as bees) and plants and those between vertebrates (such as birds
and bats) and fruits.
Some of the species drawn into mutualistic interactions become co-mutualistic, contributing
as well as benefiting from the relationship, whereas others become cheaters that only exploit
the relationship. In many interactions between bee pollinators and plants, bees collect the
nectar from the reproductive parts of the plant and are often dusted with pollen in the process.
When the bees fly to another plant of the same species, they may fertilize the plant by
depositing pollen on the plant’s stigma. In contrast, some bumblebees, such as those of
BOMBUS TERRESTRIS, obtain nectar from the plant without picking up or dropping off
pollen. They cheat by cutting through other parts of the plant instead of entering the flower.
In other cases, the behaviour or appearance of several species may converge to enhance their
mutual protection. For example, several species of heliconid butterflies that are distasteful to
predators have evolved to resemble one another. In addition, one species may evolve to
mimic the behaviour or appearance of another to garner some of the same protections enjoyed
by the model species. This evolutionary strategy has been successful for nonvenomous
snakes, such as the scarletking snake (LAMPROPELTIS TRIANGULUM ELAPSOIDES), whose
coloration closely resembles that of coral snakes, which can deliver a poisonous bite.
Coevolution is a complex process that occurs on many levels. It may appear in situations
where one species interacts closely with several others, such as the interaction between
European cuckoos (CUCULUS CANORUS) and the other species whose nests they parasitize; it
may involve many species, as in relationships between fruit-bearing plants and birds; or it
may take place in some subgroups of species but not others. It is important to note that human
activities often disrupt the process of coevolution by changing the nature and the extent of the
interactions between coevolving species. Some examples of harmful human activities include
habitat fragmentation, increased hunting pressure, favouritism of one species over another,
and the introduction of exotic species into ecosystems that are ill-equipped to handle them
Mutual attraction between the sexes is an important factor in reproduction. The males and
females of many animalspecies are similar in size and shape except for the sexual organs and
secondary sexual characteristics such as the breasts of female mammals. There are, however,
species in which the sexes exhibit striking dimorphism. Particularly in birds and mammals,
the males are often larger and stronger, more brightly coloured, or endowed with conspicuous
adornments. But bright colours make animals more visible to predators—the long plumage of
male peacocks and birds of paradise and the enormous antlers of aged male deer are
cumbersome loads in the best of cases. Darwin knew that natural selection could not be
expected to favour the evolution of disadvantageous traits, and he was able to offer a solution
to this problem. He proposed that such traits arise by “sexual selection,” which “depends not
on a struggle for existence in relation to other organic beings or to external conditions but on
a struggle between the individuals of one sex, generally the males, for the possession of the
other sex.”
The concept of sexual selection as a special form of natural selection is easily explained.
Other things being equal, organisms more proficient in securing mates have higher fitness.
There are two general circumstances leading to sexual selection. One is the preference shown
by one sex (often the females) for individuals of the other sex that exhibit certain traits. The
other is increased strength (usually among the males) that yields greater success in securing
mates.
The presence of a particular trait among the members of one sex can make them somehow
more attractive to the opposite sex. This type of “sex appeal” has been experimentally
demonstrated in all sorts of animals, from vinegar flies to pigeons, mice, dogs, and rhesus
monkeys. When, for example, DROSOPHILA flies, some with yellow bodies as a result of
spontaneous mutation and others with the normal yellowish gray pigmentation, are placed
together, normal males are preferred over yellow males by females with either body colour.
Sexual selection can also come about because a trait—the antlers of a stag, for example—
increases prowess in competition with members of the same sex. Stags, rams, and bulls use
antlers or horns in contests of strength; a winning male usually secures more female mates.
Therefore, sexual selection may lead to increased size and aggressiveness in males. Male
baboons are more than twice as large as females, and the behaviour of the docile females
contrasts with that of the aggressive males. A similar dimorphism occurs in the northernsea
lion, EUMETOPIAS JUBATA, where males weigh about 1,000 kg (2,200 pounds), about three
times as much as females. The males fight fiercely in their competition for females; large,
battle-scarred males occupy their own rocky islets, each holding a harem of as many as 20
females. Among many mammals that live in packs, troops, or herds—such as wolves, horses,
and buffaloes—there usually is a hierarchy of dominance based on age and strength, with
males that rank high in the hierarchy doing most of the mating.
The apparent altruistic behaviour of many animals is, like some manifestations of sexual
selection, a trait that at first seems incompatible with the theory of natural selection. Altruism
is a form of behaviour that benefits other individuals at the expense of the one that performs
the action; the fitness of the altruist is diminished by its behaviour, whereas individuals that
act selfishly benefit from it at no cost to themselves. Accordingly, it might be expected that
natural selection would foster the development of selfish behaviour and eliminate altruism.
This conclusion is not so compelling when it is noticed that the beneficiaries of altruistic
behaviour are usually relatives. They all carry the same genes, including the genes that
promote altruistic behaviour. Altruism may evolve by kin selection, which is simply a type of
natural selection in which relatives are taken into consideration when evaluating an
individual’s fitness.
Natural selection favours genes that increase the reproductive success of their carriers, but it
is not necessary that all individuals that share a given genotype have higher reproductive
success. It suffices that carriers of the genotype reproduce more successfully on the average
than those possessing alternative genotypes. A parent shares half of its genes with each
progeny, so a gene that promotes parental altruism is favoured by selection if the behaviour’s
cost to the parent is less than half of its average benefits to the progeny. Such a gene will be
more likely to increase in frequency through the generations than an alternative gene that
does not promote altruistic behaviour. Parental care is, therefore, a form of altruism readily
explained by kin selection. The parent spends some energy caring for the progeny because it
increases the reproductive success of the parent’s genes.
Kin selection extends beyond the relationship between parents and their offspring. It
facilitates the development of altruistic behaviour when the energy invested, or the risk
incurred, by an individual is compensated in excess by the benefits ensuing to relatives. The
closer the relationship between the beneficiaries and the altruist and the greater the number of
beneficiaries, the higher the risks and efforts warranted in the altruist. Individuals that live
together in a herd or troop usually are related and often behave toward each other in this way.
Adult zebras, for instance, will turn toward an attacking predator to protect the young in the
herd rather than fleeing to protect themselves.
Altruism also occurs among unrelated individuals when the behaviour is reciprocal and the
altruist’s costs are smaller than the benefits to the recipient. This reciprocal altruism is found
in the mutual grooming of chimpanzees and other primates as they clean each other of lice
and other pests. Another example appears in flocks of birds that post sentinels to warn of
danger. A crow sitting in a tree watching for predators while the rest of the flock forages
incurs a small loss by not feeding, but this loss is well compensated by the protection it
receives when it itself forages and others of the flock stand guard.
A particularly valuable contribution of the theory of kin selection is its explanation of the
evolution of social behaviour among ants, bees, wasps, and other social insects. In honeybee
populations, for example, the female workers build the hive, care for the young, and gather
food, but they are sterile; queen bees alone produce progeny. It would seem that the workers’
behaviour would in no way be promoted or maintained by natural selection. Any genes
causing such behaviour would seem likely to be eliminated from the population, because
individuals exhibiting the behaviour increase not their own reproductive success but that of
the queen. The situation is, however, more complex.
Queen bees produce some eggs that remain unfertilized and develop into males, or drones,
having a mother but no father. Their main role is to engage in the nuptial flight during which
one of them fertilizes a new queen. Other eggs laid by queen bees are fertilized and develop
into females, the large majority of which are workers. Some social insects, such as the
stingless Meliponinae bees, with hundreds of species across the tropics, have only one queen
in each colony. The queen typically mates with a single male during her nuptial flight; the
male’s sperm is stored in the queen’s spermatheca, from which it is gradually released as she
lays fertilized eggs. All the queen’s female progeny therefore have the same father, so that
workers are more closely related to one another and to any new sister queen than they are to
the mother queen. The female workers receive one-half of their genes from the mother and
one-half from the father, but they share among themselves three-quarters of their genes. The
half of the set from the father is the same in every worker, because the father had only one set
of genes rather than two to pass on (the male developed from an unfertilized egg, so all his
sperm carry the same set of genes). The other half of the workers’ genes come from the
mother, and on the average half of them are identical in any two sisters. Consequently, with
three-quarters of her genes present in her sisters but only half of her genes able to be passed
on to a daughter, a worker’s genes are transmitted one and a half times more effectively when
she raises a sister (whether another worker or a new queen) than if she produces a daughter of
her own.
Altruism refers to behaviour by an individual that increases the fitness of another individual
while decreasing the fitness of the actor. Altruism in this sense is different from the
philosophical concept of altruism, in which an action would only be called "altruistic" if it
was done with the conscious intention of helping another. In the behavioural sense, there is
no such requirement. As such, it is not evaluated in moral terms—it is the consequences of an
action for reproductive fitness that determine whether the action is considered altruistic, not
the intentions, if any, with which the action is performed. The term altruism was coined by
the French philosopher Auguste Comte in French, as altruisme, for an antonym of egoism.
He derived it from the Italian altrui, which in turn was derived from Latin alteri, meaning
"other people" or "somebody else".
Altruistic behaviours appear most obviously in kin relationships, such as in parenting, but
may also be evident among wider social groups, such as in social insects. They allow an
individual to increase the success of its genes by helping relatives that share those genes.
Obligate altruism is the permanent loss of direct fitness (with potential for indirect fitness
gain). For example, honey bee workers may forage for the colony. Facultative altruism is
temporary loss of direct fitness (with potential for indirect fitness gain followed by personal
reproduction). For example, a Florida scrub jay may help at the nest, then gain parental
territory.
In ethology (the study of behavior), and more generally in the study of social evolution, on
occasion, some animals do behave in ways that reduce their individual fitness but increase the
fitness of other individuals in the population; this is a functional definition of altruism.
Research in evolutionary theory has been applied to social behaviour, including altruism.
Cases of animals helping individuals to whom they are closely related can be explained by
kin selection, and are not considered true altruism. Beyond the physical exertions that in
some species mothers and in some species fathers undertake to protect their young, extreme
examples of sacrifice may occur. One example is matriphagy (the consumption of the mother
by her offspring) in the spider Stegodyphus; another example is a male spider allowing a
female fertilized by him to eat him. Hamilton's rule describes the benefit of such altruism in
terms of Wright'scoefficient of relationship to the beneficiary and the benefit granted to the
beneficiary minus the cost to the sacrificer. Should this sum be greater than zero a fitness
gain will result from the sacrifice.
When apparent altruism is not between kin, it may be based on reciprocity. A monkey will
present its back to another monkey, who will pick out parasites; after a time the roles will be
reversed. Such reciprocity will pay off, in evolutionary terms, as long as the costs of helping
are less than the benefits of being helped and as long as animals will not gain in the long run
by "cheating"—that is to say, by receiving favours without returning them. This is elaborated
on in evolutionary game theory and specifically the prisoner's dilemma as social theory.
IMPLICATIONS IN EVOLUTIONARY THEORY
The existence of altruism in nature is at first sight puzzling, because altruistic behaviour
reduces the likelihood that an individual will reproduce. The idea that group selection might
explain the evolution of altruism was first broached by Darwin himself in The Descent of
Man, and Selection in Relation to Sex, (1871). The concept of group selection has had a
chequered and controversial history in evolutionary biology but the uncritical 'good of the
species' tradition came to an abrupt halt in the 1960s, due largely to the work of George C.
Williams, and John Maynard Smith as well as Richard Dawkins. These evolutionary theorists
pointed out that natural selection acts on the individual, and that it is the individual's fitness
(number of offspring and grand-offspring produced compared to the rest of the population)
that drives evolution. A group advantage (e.g. hunting in a pack) that is disadvantageous to
the individual (who might be harmed during the hunt, when it could avoid injury by hanging
back from the pack but still share in the spoils) cannot evolve, because the selfish individual
will leave, on average, more offspring than those who join the pack and suffer injuries as a
result. If the selfishness is hereditary, this will ultimately result in the population consisting
entirely of selfish individuals. However, in the 1960s and 1970s an alternative to the "group
selection" theory emerged. This was the kin selection theory, due originally to W. D.
Hamilton. Kin selection is an instance of inclusive fitness, which is based on the notion that
an individual shares only half its genes with each offspring, but also with each full sib. From
an evolutionary genetic point of view it is therefore as advantageous to help with the
upbringing of full sibs as it is to produce and raise one's own offspring. The two activities are
evolutionarily entirely equivalent. Co-operative breeding (i.e. helping one's parents raise
sibs—provided they are full sibs) could thus evolve without the need for group-level
selection. This quickly gained prominence among biologists interested in the evolution of
social behaviour.
In 1971 Robert Trivers introduced his reciprocal altruism theory to explain the evolution of
helping at the nest of an unrelated breeding pair of birds. He argued that an individual might
act as a helper if there was a high probabilistic expectation of being helped by the recipients
at some later date. If, however, the recipients did not reciprocate when it was possible to do
so, the altruistic interaction with these recipients would be permanently terminated. But if the
recipients did not cheat then the reciprocal altruism would continue indefinitely to both
parties' advantage. This model was considered by many (e.g. West-Eberhard and Dawkins) to
be evolutionarily unstable because it is prone to invasion by cheats for the same reason that
cooperative hunting can be invaded and replaced by cheats. However, Trivers did make
reference to the Prisoner's Dilemma Game which, 10 years later, would restore interest in
Trivers' reciprocal altruism theory, but under the title of "tit-for-tat".
In its original form the Prisoner's Dilemma Game (PDG) described two awaiting trial
prisoners, A and B, each faced with the choice of betraying the other or remaining silent. The
"game" has four possible outcomes: (a) they both betray each other, and are both sentenced to
two years in prison; (b) A betrays B, which sets A free and B is sentenced to four years in
prison; (c) B betrays A, with the same result as (b) except that it is B who is set free and the
other spends four years in jail; (d) both remain silent, resulting in a six-month sentence each.
Clearly (d) ("cooperation") is the best mutual strategy, but from the point of view of the
individual betrayal is unbeatable (resulting in being set free, or getting only a two-year
sentence). Remaining silent results in a four-year or six-month sentence. This is exemplified
by a further example of the PDG: two strangers attend a restaurant together and decide to
split the bill. The mutually best ploy would be for both parties to order the cheapest items on
the menu (mutual cooperation). But if one member of the party exploits the situation by
ordering the most expensive items, then it is best for the other member to do likewise. In fact,
if the fellow diner's personality is completely unknown, and the two diners are unlikely ever
to meet again, it is always in one's own best interests to eat as expensively as possible.
Situations in nature that are subject to the same dynamics (rewards and penalties) as the PDG
define cooperative behaviour: it is never in the individual's fitness interests to cooperate, even
though mutual cooperation rewards the two contestants (together) more highly than any other
strategy. Cooperation cannot evolve under these circumstances.
However, in 1981 Axelrod and Hamilton noted that if the same contestants in the PDG meet
repeatedly (the so-called Iterated Prisoner's Dilemma game, IPD) then tit-for-tat
(foreshadowed by Robert Triver's reciprocal altruism theory) is a robust strategy which
promotes altruism. In "tit-for-tat" both players' opening moves are cooperation. Thereafter
each contestant repeats the other player's last move, resulting in a seemingly endless
sequence of mutually cooperative moves. However, mistakes severely undermine tit-for-tat's
effectiveness, giving rise to prolonged sequences of betrayal, which can only be rectified by
another mistake. Since these initial discoveries, all the other possible IPD game strategies
have been identified (16 possibilities in all, including, for instance, "generous tit-for-tat",
which behaves like "tit-for-tat", except that it cooperates with a small probability when the
opponent's last move was "betray".), but all can be outperformed by at least one of the other
strategies, should one of the players switch to such a strategy. The result is that none is
evolutionarily stable, and any prolonged series of the iterated prisoner's dilemma game, in
which alternative strategies arise at random, gives rise to a chaotic sequence of strategy
changes that never ends.
There are striking parallels between altruistic acts and exaggerated sexual ornaments
displayed by some animals, particularly certain bird species, such as, amongst others, the
peacock. Both are costly in fitness terms, and both are generally conspicuous to other
members of the population or species. This led Amotz Zahavi to suggest that both might be
fitness signals rendered evolutionarily stable by his handicap principle. If a signal is to
remain reliable, and generally resistant to falsification, the signal has to be evolutionarily
costly. Thus, if a (low fitness) liar were to use the highly costly signal, which seriously
eroded its real fitness, it would find it difficult to maintain a semblance or normality.Zahavi
borrowed the term "handicap principle" from sports handicapping systems. These systems are
aimed at reducing disparities in performance, thereby making the outcome of contests less
predictable. In a horse handicap race, provenly faster horses are given heavier weights to
carry under their saddles than inherently slower horses. Similarly, in amateur golf, better
golfers have fewer strokes subtracted from their raw scores than the less talented players. The
handicap therefore correlates with unhandicapped performance, making it possible, if one
knows nothing about the horses, to predict which unhandicapped horse would win an open
race. It would be the one handicapped with the greatest weight in the saddle. The handicaps
in nature are highly visible, and therefore a peahen, for instance, would be able to deduce the
health of a potential mate by comparing its handicap (the size of the peacock's tail) with those
of the other males. The loss of the male's fitness caused by the handicap is offset by its
increased access to females, which is as much of a fitness concern as is its health. An
altruistic act is, by definition, similarly costly. It would therefore also signal fitness, and is
probably as attractive to females as a physical handicap. If this is the case altruism is
evolutionarily stabilized by sexual selection.
There is an alternate strategy for identifying fit mates which does not rely on one gender
having exaggerated sexual ornaments or other handicaps, but is generally applicable to most,
if not all sexual creatures. It derives from the concept that the change in appearance and
functionality caused by a non-silentmutation will generally stand out in a population. This is
because that altered appearance and functionality will be unusual, peculiar, and different from
the norm within that population. The norm against which these unusual features are judged is
made up of fit attributes that have attained their plurality through natural selection, while less
adaptive attributes will be in the minority or frankly rare. Since the overwhelming majority of
mutant features are maladaptive, and it is impossible to predict evolution's future direction,
sexual creatures would be expected to prefer mates with the fewest unusual or minority
features. This will have the effect of a sexual population rapidly shedding peripheral
phenotypic features and canalizing the entire outward appearance and behavior so that all the
members of that population will begin to look remarkably similar in every detail, as
illustrated in the accompanying photograph of the African pygmy kingfisher, Ispidina picta.
Once a population has become as homogeneous in appearance as is typical of most species,
its entire repertoire of behaviors will also be rendered evolutionarily stable, including any
altruistic, cooperative and social characteristics. Thus, in the example of the selfish individual
who hangs back from the rest of the hunting pack, but who nevertheless joins in the spoils,
that individual will be recognized as being different from the norm, and will therefore find it
difficult to attract a mate. Its genes will therefore have only a very small probability of being
passed on to the next generation, thus evolutionarily stabilizing cooperation and social
interactions at whatever level of complexity is the norm in that population.
RECIPROCITY MECHANISMS
Altruism in animals describes a range of behaviors performed by animals that may be to their
own disadvantage but which benefit others. The costs and benefits are measured in terms of
reproductive fitness, or expected number of offspring. So by behaving altruistically, an
organism reduces the number of offspring it is likely to produce itself, but boosts the
likelihood that other organisms are to produce offspring. There are other forms of altruism in
nature other than risk-taking behavior, such as reciprocal altruism. This biological notion of
altruism is not identical to the everyday human concept. For humans, an action would only be
called 'altruistic' if it was done with the conscious intention of helping another. Yet in the
biological sense there is no such requirement. Instead, until we can communicate directly
with other species, an accurate theory to describe altruistic acts between species is Biological
Market Theory. Humans and other animals exchange benefits in several ways, known
technically as reciprocity mechanism. No matter what the mechanism, the common thread is
that benefits find their way back to the original giver.
Symmetry-based
Also known as the "buddy-system", mutual affection between two parties prompts similar
behavior in both directions without need to track of daily give-and-take, so long as the overall
relationship remains satisfactory. This is one of the most common mechanisms of reciprocity
in nature; this kind is present in humans, primates, and many other mammals.
Attitudinal
Also known as, "If you're nice, I'll be nice too." This mechanism of reciprocity is similar to
the heuristic of the golden rule, "Treat others how you would like to be treated." Parties
mirror one another's attitudes, exchanging favors on the spot. Instant attitudinal reciprocity
occurs among monkeys, and people often rely on it with strangers and acquaintances.
Calculated

Also known as, "what have you done for me lately?" Individuals keep track of the benefits
they exchange with particular partners, which help them decide to whom to return favors.
This mechanism is typical of chimpanzees and very common among human relationships.
Yet some opposing experimental research suggests that calculated or contingent reciprocity
does not spontaneously arise in laboratory experimental settings, despite patterns of behavior.
 UNIT 8: ORIGIN OF HIGHER EVOLUTION

8.1 Objectives
8.2 Introduction
8.3 Phylogenetic Gradualism and Punctured equilibrium
8.4 Major Trends in the Origin of Higher Categories
8.5 Micro, Macro and Mega Evolution
8.6 Evolution of Man

8.1 OBJECTIVES
The Study of Phylogenetic Gradualism and Punctured equilibrium & Micro, Macro and Mega
Evolution, We know about the Evolution of Man in this topics.

8.2 INTRODUCTION

The word phyletic derives from the Greekphūletikos, which conveys the meaning of a line of
descent. Phyletic gradualism contrasts with the theory of punctuated equilibrium, which
proposes that most evolution occurs isolated in rare episodes of rapid evolution, when a
single species splits into two distinct species, followed by a long period of stasis or non-
change. These models both contrast with variable-speed evolution ("variable speedism"),
which maintains that different species evolve at different rates, and that there is no reason to
stress one rate of change over another.
Evolutionary biologistRichard Dawkins argues that constant-rate gradualism is not present in
the professional literature; thereby the term serves only as a straw-man for punctuated-
equilibrium advocates. In his book The Blind Watchmaker, Dawkins observes that Charles
Darwin himself was not a constant-rate gradualist, as suggested by Niles Eldredge and
Stephen Jay Gould. In the first edition of On the Origin of Species, Darwin stated that
"Species of different genera and classes have not changed at the same rate, or in the same
degree. In the oldest tertiary beds a few living shells may still be found in the midst of a
multitude of extinct forms... The Silurian Lingula differs but little from the living species of
this genus".
Lingula is among the few brachiopods surviving today but also known from fossils over 500
million years old. In the fifth edition of The Origin of Species, Darwin wrote that "the periods
during which species have undergone modification, though long as measured in years, have
probably been short in comparison with the periods during which they retain the same form".

8.3 PHYLOGENETIC GRADUALISM AND PUNCTURED

EQUILIBRIUM
Phyletic gradualism is a model of evolution which theorizes that most speciation is slow,
uniform and gradual. When evolution occurs in this mode, it is usually by the steady
transformation of a whole species into a new one (through a process called anagenesis). In
this view no clear line of demarcation exists between an ancestral species and a descendant
species, unless splitting occurs. The theory is contrasted with punctuated equilibrium.

PUNCTUATED EQUILIBRIUM
In evolutionary biology, punctuated equilibrium (also called punctuated equilibria) is a
theory that proposes that once a species appears in the fossil record, the population will
become stable, showing little evolutionary change for most of its geological history. This
state of little or no morphological change is called stasis. When significant evolutionary
change occurs, the theory proposes that it is generally restricted to rare and geologically rapid
events of branching speciation called cladogenesis. Cladogenesis is the process by which a
species splits into two distinct species, rather than one species gradually transforming into
another. Punctuated equilibrium is commonly contrasted against phyletic gradualism, the idea
that evolution generally occurs uniformly and by the steady and gradual transformation of
whole lineages (called anagenesis). In this view, evolution is seen as generally smooth and
continuous. In 1972, paleontologists Niles Eldredge and Stephen Jay Gould published a
landmark paper developing their theory and called it punctuated equilibria. Their paper built
upon Ernst Mayr's model of geographic speciation, I. Michael Lerner's theories of
developmental and genetic homeostasis, and their own empirical research. Eldredge and
Gould proposed that the degree of gradualism commonly attributed to Charles Darwin is
virtually nonexistent in the fossil record, and that stasis dominates the history of most fossil
species.
Punctuated equilibrium originated as a logical consequence of Ernst Mayr's concept of
genetic revolutions by allopatric and especially peripatric speciation as applied to the fossil
record. Although the sudden appearance of species and its relationship to speciation was
proposed and identified by Mayr in 1954, historians of science generally recognize the 1972
Eldredge and Gould paper as the basis of the new paleobiological research program.
Punctuated equilibrium differs from Mayr's ideas mainly in that Eldredge and Gould placed
considerably greater emphasis on stasis, whereas Mayr was concerned with explaining the
morphological discontinuity (or "sudden jumps") found in the fossil record. Mayr later
complimented Eldredge and Gould's paper, stating that evolutionary stasis had been
"unexpected by most evolutionary biologists" and that punctuated equilibrium "had a major
impact on paleontology and evolutionary biology."
A year before their 1972 Eldredge and Gould paper, Niles Eldredge published a paper in the
journal Evolution which suggested that gradual evolution was seldom seen in the fossil record
and argued that Ernst Mayr's standard mechanism of allopatric speciation might suggest a
possible resolution. The Eldredge and Gould paper was presented at the Annual Meeting of
the Geological Society of America in 1971. The symposium focused its attention on how
modern microevolutionary studies could revitalize various aspects of paleontology and
macroevolution. Tom Schopf, who organized that year's meeting, assigned Gould the topic of
speciation. Gould recalls that "Eldredge's 1971 publication [on Paleozoictrilobites] had
presented the only new and interesting ideas on the paleontological implications of the
subject—so I asked Schopf if we could present the paper jointly." According to Gould "the
ideas came mostly from Niles, with yours truly acting as a sounding board and eventual
scribe. I coined the term punctuated equilibrium and wrote most of our 1972 paper, but Niles
is the proper first author in our pairing of Eldredge and Gould." In his book Time Frames
Eldredge recalls that after much discussion the pair "each wrote roughly half. Some of the
parts that would seem obviously the work of one of us were actually first penned by the
other—I remember for example, writing the section on Gould's snails. Other parts are harder
to reconstruct. Gould edited the entire manuscript for better consistency. We sent it in, and
Schopf reacted strongly against it—thus signaling the tenor of the reaction it has engendered,
though for shifting reasons, down to the present day."
John Wilkins and Gareth Nelson have argued that French architect Pierre Trémaux proposed
an "anticipation of the theory of punctuated equilibrium of Gould and Eldredge."
EVIDENCE FROM THE FOSSIL RECORD
The fossil record includes well documented examples of both phyletic gradualism and
punctuational evolution. As such, much debate persists over the prominence of stasis in the
fossil record. Before punctuated equilibrium, most evolutionists considered stasis to be rare
or unimportant. The paleontologist George Gaylord Simpson, for example, believed that
phyletic gradual evolution (called horotely in his terminology) comprised 90% of evolution.
More modern studies, including a meta-analysis examining 58 published studies on
speciation patterns in the fossil record showed that 71% of species exhibited stasis, and 63%
were associated with punctuated patterns of evolutionary change. According to Michael
Benton, "it seems clear then that stasis is common, and that had not been predicted from
modern genetic studies." A paramount example of evolutionary stasis is the fern Osmunda
claytoniana. Based on paleontological evidence it has remained unchanged, even at the level
of fossilized nuclei and chromosomes, for at least 180 million years.
THEORETICAL MECHANISMS
Punctuational change
When Eldredge and Gould published their 1972 paper, allopatric speciation was considered
the "standard" model of speciation. This model was popularized by Ernst Mayr in his 1954
paper "Change of genetic environment and evolution," and his classic volume Animal Species
and Evolution (1963).
Allopatric speciation suggests that species with large central populations are stabilized by
their large volume and the process of gene flow. New and even beneficial mutations are
diluted by the population's large size and are unable to reach fixation, due to such factors as
constantly changing environments. If this is the case, then the transformation of whole
lineages should be rare, as the fossil record indicates. Smaller populations on the other hand,
which are isolated from the parental stock, are decoupled from the homogenizing effects of
gene flow. In addition, pressure from natural selection is especially intense, as peripheral
isolated populations exist at the outer edges of ecological tolerance. If most evolution
happens in these rare instances of allopatric speciation then evidence of gradual evolution in
the fossil record should be rare. This hypothesis was alluded to by Mayr in the closing
paragraph of his 1954 paper:
Rapidly evolving peripherally isolated populations may be the place of origin of many
evolutionary novelties. Their isolation and comparatively small size may explain phenomena
of rapid evolution and lack of documentation in the fossil record, hitherto puzzling to the
paleontologist.
Although punctuated equilibrium generally applies to sexually reproducing organisms, some
biologists have applied the model to non-sexual species like viruses, which cannot be
stabilized by conventional gene flow. As time went on biologists like Gould moved away
from wedding punctuated equilibrium to allopatric speciation, particularly as evidence
accumulated in support of other modes of speciation. Gould, for example, was particularly
attracted to Douglas Futuyma's work on the importance of reproductive isolating
mechanisms.

STASIS
Many hypotheses have been proposed to explain the putative causes of stasis. Gould was
initially attracted to I. Michael Lerner's theories of developmental and genetic homeostasis.
However this hypothesis was rejected over time, as evidence accumulated against it. Other
plausible mechanisms which have been suggested include: habitat tracking, stabilizing
selection, the Sternest-Maynard Smith stability hypothesis, constraints imposed by the nature
of subdivided populations, normalizing clade selection, and koinophilia. Evidence for stasis
has also been corroborated from the genetics of sibling species, species which are
morphologically indistinguishable, but whose proteins have diverged sufficiently to suggest
they have been separated for millions of years. Fossil evidence of reproductively isolated
extant species of sympatric Olive Shells (Amalda sp.) also confirms morphological stasis in
multiple lineages over three million years. According to Gould, "stasis may emerge as the
theory's most important contribution to evolutionary science." Philosopher Kim Sterelny in
clarifying the meaning of stasis adds, "In claiming that species typically undergo no further
evolutionary change once speciation is complete, they are not claiming that there is no
change at all between one generation and the next. Lineages do change. But the change
between generations does not accumulate. Instead, over time, the species wobbles about its
phenotypic mean. Jonathan Weiner's The Beak of the Finch describes this very process."

HIERARCHICAL EVOLUTION
Punctuated equilibrium has also been cited as contributing to the hypothesis that species are
Darwinian individuals, and not just classes, thereby providing a stronger framework for a
hierarchical theory of evolution.

QUANTUM EVOLUTION
Quantum evolution was a controversial hypothesis advanced by Columbia University
paleontologist George Gaylord Simpson, who was regarded by Gould as "the greatest and
most biologically astute paleontologist of the twentieth century." Simpson's conjecture was
that according to the geological record, on very rare occasions evolution would proceed very
rapidly to form entirely new families, orders, and classes of organisms. This hypothesis
differs from punctuated equilibrium in several respects. First, punctuated equilibrium was
more modest in scope, in that it was addressing evolution specifically at the species level.
Simpson's idea was principally concerned with evolution at higher taxonomic groups.
Second, Eldredge and Gould relied upon a different mechanism. Where Simpson relied upon
a synergistic interaction between genetic drift and a shift in the adaptive fitness landscape,
Eldredge and Gould relied upon ordinary speciation, particularly Ernst Mayr's concept of
allopatric speciation. Lastly, and perhaps most significantly, quantum evolution took no
position on the issue of stasis. Although Simpson acknowledged the existence of stasis in
what he called the bradytelic mode, he considered it (along with rapid evolution) to be
unimportant in the larger scope of evolution. In his Major Features of Evolution Simpson
stated, "Evolutionary change is so nearly the universal rule that a state of motion is,
figuratively, normal in evolving populations. The state of rest, as in bradytely, is the
exception and it seems that some restraint or force must be required to maintain it." Despite
such differences between the two models, earlier critiques—from such eminent
commentators as Sewall Wright as well as Simpson himself—have argued that punctuated
equilibrium is little more than quantum evolution relabeled.
MULTIPLE MEANINGS OF GRADUALISM
Punctuated equilibrium is often portrayed to oppose the concept of gradualism, when it is
actually a form of gradualism. This is because even though evolutionary change appears
instantaneous between geological sedimentary layers, change is still occurring incrementally,
with no great change from one generation to the next. To this end, Gould later commented
that "Most of our paleontological colleagues missed this insight because they had not studied
evolutionary theory and either did not know about allopatric speciation or had not considered
its translation to geological time. Our evolutionary colleagues also failed to grasp the
implication(s), primarily because they did not think at geological scales".
Richard Dawkins dedicated a chapter in The Blind Watchmaker to correcting, in his view, the
wide confusion regarding rates of change. His first point is to argue that phyletic
gradualism—understood in the sense that evolution proceeds at a single uniform rate of
speed, called "constant speedism" by Dawkins—is a "caricature of Darwinism" and "does not
really exist". His second argument, which follows from the first, is that once the caricature of
"constant speedism" is dismissed, we are left with one logical alternative, which Dawkins
terms "variable speedism". Variable speedism may also be distinguished one of two ways:
"discrete variable speedism" and "continuously variable speedism". Eldredge and Gould,
proposing that evolution jumps between stability and relative rapidity, are described as
"discrete variable speediest", and "in this respect they are genuinely radical." They assert that
evolution generally proceeds in bursts, or not at all. "Continuously variable speedists", on the
other hand, advance that "evolutionary rates fluctuate continuously from very fast to very
slow and stop, with all intermediates. They see no particular reason to emphasize certain
speeds more than others. In particular, stasis, to them, is just an extreme case of ultra-slow
evolution. To a punctuationist, there is something very special about stasis." Dawkins
therefore commits himself here to an empirical claim about the geological record, in contrast
to his earlier claim that "The paleontological evidence can be argued about, and I am not
qualified to judge it." It is this particular commitment that Eldredge and Gould have aimed to
overturn.

8.4 MICRO, MACRO AND MEGA EVOLUTION

Based on the degree of change and speed of evolution three stages in evolutionary process
can be identified:

1) Origin of small evolutionary differences at sub specific level.

2) Modifications in larger groups of animals, producing species and genera by adaptive

radiation.

3) Evolution of new types from their predecessors by large genetic changes, often producing
families, orders, classes and phyla.

MICROEVOLUTION

This is also called Sequential evolution, which involves a continuous and gradual change in
an interbreeding population, usually giving rise to new subspecies and geographical races.
Basic process involves changes in gene frequencies in a population from one generation to
the next. Microevolution is produced by stabilizing or normalizing natural selections that
operate in stable environmental conditions and in short time span.

Examples: Rowe has discovered several lines of descent in sea urchin, Micraster, where he
found gradual change in characters from M. cordovans to that of M. cor-anguinum, mainly in
the shape of the test, structure of oral opening and the form of ambulacra. The changes took
place in a more or less stable environment. Similarly Fenton has described gradual
replacement of one species by another in brachiopod.

MACROEVOLUTION
This may also be called Adaptive radiation, which includes evolutionary changes above the
species level that may result in the production of new adaptive types through genetic
divergence. The changes are on account of large gene mutations or macromutations and result
in the establishment of new genera, families and orders. Macroevolution takes place in
individuals that have entered a new environmental zone, which is free of competition. Darwin
called such directional changes Orthogenesis.

Examples: Evolution of horse is a perfect example of macroevolution, in which there was an

increase in the size of body and legs and in the enlargement of teeth. All body changes were
related to life in open grasslands, fast running and feeding on harsh grasses, eventually
leading to new adaptive types. Other examples of macroevolution are: adaptive radiation in
Darwin’s finches, divergence of reptiles and evolution of camel and elephant.

MEGAEVOLUTION

This includes formation of new groups, classes or phyla due to evolution of new types from
its predecessors by general adaptation. Mega evolutionary changes are rare and have occurred
rarely in the evolutionary history. During mega evolution, organisms of the ancestral stalk
attempt to enter a new and very different environmental zone where they face strong natural
selection, for which they must possess certain pre-adaptations to enable them to survive in the
new zone. Mega evolution is brought about by large genetic changes that are capable of
producing different types and disruptive or divergent natural selection that makes the
population occupy different types of environmental zones.

Examples: Amphibians were preadapted to live on land for short periods since as fish they
already possessed lungs for air breathing and limbs to support body on land. Origin of birds
from reptiles included growth of feathers and sudden change in the fore limb to produce
wing, which enabled them to invade air and then developed beak, sternal keel and loss of tail
as post adaptations.

Origin of mammals can be traced back from series of fossil reptiles (Synapsida) of Triassic
period. During evolution, a false palate was formed, teeth became thecodont, and limbs
moved under the body for better locomotion. Emergence of bats (Order Chiroptera) from the
primitive insectivores has been a sudden event in the beginning of Coenozoic era. Skeletons
of early Eocene bats show fully developed wings, much like our modern day species possess.
No transitional forms are known; suggesting that bats emerged by a mega evolutionary event.
Mega evolution is always followed by micro-and macroevolution.
MOLECULAR EVOLUTION

Changes in the base pair sequences in DNA or RNA molecules and changes in amino acid
sequences and their molecular configuration in different proteins, from generation to
generation are known as molecular evolution. It is possible to measure differences between
these molecules obtained from different organisms (such as humans, apes, monkeys,
prosimians etc.) on a unit scale of amino acids or nucleotides and demonstrate their
relationships. As the molecular sequences are heritable, their variations produce molecular
records that have been transferred from generation to generation during evolution. A triplet
made of three pairs of nucleotides is called a codon. A codon will change if one of the three
bases changes and it may or may not end up in a change in the amino acid synthesized by it.
Majority of these changes are small and inconsequential but accumulate over long periods to
bring about large alterations in the gene frequencies in populations. Two kinds of such
changes are possible:

Silent site substitution: These are such changes in DNA sequences which do not result in any
change in amino acid synthesis and hence composition of proteins is not changed. They are
usually changes in the last base pair of the codon. For example in mRNA strand GCA codes
for alanine and if adenine is replaced by guanine, the resulting GCG will still code for the
same amino acid alanine. Silent site substitutions do not bring about any phenotypic changes.

Replacement substitution: They are changes in the bases of codons that result in synthesis of
new amino acids and are capable of altering the structure of proteins that are controlled by
them and thus changing the phenotype. Silent site substitutions have much higher rate of
change as compared to the replacement substitutions, since the former do not produce
changes that can be exposed to natural selection but the latter do. For the same reason genes
which are less vital to the cell can undergo rapid changes by replacement substitution without
showing harmful effects.Pseudogenes, which are duplicated sequences of bases and do not
code for proteins and hence are not exposed to natural selection, are known to undergo higher
rate of evolutionary changes.

Sequencing amino acids:

Comparing amino acid sequences in a protein in different species by using biochemical

techniques is one of the most popular methods to determine phylogeny. For example, in
hemoglobin two pairs of alpha and beta sequences of polypeptide chains form a tetramer that
can be distinguished by different amino acid sequences in different species. In vertebrates
different types of globin chains appeared during evolution and in each species they followed
their own evolutionary path by changes in the amino acid sequences. They are all variations
of a single globin ancestor that is controlled by similar globin genes which are believed to
have originated by gene duplication of the original type.

NEUTRAL THEORY OF MOLECULAR EVOLUTION

Moto Kimura (1986) proposed that a vast majority of base substitutions that are preserved in
a population are neutral with regards to natural selection. Positive substitutions are so rare
that they are inconsequential in molecular evolution, while negative changes are quickly
eliminatedby natural selection. Natural selection seems to favour neutral changes which
determine the overall rate of sequential evolution. For instance, pseudogenes have the highest
substitution rate among the genes but the changes are completely neutral with regard to
selection.

The theory was tested by J. McDonald and M. Kreitman (1991) by comparing base sequences
of alcohol dehydrogenase gene of Drosophila melanogaster, D. simulans and D. yakuba.
Kimura’s theory not only contradicts classical Darwinism but also does not explain fixation
of various types of alleles in different sizes of population. The theory holds that the rate of
fixation of neutral mutations does not depend on population size butthe genes are fixed or
eliminated by genetic drift. The neutral theory provides theoretical framework for testing and
predicting molecular evolution in the absence of positive selection.

8.5 DIFFERENCE BETWEEN MICRO-EVOLUTION AND MACRO-

EVOLUTION

Given below points are the essential one to distinguish between micro-evolution and macro-
evolution:
1. The heritable change in the gene frequency is called as evolution when the evolution
occurs on a small scale and within a single population is micro-evolution, while the
evolution that occurs on a large and surpasses the level of the single species is macro-
evolution.

2. Micro-evolution gives rise to changes in the gene pool , which results in few changes
in the same species also called Intra-species genetic change, whereas the macro-
evolution results in the formation of new species.
3. The changes in micro-evolution occur over short-time scales, whereas the changes
observed in macro-evolution occur over long-time scales.
 4. Genetic information gets altered or rearranged in micro-evolution, whereas there is
the new addition, deletion in the genetic structure, resulting in the formation of new
species in macroevolution.
5. Creationists support micro-evolution as this process has been experimentally proven
and is observed frequently, although there are many barriers in providing
experimental proof and so creationists do not support this kind of evolution as it takes
a lot of time to occur.
6. Example of the micro-evolution is the peppered moth, new strains of flu viruses,
Galapagos finch beaks, etc. and Origin of different phyla, development of vertebrates
from invertebrates, development of feathers is the examples of macro-evolution.

8.6 EVOLUTION OF MAN

Human evolution is the evolutionary process within the history of primates that led to the
emergence of Homo sapiens as a distinct species of the hominid family, which includes the
great apes. This process involved the gradual development of traits such as human bipedalism
and language, as well as interbreeding with other hominines, which indicate that human
evolution was not linear but a web.
The study of human evolution involves several scientific disciplines, including physical
anthropology, primatology, archaeology, paleontology, neurobiology, ethology, linguistics,
evolutionary psychology, embryology and genetics. Genetic studies show that primates
diverged from other mammals about 85 million years ago, in the Late Cretaceous period, and
the earliest fossils appear in the Paleocene, around 55 million years ago.
Within the superfamily Hominoidea, the family Hominidae diverged from the family
Hylobatidae some 15–20 million years ago; subfamily Homininae (African apes) diverged
from Ponginae (orangutans) about 14 million years ago; the tribe Hominini (including
humans, Australopithecus, and chimpanzees) parted from the tribe Gorillini (gorillas)
between 8–9 million years ago; and, in turn, the subtribes Hominina (humans and extinct
biped ancestors) and Panina (chimpanzees) separated 4–7 million years ago.

Anatomical changes
The hominoids are descendants of a common ancestor
Human evolution from its first separation from the last common ancestor of humans and
chimpanzees is characterized by a number of morphological, developmental, physiological
physiological,
and behavioral changes. The most significant of these adaptations are bipedalism, increased
brain size, lengthened ontogeny (gestation and infancy), and decreased sexual dimorphism.
dimorphism
The relationship between these changes is the subject of ongoing debate. Other significant
morphological changes included the evolution of a power and precision grip,, a change first
occurring in H. erectus.

Bipedalism
Bipedalism is the basic adaptation of the hominid and is considered the main cause behind a
suite of skeletal changes shared by all bipedal hominids. The earliest hominid, of presumably
primitive
ve bipedalism, is considered to be either Sahelanthropus or Orrorin,, both of which
arose some 6 to 7 million years
rs ago. The non
non-bipedal knuckle-walkers,
walkers, the gorillas and
chimpanzees, diverged from the hominin line over a period covering the same time, so either
Sahelanthropus or Orrorin may be our last shared ancestor. Ardipithecus,, a full biped, arose
approximately 5.6 million years ago.
The early bipeds eventually
ally evolved into the australopithecines and still later into the genus
Homo.. There are several theories of the adaptation value of bipedalism. It is possible that
bipedalism was favored because it freed the hands for reaching and carrying food, saved
energy
gy during locomotion, enabled long
long-distance
distance running and hunting, provided an enhanced
field of vision, and helped avoid hyperthermia by reducing the surface area exposed to direct
sun; features all advantageous for thriving in the new savanna and woodland environment
created as a result of the East African Rift Valley uplift versus the previous closed forest
habitat. A 2007 study provides support for the hypothesis that walking on two legs, or
bipedalism, evolved because it used less energy than quadrupedal knuckle
knuckle-walking.
However, recent studies suggest that bipedalism without the ability to use fire would not have
allowed global dispersal. This change in gait saw a lengthening of the legs proportionately
when compared to the length of the arms, which were shortened through the removal of the
need for brachiating. Another change is the shape of the big toe. Recent studies suggest that
australopithecines still lived part of the time in trees as a result of maintaining a grasping big
toe. This was progressively lost in habilines.
Anatomically, the evolution of bipedalism has been accompanied by a large number of
skeletal changes, not just to the legs and pelvis, but also to the vertebral column, feet and
ankles, and skull. The femur evolved into a slightly more angular position to move the center
of gravity toward the geometric center of the body. The knee and ankle joints became
increasingly robust to better support increased weight. To support the increased weight on
each vertebra in the upright position, the human vertebral column became S-shaped and the
lumbar vertebrae became shorter and wider. In the feet the big toe moved into alignment with
the other toes to help in forward locomotion. The arms and forearms shortened relative to the
legs making it easier to run. The foramen magnum migrated under the skull and more
anterior.
The most significant changes occurred in the pelvic region, where the long downward facing
iliac blade was shortened and widened as a requirement for keeping the center of gravity
stable while walking; bipedal hominids have a shorter but broader, bowl-like pelvis due to
this. A drawback is that the birth canal of bipedal apes is smaller than in knuckle-walking
apes, though there has been a widening of it in comparison to that of australopithecine and
modern humans, permitting the passage of newborns due to the increase in cranial size but
this is limited to the upper portion, since further increase can hinder normal bipedal
movement.
The shortening of the pelvis and smaller birth canal evolved as a requirement for bipedalism
and had significant effects on the process of human birth which is much more difficult in
modern humans than in other primates. During human birth, because of the variation in size
of the pelvic region, the fetal head must be in a transverse position (compared to the mother)
during entry into the birth canal and rotate about 90 degrees upon exit. The smaller birth
canal became a limiting factor to brain size increases in early humans and prompted a shorter
gestation period leading to the relative immaturity of human offspring, who are unable to
walk much before 12 months and have greater neoteny, compared to other primates, who are
mobile at a much earlier age. The increased brain growth after birth and the increased
dependency of children on mothers had a major effect upon the female reproductive cycle,
and the more frequent appearance oof alloparenting in humans when compared with other
hominids. Delayed human sexual maturity also led to the evolution of menopause with one
explanation providing that elderly women could better pass on their genes by taking care of
their daughter's offspring, as compared to having more children of their own.

Encephalization

Skulls of successive (or near-successive,

successive, depending on the source) human evolutionary
ancestors, up until 'modern' Homo sapiens. The human species eventually developed a much
larger brain than that of other primates—typically
primates 1,330 cm3 (81 cu in) in modern humans,
nearly three times the size of a chimpanzee or gorilla brain. After a period of stasis with
Australopithecus anamensis and Ardipithecus,, species which had smaller brains as a result of
their bipedal locomotion, the pattern of encephalization started with Homo habilis
habilis, whose
600 cm3 (37 cu in) brain was slightly larger than that of chimpanzees. This evolution
continued in Homo erectus with 800–1,100
800 cm3 (49–67 cu in), and reached a maximum in
Neanderthals with 1,200–1,900 cm3 (73–116 cu in), larger even than modern Homo sapiens.
sapiens
This brain increase manifested during postnatal brain growth,, far exceeding that of other apes
(heterochrony).
). It also allowed for extended periods of social learning and language
acquisition in juvenile humans, beginning as much as 2 million years ago.
Furthermore, the changes in the structure
st of human brains may be even more significant than
the increase in size. The size and shape of the skull changed over time. The leftmost, and
largest, is a replica of a modern human skull. The temporal lobes,, which contain centers for
language processing, have increased disproportionately, as has the prefrontal cortex,
cortex which
has been related to complex decision-making
decision king and moderating social behavior.
Encephalization has been tied to increased meat and starches in the diet, and the development
of cooking, and it has been proposed that intelligence increased as a response to an increased
necessity for solving social problems as human society became more complex. Changes in
skull morphology, such as smaller mandibles and mandible muscle attachments, allowed
more room for the brain to grow.
The increase in volume of the neocortex also included a rapid increase in size of the
cerebellum. Its function has traditionally been associated with balance and fine motor control,
but more recently with speech and cognition. The great apes, including hominids, had a more
pronounced cerebellum relative to the neocortex than other primates. It has been suggested
that because of its function of sensory-motor control and learning complex muscular actions,
the cerebellum may have underpinned human technological adaptations, including the
preconditions of speech.
The immediate survival advantage of cephalization is difficult to discern, as the major brain
changes from Homo erectus to Homo heidelbergensis were not accompanied by major
changes in technology. It has been suggested that the changes were mainly social and
behavioural, including increased empathic abilities, increases in size of social groups, and
increased behavioural plasticity. Encephalization may be due to a dependency on calorie-
dense, difficult-to-acquire food.

SEXUAL DIMORPHISM
The reduced degree of sexual dimorphism in humans is visible primarily in the reduction of
the male canine tooth relative to other ape species (except gibbons) and reduced brow ridges
and general robustness of males. Another important physiological change related to sexuality
in humans was the evolution of hidden estrus. Humans are the only hominoids in which the
female is fertile year round and in which no special signals of fertility are produced by the
body (such as genital swelling or overt changes in proceptivity during estrus).
Nonetheless, humans retain a degree of sexual dimorphism in the distribution of body hair
and subcutaneous fat, and in the overall size, males being around 15% larger than females.
These changes taken together have been interpreted as a result of an increased emphasis on
pair bonding as a possible solution to the requirement for increased parental investment due
to the prolonged infancy of offspring.
Ulnar opposition
The ulnar opposition—the contact between the thumb and the tip of the little finger of the
same hand—is unique to the genus Homo, including Neanderthals, the Sima de los
Huesoshominins and anatomically modern humans. In other primates, the thumb is short and
unable to touch the little finger. The ulnar opposition facilitates the precision grip and power
grip of the human hand, underlying all the skilled manipulations.
Other changes
A number of other changes have also characterized the evolution of humans, among them an
increased importance on vision rather than smell; a longer juvenile developmental period and
higher infant dependency; a smaller gut; faster basal metabolism; loss of body hair; evolution
of sweat glands; a change in the shape of the dental arcade from being u-shaped to being
parabolic; development of a chin (found in Homo sapiens alone); development of styloid
processes; and the development of a descended larynx.

History of study
Before Darwin
The word homo, the name of the biological genus to which humans belongs, is Latin for
"human". It was chosen originally by Carl Linnaeus in his classification system. The word
"human" is from the Latin humanus, the adjectival form of homo. The Latin "homo" derives
from the Indo-European root *dhghem, or "earth". Linnaeus and other scientists of his time
also considered the great apes to be the closest relatives of humans based on morphological
and anatomical similarities.

Darwin
The possibility of linking humans with earlier apes by descent became clear only after 1859
with the publication of Charles Darwin's On the Origin of Species, in which he argued for the
idea of the evolution of new species from earlier ones. Darwin's book did not address the
question of human evolution, saying only that "Light will be thrown on the origin of man and
his history”. The first debates about the nature of human evolution arose between Thomas
Henry Huxley and Richard Owen. Huxley argued for human evolution from apes by
illustrating many of the similarities and differences between humans and other apes, and did
so particularly in his 1863 book Evidence as to Man's Place in Nature. Many of Darwin's
early supporters (such as Alfred Russel Wallace and Charles Lyell) did not initially agree that
the origin of the mental capacities and the moral sensibilities of humans could be explained
by natural selection, though this later changed. Darwin applied the theory of evolution and
sexual selection to humans in his 1871 book The Descent of Man, and Selection in Relation
to Sex.

FIRST FOSSILS
A major problem in the 19th century was the lack of fossil intermediaries. Neanderthal
remains were discovered in a limestone quarry in 1856, three years before the publication of
On the Origin of Species, and Neanderthal fossils had been discovered in Gibraltar even
earlier, but it was originally claimed that these were the remains of a modern human who had
suffered some kind of illness. Despite the 1891 discovery by Eugène Dubois of what is now
called Homo erectus at Trinil, Java, it was only in the 1920s when such fossils were
discovered in Africa, that intermediate species began to accumulate. In 1925, Raymond Dart
described Australopithecus africanus. The type specimen was the Taung Child, an
australopithecine infant which was discovered in a cave. The child's remains were a
remarkably well-preserved tiny skull and an endocast of the brain.
Although the brain was small (410 cm3), its shape was rounded, unlike that of chimpanzees
and gorillas, and more like a modern human brain. Also, the specimen showed short canine
teeth, and the position of the foramen magnum (the hole in the skull where the spine enters)
was evidence of bipedal locomotion. All of these traits convinced Dart that the Taung Child
was a bipedal human ancestor, a transitional form between apes and humans.
THE EAST AFRICAN FOSSILS
During the 1960s and 1970s, hundreds of fossils were found in East Africa in the regions of
the Olduvai Gorge and Lake Turkana. These searches were carried out by the Leakey family,
with Louis Leakey and his wife Mary Leakey, and later their son Richard and daughter-in-
law Meave, fossil hunters and paleoanthropologists. From the fossil beds of Olduvai and
Lake Turkana they amassed specimens of the early hominins: the australopithecines and
Homo species, and even Homo erectus.
These finds cemented Africa as the cradle of humankind. In the late 1970s and the 1980s,
Ethiopia emerged as the new hot spot of paleoanthropology after "Lucy", the most complete
fossil member of the species Australopithecus afarensis, was found in 1974 by Donald
Johanson near Hadar in the desertic Afar Triangle region of northern Ethiopia. Although the
specimen had a small brain, the pelvis and leg bones were almost identical in function to
those of modern humans, showing with certainty that these hominins had walked erect. Lucy
was classified as a new species, Australopithecus afarensis, which is thought to be more
closely related to the genus Homo as a direct ancestor, or as a close relative of an unknown
ancestor, than any other known hominid or hominin from this early time range; seeterms
"hominid" and "hominin". (The specimen was nicknamed "Lucy" after the Beatles' song
"Lucy in the Sky with Diamonds", which was played loudly and repeatedly in the camp
during the excavations). The Afar Triangle area would later yield discovery of many more
hominin fossils, particularly those uncovered or described by teams headed by Tim D. White
in the 1990s, including Ardipithecus ramidus and Ardipithecus kadabba.
In 2013, fossil skeletons of Homo naledi, an extinct species of hominin assigned
(provisionally) to the genusHomo, were found in the Rising Star Cave system, a site in South
Africa's Cradle of Humankind region in Gauteng province near Johannesburg. As of
September 2015, fossils of at least fifteen individuals, amounting to 1,550 specimens, have
been excavated from the cave. The species is characterized by a body mass and stature
similar to small-bodied human populations, a smaller endocranial volume similar to
Australopithecus, and a cranialmorphology (skull shape) similar to early Homo species. The
skeletal anatomy combines primitive features known from australopithecines with features
known from early hominins. The individuals show signs of having been deliberately disposed
of within the cave near the time of death. The fossils were dated close to 250,000 years ago,
and thus are not a direct ancestor but a contemporary with the first appearance of larger-
brained anatomically modern humans.
THE GENETIC REVOLUTION
The genetic revolution in studies of human evolution started when Vincent Sarich and Allan
Wilson measured the strength of immunological cross-reactions of blood serumalbumin
between pairs of creatures, including humans and African apes (chimpanzees and gorillas).
The strength of the reaction could be expressed numerically as an immunological distance,
which was in turn proportional to the number of amino acid differences between homologous
proteins in different species. By constructing a calibration curve of the ID of species' pairs
with known divergence times in the fossil record, the data could be used as a molecular clock
to estimate the times of divergence of pairs with poorer or unknown fossil records.
In their seminal 1967 paper in Science, Sarich and Wilson estimated the divergence time of
humans and apes as four to five million years ago, at a time when standard interpretations of
the fossil record gave this divergence as at least 10 to as much as 30 million years.
Subsequent fossil discoveries, notably "Lucy", and reinterpretation of older fossil materials,
notably Ramapithecus, showed the younger estimates to be correct and validated the albumin
method.
Progress in DNA sequencing, specifically mitochondrial DNA (mtDNA) and then Y-
chromosome DNA (Y-DNA) advanced the understanding of human origins. Application of
the molecular clock principle revolutionized the study of molecular evolution.
On the basis of a separation from the orangutan between 10 and 20 million years ago, earlier
studies of the molecular clock suggested that there were about 76 mutations per generation
that were not inherited by human children from their parents; this evidence supported the
divergence time between hominins and chimpanzees noted above. However, a 2012 study in
Iceland of 78 children and their parents suggests a mutation rate of only 36 mutations per
generation; this datum extends the separation between humans and chimpanzees to an earlier
period greater than 7 million years ago (Ma). Additional research with 226 offspring of wild
chimpanzee populations in eight locations suggests that chimpanzees reproduce at age 26.5
years on average; which suggests the human divergence from chimpanzees occurred between
7 and 13 million years ago. And these data suggest that Ardipithecus (4.5 Ma), Orrorin (6
Ma) and Sahelanthropus (7 Ma) all may be on the hominid lineage, and even that the
separation may have occurred outside the East African Rift region.
Furthermore, analysis of the two species' genes in 2006 provides evidence that after human
ancestors had started to diverge from chimpanzees, interspecies mating between "proto-
human" and "proto-chimpanzees" nonetheless occurred regularly enough to change certain
genes in the new gene pool:

• A new comparison of the human and chimpanzee genomes suggests that after the two
lineages separated, they may have begun interbreeding... A principal finding is that the X
chromosomes of humans and chimpanzees appear to have diverged about 1.2 million
years more recently than the other chromosomes.
• There were in fact two splits between the human and chimpanzee lineages, with the first
being followed by interbreeding between the two populations and then a second split.
The suggestion of hybridization has startled paleoanthropologists, who nonetheless are
treating the new genetic data seriously.
HUMAN DISPERSAL
Anthropologists in the 1980s were divided regarding some details of reproductive barriers
and migratory dispersals of the genus Homo. Subsequently, genetics has been used to
investigate and resolve these issues. According to the Sahara pump theory evidence suggests
that the genus Homo have migrated out of Africa at least three and possibly four times (e.g.
Homo erectus, Homo heidelbergensis and two or three times for Homo sapiens). Recent
evidence suggests these dispersals are closely related to fluctuating periods of climate
change.
Recent evidence suggests that humans may have left Africa half a million years earlier than
previously thought. A joint Franco-Indian team has found human artifacts in the Siwalk Hills
north of New Delhi dating back at least 2.6 million years. This is earlier than the previous
earliest finding of genus Homo at Dmanisi, in Georgia, dating to 1.85 million years. Although
controversial, tools found at a Chinese cave strengthen the case that humans used tools as far
back as 2.48 million years ago. This suggests that the Asian "Chopper" tool tradition, found
in Java and northern China may have left Africa before the appearance of the Acheulian hand
axe.

Dispersal of modern Homo sapiens

Up until the genetic evidence became available, there were two dominant models for the
dispersal of modern humans. The multiregional hypothesis proposed that the genus Homo
contained only a single interconnected population as it does today (not separate species), and
that its evolution took place worldwide continuously over the last couple of million years.
This model was proposed in 1988 by Milford H. Wolpoff. In contrast, the "out of Africa"
model proposed that modern H. sapiensspeciated in Africa recently (that is, approximately
200,000 years ago) and the subsequent migration through Eurasia resulted in the nearly
complete replacement of other Homo species. This model has been developed by Chris B.
Stringer and Peter Andrews.
Sequencing mtDNA and Y-DNA sampled from a wide range of indigenous populations
revealed ancestral information relating to both male and female genetic heritage, and
strengthened the "out of Africa" theory and weakened the views of multiregional
evolutionism. Aligned in genetic tree differences were interpreted as supportive of a recent
single origin. Analyses have shown a greater diversity of DNA patterns throughout Africa,
consistent with the idea that Africa is the ancestral home of mitochondrial Eve and Y-
chromosomal Adam, and that modern human dispersal out of Africa has only occurred over
the last 55,000 years.
"Out of Africa" has thus gained much support from research using female mitochondrial
DNA and the male Y chromosome. After analysing genealogy trees constructed using 133
types of mtDNA, researchers concluded that all were descended from a female African
progenitor, dubbed Mitochondrial Eve. "Out of Africa" is also supported by the fact that
mitochondrial genetic diversity is highest among African populations.
A broad study of African genetic diversity, headed by Sarah Tishkoff, found the San people
had the greatest genetic diversity among the 113 distinct populations sampled, making them
one of 14 "ancestral population clusters". The research also located a possible origin of
modern human migration in southwestern Africa, near the coastal border of Namibia and
Angola. The fossil evidence was insufficient for archaeologist Richard Leakey to resolve the
debate about exactly where in Africa modern humans first appeared. Studies of haplogroups
in Y-chromosomal DNA and mitochondrial DNA have largely supported a recent African
origin. All the evidence from autosomal DNA also predominantly supports a Recent African
origin. However, evidence for archaic admixture in modern humans, both in Africa and later,
throughout Eurasia has recently been suggested by a number of studies.
Recent sequencing of Neanderthal and Denisovan genomes shows that some admixture with
these populations has occurred. All modern human groups outside Africa have 1–4% or
(according to more recent research) about 1.5–2.6% Neanderthal alleles in their genome, and
some Melanesians have an additional 4–6% of Denisovan alleles. These new results do not
contradict the "out of Africa" model, except in its strictest interpretation, although they make
the situation more complex. After recovery from a genetic bottleneck that some researchers
speculate might be linked to the Toba supervolcano catastrophe, a fairly small group left
Africa and interbred with Neanderthals, probably in the Middle East, on the Eurasian steppe
or even in North Africa before their departure. Their still predominantly African descendants
spread to populate the world. A fraction in turn interbred with Denisovans, probably in
southeastern Asia, before populating Melanesia. HLA haplotypes of Neanderthal and
Denisova origin have been identified in modern Eurasian and Oceanian populations. The
Denisovan EPAS1 gene has also been found in Tibetan populations. Studies of the human
genome using machine learning have identified additional genetic contributions in Eurasians
from an "unknown" ancestral population potentially related to the Neanderthal-Denisovan
lineage.
There are still differing theories on whether there was a single exodus from Africa or several.
A multiple dispersal model involves the Southern Dispersal theory, which has gained support
in recent years from genetic, linguistic and archaeological evidence. In this theory, there was
a coastal dispersal of modern humans from the Horn of Africa crossing the Bab el Mandib to
Yemen at a lower sea level around 70,000 years ago. This group helped to populate Southeast
Asia and Oceania, explaining the discovery of early human sites in these areas much earlier
than those in the Levant. This group seems to have been dependent upon marine resources for
their survival.
Stephen Oppenheimer has proposed a second wave of humans may have later dispersed
through the Persian Gulf oases, and the Zagros mountains into the Middle East. Alternatively
it may have come across the Sinai Peninsula into Asia, from shortly after 50,000 yrs BP,
resulting in the bulk of the human populations of Eurasia. It has been suggested that this
second group possibly possessed a more sophisticated "big game hunting" tool technology
and was less dependent on coastal food sources than the original group. Much of the evidence
for the first group's expansion would have been destroyed by the rising sea levels at the end
of each glacial maximum. The multiple dispersal model is contradicted by studies indicating
that the populations of Eurasia and the populations of Southeast Asia and Oceania are all
descended from the same mitochondrial DNA L3 lineages, which support a single migration
out of Africa that gave rise to all non-African populations. On the basis of the early date of
Badoshan Iranian Aurignacian, Oppenheimer suggests that this second dispersal may have
occurred with a pluvial period about 50,000 years before the present, with modern human
big-game hunting cultures spreading up the Zagros Mountains, carrying modern human
genomes from Oman, throughout the Persian Gulf, northward into Armenia and Anatolia,
with a variant travelling south into Israel and to Cyrenicia. Recent genetic evidence suggests
that all modern non-African populations, including those of Eurasia and Oceania, are
descended from a single wave that left Africa between 65,000 and 50,000 years ago.

EVIDENCE
The evidence on which scientific accounts of human evolution are based comes from many
fields of natural science. The main source of knowledge about the evolutionary process has
traditionally been the fossil record, but since the development of genetics beginning in the
1970s, DNA analysis has come to occupy a place of comparable importance. The studies of
ontogeny, phylogeny and especially evolutionary developmental biology of both vertebrates
and invertebrates offer considerable insight into the evolution of all life, including how
humans evolved. The specific study of the origin and life of humans is anthropology,
particularly paleoanthropology which focuses on the study of human prehistory.

Evidence from molecular biology

Family tree showing the extant hominoids: humans (genus Homo), chimpanzees and bonobos
(genus Pan), gorillas (genus Gorilla),
Gorilla orangutans (genus Pongo),
), and gibbons (four genera of
the family Hylobatidae: Hylobates,
Hylobates Hoolock, Nomascus, and Symphalangus
Symphalangus). All except
gibbons are hominids.
The closest living relatives of humans are bonobos and chimpanzees (both genus Pan) and
gorillas (genus Gorilla).
). With the sequencing of both the human and chimpanzee genome, as
of 2012 estimates
imates of the similarity between their DNA sequences range between 95% and
99%. By using the technique called the molecular clock which estimates the time required for
the number
ber of divergent mutations to accumulate between two lineages, the approximate date
for the split between lineages can be calculated.
The gibbons (family Hylobatidae) and then the orangutans (genus Pongo)) were the first
groups to split from the line leading to the hominins, including humans—followed
humans followed by gorillas
(genus Gorilla),
), and, ultimately, by the chimpanzees (genus Pan).
). The splitting date between
hominin and chimpanzee lineages is placed by some between 4 to 8million
million years ago
ago, that is,
during the Late Miocene. Speciation,
Speciation, however, appears to have been unusually drawn out.
Initial divergence occurred sometime between 7 to 13million years ago,, but ongoing
hybridization blurred the separation and delayed complete separation during several millions
of years. Patterson (2006) dated the final divergence at 5 to 6million years ago.
Genetic evidence has also been employed to resolve the question
question of whether there was any
gene flow between early modern humans and Neanderthals,
Neanderthals, and to enhance our
understanding of the
he early human migration patterns and splitting dates. By comparing the
parts of the genome that are not under natural selection and which therefore accumulate
mutations at a fairly steady rate, it is possible to reconstruct a genetic tree incorporating th
the
entire human species since the last shared ancestor.
Each time a certain mutation (single-nucleotide polymorphism) appears in an individual and
is passed on to his or her descendants, a haplo group is formed including all of the
descendants of the individual who will also carry that mutation. By comparing mitochondrial
DNA which is inherited only from the mother, geneticists have concluded that the last female
common ancestor whose genetic marker is found in all modern humans, the so-called
mitochondrial Eve, must have lived around 200,000 years ago.

GENETICS
Human evolutionary genetics studies how one human genome differs from the other, the
evolutionary past that gave rise to it, and its current effects. Differences between genomes
have anthropological, medical and forensic implications and applications. Genetic data can
provide important insight into human evolution.

EVIDENCE FROM THE FOSSIL RECORD

There is little fossil evidence for the divergence of the gorilla, chimpanzee and hominin
lineages. The earliest fossils that have been proposed as members of the hominin lineage are
Sahelanthropus tchadensis dating from 7 million years ago, Orrorin tugenensis dating from
5.7 million years ago, and Ardipithecus kadabba dating to 5.6 million years ago. Each of
these has been argued to be a bipedal ancestor of later hominins but, in each case, the claims
have been contested. It is also possible that one or more of these species are ancestors of
another branch of African apes, or that they represent a shared ancestor between hominins
and other apes.
The question then of the relationship between these early fossil species and the hominin
lineage is still to be resolved. From these early species, the australopithecines arose around
4 million years ago and diverged into robust (also called Paranthropus) and gracile branches,
one of which (possibly A. garhi) probably went on to become ancestors of the genus Homo.
The australopithecine species that is best represented in the fossil record is Australopithecus
afarensis with more than 100 fossil individuals represented, found from Northern Ethiopia
(such as the famous "Lucy"), to Kenya, and South Africa. Fossils of robust australopithecines
such as Au. robustus (or alternatively Paranthropus robustus) and Au./P. boisei are
particularly abundant in South Africa at sites such as Kromdraai and Swartkrans, and around
Lake Turkana in Kenya.
The earliest member of the genus Homo is Homo habilis which evolved around 2.8 million
years ago. Homo habilis is the first species for which we have positive evidence of the use of
stone tools. They developed the Oldowan lithic technology, named after the Olduvai Gorge in
which the first specimens were found. Some scientists consider Homo rudolfensis, a larger
bodied group of fossils with similar morphology to the original H. habilis fossils, to be a
separate species, while others consider them to be part of H. habilis—simply representing
intraspecies variation, or perhaps even sexual dimorphism. The brains of these early hominins
were about the same size as that of a chimpanzee, and their main adaptation was bipedalism
as an adaptation to terrestrial living.
During the next million years, a process of encephalization began and, by the arrival (about
1.9 million years ago) of Homo erectus in the fossil record, cranial capacity had doubled.
Homo erectus was the first of the hominins to emigrate from Africa, and, from
1.8 to 1.3million years ago, this species spread through Africa, Asia, and Europe. One
population of H. erectus, also sometimes classified as a separate species Homo ergaster,
remained in Africa and evolved into Homo sapiens. It is believed that these species, H.
erectus and H. ergaster, were the first to use fire and complex tools.
The earliest transitional fossils between H. ergaster/erectus and archaic H. sapiens are from
Africa, such as Homo rhodesiensis. These descendants of African H. erectus spread through
Eurasia from ca. 500,000 years ago, evolving into H. antecessor, H. heidelbergensis and H.
neanderthalensis. The earliest fossils of anatomically modern humans are from the Middle
Paleolithic, about 300–200,000 years ago such as the Herto and Omo remains of Ethiopia,
Jebel Irhoud remains of Morocco, and Florisbad remains of South Africa; later fossils from
Es Skhul cave in Israel and Southern Europe begin around 90,000 years ago (0.09 million
years ago).
As modern humans spread out from Africa, they encountered other hominins such as Homo
neanderthalensis and the Denisovans, who may have evolved from populations of Homo
erectus that had left Africa around 2 million years ago. The nature of interaction between
early humans and these sister species has been a long-standing source of controversy, the
question being whether humans replaced these earlier species or whether they were in fact
similar enough to interbreed, in which case these earlier populations may have contributed
genetic material to modern humans.
This migration out of Africa is estimated to have begun about 70–50,000 years BP and
modern humans subsequently spread globally, replacing earlier hominins either through
competition or hybridization. They inhabited Eurasia and Oceania by 40,000 years BP, and
the Americas by at least 14,500 years BP.

INTER-SPECIES BREEDING
The hypothesis of interbreeding, also known as hybridization, admixture or hybrid-origin
theory, has been discussed ever since the discovery of Neanderthal remains in the 19th
century. The linear view of human evolution began to be abandoned in the 1970s as different
species of humans were discovered that made the linear concept increasingly unlikely. In the
21st century with the advent of molecular biology techniques and computerization, whole-
genome sequencing of Neanderthal and human genome were performed, confirming recent
admixture between different human species. In 2010, evidence based on molecular biology
was published, revealing unambiguous examples of interbreeding between archaic and
modern humans during the Middle Paleolithic and early Upper Paleolithic. It has been
demonstrated that interbreeding happened in several independent events that included
Neanderthals and Denisovans, as well as several unidentified hominins. Today,
approximately 2% of DNA from all non-African populations (including Europeans, Asians,
and Oceanians) is Neanderthal, with traces of Denisovan heritage. Also, 4–6% of modern
Melanesian genetics are Denisovan. Comparisons of the human genome to the genomes of
Neandertals, Denisovans and apes can help identify features that set modern humans apart
from other hominin species. In a 2016 comparative genomics study, a Harvard Medical
School/UCLA research team made a world map on the distribution and made some
predictions about where Denisovan and Neanderthal genes may be impacting modern human
biology.
For example, comparative studies in the mid-2010s found several traits related to
neurological, immunological, developmental, and metabolic phenotypes that were developed
by archaic humans to European and Asian environments and inherited to modern humans
through admixture with local hominins.
Although the narratives of human evolution are often contentious, several discoveries since
2010 show that human evolution should not be seen as a simple linear or branched
progression, but a mix of related species. In fact, genomic research has shown that
hybridization between substantially diverged lineages is the rule, not the exception, in human
evolution. Furthermore, it is argued that hybridization was an essential creative force in the
emergence of modern humans.
EARLY EVOLUTION OF PRIMATES
The evolutionary history of the primates can be traced back 65 million years. One of the
oldest known primate-like mammal species, the Plesiadapis, came from North America;
another, Archicebus, came from China. Other similar basal primates were widespread in
Eurasia and Africa during the tropical conditions of the Paleocene and Eocene.
David R. Begun concluded that early primates flourished in Eurasia and that a lineage leading
to the African apes and humans, including to Dryopithecus, migrated south from Europe or
Western Asia into Africa. The surviving tropical population of primates—which is seen most
completely in the Upper Eocene and lowermost Oligocene fossil beds of the Faiyum
depression southwest of Cairo—gave rise to all extant primate species, including the lemurs
of Madagascar, lorises of Southeast Asia, galagos or "bush babies" of Africa, and to the
anthropoids, which are the Platyrrhines or New World monkeys, the Catarrhines or Old
World monkeys, and the great apes, including humans and other hominids.
The earliest known catarrhine is Kamoyapithecus from uppermost Oligocene at Eragaleit in
the northern Great Rift Valley in Kenya, dated to 24 million years ago. Its ancestry is thought
to be species related to Aegyptopithecus, Propliopithecus, and Parapithecus from the Faiyum,
at around 35 million years ago. In 2010, Saadanius was described as a close relative of the
last common ancestor of the crown catarrhines, and tentatively dated to 29–28 million years
ago, helping to fill an 11-million-year gap in the fossil record.
In the Early Miocene, about 22 million years ago, the many kinds of arboreally adapted
primitive catarrhines from East Africa suggest a long history of prior diversification. Fossils
at 20 million years ago include fragments attributed to Victoriapithecus, the earliest Old
World monkey. Among the genera thought to be in the ape lineage leading up to 13 million
years ago are Proconsul, Rangwapithecus, Dendropithecus, Limnopithecus, Nacholapithecus,
Equatorius, Nyanzapithecus, Afropithecus, Heliopithecus, and Kenyapithecus, all from East
Africa.
The presence of other generalized non-cercopithecids of Middle Miocene from sites far
distant—Otavipithecus from cave deposits in Namibia, and Pierolapithecus and Dryopithecus
from France, Spain and Austria—is evidence of a wide diversity of forms across Africa and
the Mediterranean basin during the relatively warm and equable climatic regimes of the Early
and Middle Miocene. The youngest of the Miocene hominoids, Oreopithecus, is from coal
beds in Italy that have been dated to 9 million years ago.
Molecular evidence indicates that the lineage of gibbons (family Hylobatidae) diverged from
the line of great apes some 18–12 million years ago, and that of orangutans (subfamily
Ponginae) diverged from the other great apes at about 12 million years; there are no fossils
that clearly document the ancestry of gibbons, which may have originated in a so-far-
unknown Southeast Asian hominoid population, but fossil proto-orangutans may be
represented by Sivapithecus from India and Griphopithecus from Turkey, dated to around
10 million years ago.
DIVERGENCE OF THE HUMAN CLADE FROM OTHER GREAT APES
Species close to the last common ancestor of gorillas, chimpanzees and humans may be
represented by Nakalipithecus fossils found in Kenya and Ouranopithecus found in Greece.
Molecular evidence suggests that between 8 and 4 million years ago, first the gorillas, and
then the chimpanzees (genus Pan) split off from the line leading to the humans. Human DNA
is approximately 98.4% identical to that of chimpanzees when comparing single nucleotide
polymorphisms. The fossil record, however, of gorillas and chimpanzees is limited; both poor
preservation – rain forest soils tend to be acidic and dissolve bone – and sampling bias
probably contribute to this problem.
Other hominins probably adapted to the drier environments outside the equatorial belt; and
there they encountered antelope, hyenas, dogs, pigs, elephants, horses, and others. The
equatorial belt contracted after about 8 million years ago, and there is very little fossil
evidence for the split—thought to have occurred around that time—of the hominin lineage
from the lineages of gorillas and chimpanzees. The earliest fossils argued by some to belong
to the human lineage are Sahelanthropus tchadensis (7 Ma) and Orrorin tugenensis (6 Ma),
followed by Ardipithecus (5.5–4.4 Ma), with species Ar. kadabba and Ar. ramidus.
It has been argued in a study of the life history of Ar. ramidus that the species provides
evidence for a suite of anatomical and behavioral adaptations in very early hominins unlike
any species of extant great ape. This study demonstrated affinities between the skull
morphology of Ar. ramidus and that of infant and juvenile chimpanzees, suggesting the
species evolved a juvenalised or paedomorphic craniofacial morphology via heterochronic
dissociation of growth trajectories. It was also argued that the species provides support for the
notion that very early hominins, akin to bonobos (Pan paniscus) the less aggressive species
of the genus Pan, may have evolved via the process of self-domestication. Consequently,
arguing against the so-called "chimpanzee referential model”. The authors suggest it is no
longer tenable to use chimpanzee (Pan troglodytes) social and mating behaviors in models of
early hominin social evolution.
Genus Australopithecus
The genus Australopithecus evolved in eastern Africa around 4 million years ago before
spreading throughout the continent and eventually becoming extinct 2 million years ago.
During this time period various forms of australopiths existed, including Australopithecus
anamensis, Au. afarensis, Au. sediba, and Au. africanus. There is still some debate among
academics whether certain African hominid species of this time, such as Au. robustus and Au.
boisei, constitute members of the same genus; if so, they would be considered to be Au.
robust australopiths whilst the others would be considered Au. gracile australopiths.
However, if these species do indeed constitute their own genus, then they may be given their
own name, Paranthropus.
• Australopithecus (4–1.8 Ma), with species Au. anamensis, Au. afarensis, Au.
africanus, Au. bahrelghazali, Au. garhi, and Au. sediba;
• Kenyanthropus (3–2.7 Ma), with species K. platyops;
• Paranthropus (3–1.2 Ma), with species P. aethiopicus, P. boisei, and P. robustus
A new proposed species Australopithecus deyiremeda is claimed to have been discovered
living at the same time period of Au. afarensis. There is debate if Au.deyiremeda is a new
species or is Au. afarensis.Australopithecus prometheus, otherwise known as Little Foot has
recently been dated at 3.67 million years old through a new dating technique, making the
genus Australopithecus as old as afarensis. Given the opposable big toe found on Little Foot,
it seems that he was a good climber, and it is thought given the night predators of the region,
he probably, like gorillas and chimpanzees, built a nesting platform at night, in the trees.

Evolution of genus Homo

The earliest documented representative of the genus Homo is Homo habilis, which evolved
around 2.8 million years ago, and is arguably the earliest species for which there is positive
evidence of the use of stone tools. The brains of these early hominins were about the same
size as that of a chimpanzee, although it has been suggested that this was the time in which
the human SRGAP2gene doubled, producing a more rapid wiring of the frontal cortex.
During the next million years a process of rapid encephalization occurred, and with the
arrival of Homo erectus and Homo ergaster in the fossil record, cranial capacity had doubled
to 850 cm3. (Such an increase in human brain size is equivalent to each generation having
125,000 more neurons than their parents.) It is believed that Homo erectus and Homo
ergaster were the first to use fire and complex tools, and were the first of the hominin line to
leave Africa, spreading throughout Africa, Asia, and Europe between 1.3 to 1.8million years
ago.
A model of the phylogeny of H. sapiens during the Middle Paleolithic. The horizontal axis
represents geographic location; the vertical axis represents time in thousands of years ago.
Homo heidelbergensis is shown as diverging into Neanderthals, Denisovans and H. sapiens.
With the expansion of H. sapiens after 200 kya, Neanderthals, Denisovans and unspecified
archaic African hominins are shown as again subsumed into the H. sapiens lineage. In
addition, admixture events in modern African populations are indicated.
According to the recent African origin of modern humans theory, modern humans evolved in
Africa possibly from Homo heidelbergensis, Homo rhodesiensis or Homo antecessor and
migrated out of the continent some 50,000 to 100,000 years ago, gradually replacing local
populations of Homo erectus, Denisova hominins, Homo floresiensis, Homo luzonensis and
Homo neanderthalensis. Archaic Homo sapiens, the forerunner of anatomically modern
humans, evolved in the Middle Paleolithic between 400,000 and 250,000 years ago. Recent
DNA evidence suggests that several haplotypes of Neanderthal origin are present among all
non-African populations, and Neanderthals and other hominins, such as Denisovans, may
have contributed up to 6% of their genome to present-day humans, suggestive of a limited
interbreeding between these species. The transition to behavioral modernity with the
development of symbolic culture, language, and specialized lithic technology happened
around 50,000 years ago, according to some anthropologists, although others point to
evidence that suggests that a gradual change in behavior took place over a longer time span.
Homo sapiens is the only extant species of its genus, Homo. While some (extinct) Homo
species might have been ancestors of Homo sapiens, many, perhaps most, were likely
"cousins", having speciated away from the ancestral hominin line. There is yet no consensus
as to which of these groups should be considered a separate species and which should be a
subspecies; this may be due to the dearth of fossils or to the slight differences used to classify
species in the genus Homo. The Sahara pump theory (describing an occasionally passable
"wet" Sahara desert) provides one possible explanation of the early variation in the genus
Homo.
Based on archaeological and paleontological evidence, it has been possible to infer, to some
extent, the ancient dietary practices of various Homo species and to study the role of diet in
physical and behavioral evolution within Homo.
Some anthropologists and archaeologists subscribe to the Toba catastrophe theory, which
posits that the supereruption of Lake Toba on Sumatran island in Indonesia some 70,000
years ago caused global consequences, killing the majority of humans and creating a
population bottleneck that affected the genetic inheritance of all humans today. The genetic
and archaeological evidence for this remains in question however.
H. habilis and H. gautengensis
Homo habilis lived from about 2.8 to 1.4 Ma. The species evolved in South and East Africa
in the Late Pliocene or Early Pleistocene, 2.5–2 Ma, when it diverged from the
australopithecines. Homo habilis had smaller molars and larger brains than the
australopithecines, and made tools from stone and perhaps animal bones. One of the first
known hominins was nicknamed 'handy man' by discoverer Louis Leakey due to its
association with stone tools. Some scientists have proposed moving this species out of Homo
and into Australopithecus due to the morphology of its skeleton being more adapted to living
on trees rather than to moving on two legs like Homo sapiens.

H. rudolfensis and H. georgicus

These are proposed species names for fossils from about 1.9–1.6 Ma, whose relation to Homo
habilis is not yet clear.
• Homo rudolfensis refers to a single, incomplete skull from Kenya. Scientists have
suggested that this was another Homo habilis, but this has not been confirmed.
• Homo georgicus, from Georgia, may be an intermediate form between Homo habilis
and Homo erectus, or a subspecies of Homo erectus.

H. ergaster and H. erectus

The first fossils of Homo erectus were discovered by Dutch physician Eugene Dubois in 1891
on the Indonesian island of Java. He originally named the material Anthropopithecus erectus
(1892–1893, considered at this point as a chimpanzee-like fossil primate) and
Pithecanthropus erectus (1893–1894, changing his mind as of based on its morphology,
which he considered to be intermediate between that of humans and apes). Years later, in the
20th century, the German physician and paleoanthropologistFranz Weidenreich (1873–1948)
compared in detail the characters of Dubois' Java Man, then named Pithecanthropus erectus,
with the characters of the Peking Man, then named Sinanthropus pekinensis. Weidenreich
concluded in 1940 that because of their anatomical similarity with modern humans it was
necessary to gather all these specimens of Java and China in a single species of the genus
Homo, the species Homo erectus. Homo erectus lived from about 1.8 Ma to about 70,000
years ago – which would indicate that they were probably wiped out by the Toba catastrophe;
however, nearby Homo floresiensis survived it. The early phase of Homo erectus, from 1.8 to
1.25 Ma, is considered by some to be a separate species, Homo ergaster, or as Homo erectus
ergaster, a subspecies of Homo erectus. In Africa in the Early Pleistocene, 1.5–1 Ma, some
populations of Homo habilis are thought to have evolved larger brains and to have made
more elaborate stone tools; these differences and others are sufficient for anthropologists to
classify them as a new species, Homo erectus—in Africa. The evolution of locking knees and
the movement of the foramen magnum are thought to be likely drivers of the larger
population changes. This species also may have used fire to cook meat. Richard Wrangham
suggests that the fact that Homo seems to have been ground dwelling, with reduced intestinal
length, smaller dentition, "and swelled our brains to their current, horrendously fuel-
inefficient size", suggest that control of fire and releasing increased nutritional value through
cooking was the key adaptation that separated Homo from tree-sleeping Australopithecines.
A famous example of Homo erectus is Peking Man; others were found in Asia (notably in
Indonesia), Africa, and Europe. Many paleoanthropologists now use the term Homo ergaster
for the non-Asian forms of this group, and reserve Homo erectus only for those fossils that
are found in Asia and meet certain skeletal and dental requirements which differ slightly from
H. ergaster.
H. cepranensis and H. antecessor
These are proposed as species that may be intermediate between H. erectus and H.
heidelbergensis.
• H. antecessor is known from fossils from Spain and England that are dated 1.2 Ma–
500 ka.
• H. cepranensis refers to a single skull cap from Italy, estimated to be about 800,000
years old.
H. heidelbergensis
H. heidelbergensis ("Heidelberg Man") lived from about 800,000 to about 300,000 years ago.
Also proposed as Homo sapiens heidelbergensis or Homo sapiens paleohungaricus.

H. rhodesiensis, and the Gawis cranium

• H. rhodesiensis, estimated to be 300,000–125,000 years old. Most current researchers
place Rhodesian Man within the group of Homo heidelbergensis, though other
designations such as archaic Homo sapiens and Homo sapiens rhodesiensis have been
proposed.
• In February 2006 a fossil, the Gawis cranium, was found which might possibly be a
species intermediate between H. erectus and H. sapiens or one of many evolutionary
dead ends. The skull from Gawis, Ethiopia, is believed to be 500,000–250,000 years
old. Only summary details are known, and the finders have not yet released a peer-
 reviewed study. Gawis man's facial features suggest its being either an intermediate
species or an example of a "Bodo man" female.

NEANDERTHAL AND DENISOVAN

Homo neanderthalensis, alternatively designated as Homo sapiens neanderthalensis, lived in
Europe and Asia from 400,000 to about 28,000 years ago. There are a number of clear
anatomical differences between anatomically modern humans (AMH) and Neanderthal
populations. Many of these relate to the superior adaptation to cold environments possessed
by the Neanderthal populations. Their surface to volume ratio is an extreme version of that
found amongst Inuit populations, indicating that they were less inclined to lose body heat
than were AMH. From brain Endocasts, Neanderthals also had significantly larger brains.
This would seem to indicate that the intellectual superiority of AMH populations may be
questionable. More recent research by Eiluned Pearce, Chris Stringer, R.I.M. Dunbar,
however, have shown important differences in brain architecture. For example, in both the
orbital chamber size and in the size of the occipital lobe, the larger size suggests that the
Neanderthal had a better visual acuity than modern humans. This would give a superior
vision in the inferior light conditions found in Glacial Europe. It also seems that the higher
body mass of Neanderthals had a correspondingly larger brain mass required for body care
and control.
The Neanderthal populations seem to have been physically superior to AMH populations.
These differences may have been sufficient to give Neanderthal populations an
environmental superiority to AMH populations from 75,000 to 45,000 years BP. With these
differences, Neanderthal brains show a smaller area was available for social functioning.
Plotting group size possible from endocranial volume, suggests that AMH populations (minus
occipital lobe size), had a Dunbars number of 144 possible relationships. Neanderthal
populations seem to have been limited to about 120 individuals. This would show up in a
larger number of possible mates for AMH humans, with increased risks of inbreeding
amongst Neanderthal populations. It also suggests that humans had larger trade catchment
areas than Neanderthals (confirmed in the distribution of stone tools). With larger
populations, social and technological innovations were easier to fix in human populations,
which may have all contributed to the fact that modern Homo sapiens replaced the
Neanderthal populations by 28,000 BP.
Earlier evidence from sequencing mitochondrial DNA suggested that no significant gene
flow occurred between H. neanderthalensis and H. sapiens, and that the two were separate
species that shared a common ancestor about 660,000 years ago. However, a sequencing of
the Neanderthal genome in 2010 indicated that Neanderthals did indeed interbreed with
anatomically modern humans circa 45,000 to 80,000 years ago (at the approximate time that
modern humans migrated out from Africa, but before they dispersed into Europe, Asia and
elsewhere). The genetic sequencing of a 40,000-year-old human skeleton from Romania
showed that 11% of its genome was Neanderthal, and it was estimated that the individual had
a Neanderthal ancestor 4–6 generations previously, in addition to a contribution from earlier
interbreeding in the Middle East. Though this interbred Romanian population seems not to
have been ancestral to modern humans, the finding indicates that interbreeding happened
repeatedly.
All modern non-African humans have about 1% to 4% or, according to more recent data,
about 1.5% to 2.6% of their DNA derived from Neanderthal DNA, and this finding is
consistent with recent studies indicating that the divergence of some human alleles dates to
one Ma, although the interpretation of these studies has been questioned. Neanderthals and
Homo sapiens could have co-existed in Europe for as long as 10,000 years, during which
human populations exploded vastly outnumbering Neanderthals, possibly outcompeting them
by sheer numerical strength. In 2008, archaeologists working at the site of Denisova Cave in
the Altai Mountains of Siberia uncovered a small bone fragment from the fifth finger of a
juvenile member of Denisovans. Artifacts, including a bracelet, excavated in the cave at the
same level were carbon dated to around 40,000 BP. As DNA had survived in the fossil
fragment due to the cool climate of the Denisova Cave, both mtDNA and nuclear DNA were
sequenced.
While the divergence point of the mtDNA was unexpectedly deep in time, the full genomic
sequence suggested the Denisovans belonged to the same lineage as Neanderthals, with the
two diverging shortly after their line split from the lineage that gave rise to modern humans.
Modern humans are known to have overlapped with Neanderthals in Europe and the Near
East for possibly more than 40,000 years, and the discovery raises the possibility that
Neanderthals, Denisovans, and modern humans may have co-existed and interbred. The
existence of this distant branch creates a much more complex picture of humankind during
the Late Pleistocene than previously thought. Evidence has also been found that as much as
6% of the DNA of some modern Melanesians derive from Denisovans, indicating limited
interbreeding in Southeast Asia.
Alleles thought to have originated in Neanderthals and Denisovans have been identified at
several genetic loci in the genomes of modern humans outside of Africa. HLA haplotypes
from Denisovans and Neanderthal represent more than half the HLA alleles of modern
Eurasians, indicating strong positive selection for these introgressed alleles. Corinne Simoneti
at Vanderbilt University, in Nashville and her team have found from medical records of
28,000 people of European descent that the presence of Neanderthal DNA segments may be
associated with a likelihood to suffer depression more frequently.
The flow of genes from Neanderthal populations to modern humans was not all one way.
Sergi Castellano of the Max Planck Institute for Evolutionary Anthropology in Leipzig,
Germany, has in 2016 reported that while Denisovan and Neanderthal genomes are more
related to each other than they are to us, Siberian Neanderthal genomes show similarity to the
modern human gene pool, more so than to European Neanderthal populations. The evidence
suggests that the Neanderthal populations interbred with modern humans possibly 100,000
years ago, probably somewhere in the Near East. Studies of a Neanderthal child at Gibraltar
show from brain development and teeth eruption that Neanderthal children may have matured
more rapidly than is the case for Homo sapiens.

H. floresiensis
H. floresiensis, which lived from approximately 190,000 to 50,000 years before present (BP),
has been nicknamed the hobbit for its small size, possibly a result of insular dwarfism. H.
floresiensis is intriguing both for its size and its age, being an example of a recent species of
the genus Homo that exhibits derived traits not shared with modern humans. In other words,
H. floresiensis shares a common ancestor with modern humans, but split from the modern
human lineage and followed a distinct evolutionary path. The main find was a skeleton
believed to be a woman of about 30 years of age. Found in 2003, it has been dated to
approximately 18,000 years old. The living woman was estimated to be one meter in height,
with a brain volume of just 380 cm3 (considered small for a chimpanzee and less than a third
of the H. sapiens average of 1400 cm3).
However, there is an ongoing debate over whether H. floresiensis is indeed a separate
species. Some scientists hold that H. floresiensis was a modern H. sapiens with pathological
dwarfism. This hypothesis is supported in part, because some modern humans who live on
Flores, the Indonesian island where the skeleton was found, are pygmies. This, coupled with
pathological dwarfism, could have resulted in a significantly diminutive human. The other
major attack on H. floresiensis as a separate species is that it was found with tools only
associated with H. sapiens.
The hypothesis of pathological dwarfism, however, fails to explain additional anatomical
features that are unlike those of modern humans (diseased or not) but much like those of
ancient members of our genus. Aside from cranial features, these features include the form of
bones in the wrist, forearm, shoulder, knees, and feet. Additionally, this hypothesis fails to
explain the find of multiple examples of individuals with these same characteristics,
indicating they were common to a large population, and not limited to one individual.

H. luzonensis
A small number of specimens from the island of Luzon, dated 50,000 to 67,000 years ago,
have recently been assigned by their discoverers, based on dental characteristics, to a novel
human species, H. luzonensis.

H. sapiens
H. sapiens (the adjective sapiens is Latin for "wise" or "intelligent") emerged in Africa
around 300,000 years ago, likely derived from Homo heidelbergensis or a related lineage. In
September 2019, scientists reported the computerized determination, based on 260 CT scans,
of a virtual skull shape of the last common human ancestor to modern humans/H. sapiens,
representative of the earliest modern humans, and suggested that modern humans arose
between 260,000 and 350,000 years ago through a merging of populations in East and South
Africa. Between 400,000 years ago and the second interglacial period in the Middle
Pleistocene, around 250,000 years ago, the trend in intra-cranial volume expansion and the
elaboration of stone tool technologies developed, providing evidence for a transition from H.
erectus to H. sapiens. The direct evidence suggests there was a migration of H. erectus out of
Africa, then a further speciation of H. sapiens from H. erectus in Africa. A subsequent
migration (both within and out of Africa) eventually replaced the earlier dispersed H. erectus.
This migration and origin theory is usually referred to as the "recent single-origin hypothesis"
or "out of Africa" theory. H. sapiensinterbred with archaic humans both in Africa and in
Eurasia, in Eurasia notably with Neanderthals and Denisovans. The Toba catastrophe theory,
which postulates a population bottleneck for H. sapiens about 70,000 years ago, was
controversial from its first proposal in the 1990s and by the 2010s had very little support.
Distinctive human genetic variability has arisen as the result of the founder effect, by archaic
admixture and by recent evolutionary pressures.

USE OF TOOLS
The use of tools has been interpreted as a sign of intelligence, and it has been theorized that
tool use may have stimulated certain aspects of human evolution, especially the continued
expansion of the human brain. Paleontology has yet to explain the expansion of this organ
over millions of years despite being extremely demanding in terms of energy consumption.
The brain of a modern human consumes about 13 watts (260 kilocalories per day), a fifth of
the body's resting power consumption. Increased tool use would allow hunting for energy-
rich meat products, and would enable processing more energy-rich plant products.
Researchers have suggested that early hominins were thus under evolutionary pressure to
increase their capacity to create and use tools.
Precisely when early humans started to use tools is difficult to determine, because the more
primitive these tools are (for example, sharp-edged stones) the more difficult it is to decide
whether they are natural objects or human artifacts. There is some evidence that the
australopithecines (4 Ma) may have used broken bones as tools, but this is debated.
Many species make and use tools, but it is the human genus that dominates the areas of
making and using more complex tools. The oldest known tools are flakes from West Turkana,
Kenya, which date to 3.3 million years ago. The next oldest stone tools are from Gona,
Ethiopia, and are considered the beginning of the Oldowan technology. These tools date to
about 2.6 million years ago. A Homo fossil was found near some Oldowan tools, and its age
was noted at 2.3 million years old, suggesting that maybe the Homo species did indeed create
and use these tools. It is a possibility but does not yet represent solid evidence. The third
metacarpal styloid process enables the hand bone to lock into the wrist bones, allowing for
greater amounts of pressure to be applied to the wrist and hand from a grasping thumb and
fingers. It allows humans the dexterity and strength to make and use complex tools. This
unique anatomical feature separates humans from apes and other nonhuman primates, and is
not seen in human fossils older than 1.8 million years.
Bernard Wood noted that Paranthropus co-existed with the early Homo species in the area of
the "Oldowan Industrial Complex" over roughly the same span of time. Although there is no
direct evidence which identifies Paranthropus as the tool makers, their anatomy lends to
indirect evidence of their capabilities in this area. Most paleoanthropologists agree that the
early Homo species were indeed responsible for most of the Oldowan tools found. They
argue that when most of the Oldowan tools were found in association with human fossils,
Homo was always present, but Paranthropus was not.
In 1994, Randall Susman used the anatomy of opposable thumbs as the basis for his argument
that both the Homo and Paranthropus species were toolmakers. He compared bones and
muscles of human and chimpanzee thumbs, finding that humans have 3 muscles which are
lacking in chimpanzees. Humans also have thicker metacarpals with broader heads, allowing
more precise grasping than the chimpanzee hand can perform. Susman posited that modern
anatomy of the human opposable thumb is an evolutionary response to the requirements
associated with making and handling tools and that both species were indeed toolmakers.
STONE TOOLS
Stone tools are first attested around 2.6 million years ago, when hominins in Eastern Africa
used so-called core tools, choppers made out of round cores that had been split by simple
strikes. This marks the beginning of the Paleolithic, or Old Stone Age; its end is taken to be
the end of the last Ice Age, around 10,000 years ago. The Paleolithic is subdivided into the
Lower Paleolithic (Early Stone Age), ending around 350,000–300,000 years ago, the Middle
Paleolithic (Middle Stone Age), until 50,000–30,000 years ago, and the Upper Paleolithic,
(Late Stone Age), 50,000–10,000 years ago.
Archaeologists working in the Great Rift Valley in Kenya have discovered the oldest known
stone tools in the world. Dated to around 3.3 million years ago, the implements are some
700,000 years older than stone tools from Ethiopia that previously held this distinction. The
period from 700,000 to 300,000 years ago is also known as the Acheulean, when H. ergaster
(or erectus) made large stone hand axes out of flint and quartzite, at first quite rough (Early
Acheulian), later "retouched" by additional, more-subtle strikes at the sides of the flakes.
After 350,000 BP the more refined so-called Levallois technique was developed, a series of
consecutive strikes, by which scrapers, slicers ("racloirs"), needles, and flattened needles
were made. Finally, after about 50,000 BP, ever more refined and specialized flint tools were
made by the Neanderthals and the immigrant Cro-Magnons (knives, blades, skimmers). Bone
tools were also made by H. sapiens in Africa by 90–70,000 years ago and are also known
from early H. sapiens sites in Eurasia by about 50,000 years ago.
TRANSITION TO BEHAVIORAL MODERNITY
Until about 50,000–40,000 years ago, the use of stone tools seems to have progressed
stepwise. Each phase (H. habilis, H. ergaster, H. neanderthalensis) started at a higher level
than the previous one, but after each phase started, further development was slow. Currently
paleoanthropologists are debating whether these Homo species possessed some or many of
the cultural and behavioral traits associated with modern humans such as language, complex
symbolic thinking, technological creativity etc. It seems that they were culturally
conservative maintaining simple technologies and foraging patterns over very long periods.
Around 50,000 BP, modern human culture started to evolve more rapidly. The transition to
behavioral modernity has been characterized by some as a "Great Leap Forward", or as the
"Upper Palaeolithic Revolution", due to the sudden appearance of distinctive signs of modern
behavior and big game hunting in the archaeological record. Evidence of behavioral
modernity significantly earlier also exists from Africa, with older evidence of abstract
imagery, widened subsistence strategies, more sophisticated tools and weapons, and other
"modern" behaviors, and many scholars have recently argued that the transition to modernity
occurred sooner than previously believed. Some other scholars consider the transition to have
been more gradual, noting that some features had already appeared among archaic African
Homo sapiens since 300–200,000 years ago. Recent evidence suggests that the Australian
Aboriginal population separated from the African population 75,000 years ago, and that they
made a sea journey of up to 160 km 60,000 years ago, which may diminish the evidence of
the Upper Paleolithic Revolution.
Modern humans started burying their dead, using animal hides to make clothing, hunting with
more sophisticated techniques (such as using trapping pits or driving animals off cliffs), and
engaging in cave painting. As human culture advanced, different populations of humans
introduced novelty to existing technologies: artifacts such as fish hooks, buttons, and bone
needles show signs of variation among different populations of humans, something that had
not been seen in human cultures prior to 50,000 BP. Typically, H. neanderthalensis
populations do not vary in their technologies, although the Chatelperronian assemblages have
been found to be Neanderthal innovations produced as a result of exposure to the Homo
sapiens Aurignacian technologies.
Among concrete examples of modern human behavior, anthropologists include specialization
of tools, use of jewellery and images (such as cave drawings), organization of living space,
rituals (for example, burials with grave gifts), specialized hunting techniques, exploration of
less hospitable geographical areas, and barter trade networks. Debate continues as to whether
a "revolution" led to modern humans ("the big bang of human consciousness"), or whether
the evolution was more "gradual".

RECENT AND ONGOING HUMAN EVOLUTION

Anatomically modern human populations continue to evolve, as they are affected by both
natural selection and genetic drift. Although selection pressure on some traits, such as
resistance to smallpox, has decreased in the modern age, humans are still undergoing natural
selection for many other traits. Some of these are due to specific environmental pressures,
while others are related to lifestyle changes since the development of agriculture (10,000
years ago), urbanization (5,000), and industrialization (250 years ago). It has been argued that
human evolution has accelerated since the development of agriculture 10,000 years ago and
civilization some 5,000 years ago, resulting, it is claimed, in substantial genetic differences
between different current human populations, and more recent research indicates that for
some traits, the developments and innovations of human culture have driven a new form of
selection that coexists with, and in some cases has largely replaced, natural selection.
Particularly conspicuous is variation in superficial characteristics, such as Afro-textured hair,
or the recent evolution of light skin and blond hair in some populations, which are attributed
to differences in climate. Particularly strong selective pressures have resulted in high-altitude
adaptation in humans, with different ones in different isolated populations. Studies of the
genetic basis show that some developed very recently, with Tibetans evolving over 3,000
years to have high proportions of an allele of EPAS1 that is adaptive to high altitudes.
Other evolution is related to endemic diseases: the presence of malaria selects for sickle cell
trait (the heterozygous form of sickle cell gene), while in the absence of malaria, the health
effects of sickle-cell anemia select against this trait. For another example, the population at
risk of the severe debilitating disease kuru has significant over-representation of an immune
variant of the prion protein gene G127V versus non-immune alleles. The frequency of this
genetic variant is due to the survival of immune persons. Some reported trends remain
unexplained and the subject of ongoing research in the novel field of evolutionary medicine:
polycystic ovary syndrome (PCOS) reduces fertility and thus is expected to be subject to
extremely strong negative selection, but its relative commonality in human populations
suggests a counteracting selection pressure. The identity of that pressure remains the subject
of some debate. Recent human evolution related to agriculture includes genetic resistance to
infectious disease that has appeared in human populations by crossing the species barrier
from domesticated animals, as well as changes in metabolism due to changes in diet, such as
lactase persistence.
Culturally-driven evolution can defy the expectations of natural selection: while human
populations experience some pressure that drives a selection for producing children at
younger ages, the advent of effective contraception, higher education, and changing social
norms have driven the observed selection in the opposite direction. However, culturally-
driven selection need not necessarily work counter or in opposition to natural selection: some
proposals to explain the high rate of recent human brain expansion indicate a kind of
feedback whereupon the brain's increased social learning efficiency encourages cultural
developments that in turn encourage more efficiency, which drive more complex cultural
developments that demand still-greater efficiency, and so forth. Culturally-driven evolution
has an advantage in that in addition to the genetic effects, it can be observed also in the
archaeological record: the development of stone tools across the Palaeolithic period connects
to culturally-driven cognitive development in the form of skill acquisition supported by the
culture and the development of increasingly complex technologies and the cognitive ability to
elaborate them.
In contemporary times, since industrialization, some trends have been observed: for instance,
menopause is evolving to occur later. Other reported trends appear to include lengthening of
the human reproductive period and reduction in cholesterol levels, blood glucose and blood
pressure in some populations.