Taxonomy and Phylogeny of

Animals
JASPER KIT TANGAL, RFP
INTRODUCTION
Aquatic organisms are a diverse group of animals that
inhabit aquatic environments such as oceans, rivers, lakes,
and ponds. They have adapted to live and thrive in various
aquatic conditions, and they play a critical role in the
ecological balance of these environments. In this
presentation, we will explore the taxonomy and phylogeny of
aquatic organisms, focusing on their classification and
evolutionary relationships.
Linnaeus and Taxonomy
● He was born in Råshult, Sweden, on May 23, 1707, and died in
Uppsala, Sweden, on January 10, 1778.
● He studied medicine at the University of Lund and the University
of Uppsala, where he later became a professor of botany and
medicine.
● He traveled extensively in Sweden and abroad to collect and
observe plants and animals. He also corresponded with many other
naturalists and exchanged specimens with them.
● He devised a system of classification that divided living things
into three kingdoms: animal, vegetable, and mineral. Within each
kingdom, he further classified organisms into classes, orders,
genera, and species. He gave each species a unique Latin name
consisting of a genus name and a specific epithet. For example,
the scientific name for humans is Homo sapiens.
● He named more than 12,000 plant and animal species and described many new
ones. He also coined many terms that are still used in biology today, such
as mammal, amphibian, reptile, and ecology.
● He published more than 70 works on various topics related to natural
history. His most influential work was "Systema Naturae," which he first
published in 1735 as a 12-page pamphlet and later expanded to a 12-volume
encyclopedia. It contained descriptions of all the known species of plants
and animals at the time.
● He was honored with many awards and titles during his lifetime and after
his death. He was ennobled by King Adolf Frederick of Sweden in 1761 and
took the name Carl von Linné. He was also a member of several scientific
societies and academies in Europe. He is widely regarded as one of the
greatest naturalists of all time and the father of modern taxonomy.
● Taxonomy is the science of naming, describing and classifying organisms into
groups based on their similarities and differences.
● Taxonomy helps to organize the diversity of life on Earth and to understand
the evolutionary relationships among living beings.
● Taxonomy follows a hierarchical system of classification, where each level is
called a taxon (plural: taxa) and represents a group of organisms that share
common characteristics.
● The most widely used taxonomic system is the Linnaean system, which has seven
main levels: kingdom, phylum, class, order, family, genus and species. For
example, humans belong to the kingdom Animalia, the phylum Chordata, the class
Mammalia, the order Primates, the family Hominidae, the genus Homo and the
species sapiens.
● The scientific name of an organism is composed of its genus and species names,
written in italics and with the first letter of the genus capitalized. For
example, the scientific name of humans is Homo sapiens.
● Taxonomy is not a fixed or static system, but rather a dynamic and evolving
one that reflects the current state of knowledge and evidence. New taxa may be
discovered or revised as new data and methods become available.
Species
- A species is a group of organisms that can interbreed and produce fertile offspring.

- The concept of species is based on the biological species concept, which defines a
species as a population or group of populations that are reproductively isolated from
other groups.

- There are other ways to define a species, such as the morphological species concept,
which relies on physical characteristics, or the phylogenetic species concept, which
uses evolutionary relationships.

- The number of species on Earth is estimated to be between 8.7 million and 2 billion,
but only about 1.9 million have been formally described and named.

- Species are classified into hierarchical groups called taxa, such as kingdom,
phylum, class, order, family, genus and species. The scientific name of a species
consists of two parts: the genus name and the specific epithet.
Taxonomic Characters
Taxonomic are the observable features or traits of an organism that can be used to identify and classify
it into a taxonomic group.
- Taxonomic characters can be morphological, anatomical, physiological, biochemical, genetic,
behavioral, ecological or molecular.
- Taxonomic characters can be qualitative or quantitative, depending on whether they are based on
discrete categories or continuous measurements.
- Taxonomic characters can be homologous or analogous, depending on whether they are derived from a
common ancestor or evolved independently in different lineages.
- Taxonomic characters can be primitive or derived, depending on whether they are shared with the
ancestral form or evolved later in the evolutionary history of the group.
- Taxonomic characters can be useful or misleading, depending on whether they reflect the true
evolutionary relationships among the organisms or are affected by convergent evolution, parallel
evolution, reversal evolution or homoplasy.
Phylogenetic reconstruction
- Phylogenetic reconstruction is the process of inferring the evolutionary history and relationships of different groups of organisms
based on their genetic or morphological data.
- Phylogenetic reconstruction can be done using various methods, such as parsimony, maximum likelihood, Bayesian inference, or
distance-based methods.
- Phylogenetic reconstruction can help answer questions such as: How are different species related to each other? When did they
diverge from a common ancestor? What are the patterns of gene flow and hybridization among populations?
- Phylogenetic reconstruction can also have applications in fields such as biogeography, epidemiology, conservation biology, and
molecular evolution.
Parsimony
Parsimony is a principle that states that the simplest
explanation for a set of observations is the most likely
one. In phylogenetics, parsimony methods try to find the
tree that minimizes the number of evolutionary changes (such
as mutations or substitutions) required to explain the data.
Maximum likelihood
Maximum likelihood is a statistical approach that estimates
the probability of observing the data given a model and a
set of parameters. In phylogenetics, maximum likelihood
methods try to find the tree that maximizes the likelihood
of the data under a specific model of evolution (such as
Jukes-Cantor or Kimura).
Bayesian inference & Distance-based methods

- Bayesian inference is a probabilistic framework that incorporates prior

knowledge and uncertainty into the analysis. In phylogenetics, Bayesian
methods try to find the posterior distribution of trees given the data and a
prior distribution of trees and parameters. The posterior distribution
reflects the degree of belief in each possible tree after observing the data.

- Distance-based methods are a class of methods that rely on calculating

pairwise distances between sequences and then constructing a tree based on
those distances. In phylogenetics, distance-based methods can use different
algorithms to build the tree, such as UPGMA, NJ, or Fitch-Margoliash.
Distance-based methods are usually fast and simple, but they may not account
for complex evolutionary processes or uncertainties in the data.
Theories of Taxonomy
- Theories of Taxonomy are the principles that we use to
recognize and rank taxonomic groups, which are the arrangements
of organisms into hierarchies of superior and subordinate groups
based on their relationships .
- There are two currently popular theories of taxonomy: (1)
traditional evolutionary taxonomy and (2) phylogenetic
systematics (cladistics). Both are based on evolutionary
principles, but they differ on how they use them.
- Traditional evolutionary taxonomy incorporates two different
evolutionary principles for recognizing and ranking higher taxa:
common descent and amount of adaptive evolutionary change.
Evolutionary taxa must have a single evolutionary origin and
must show unique adaptive features.
Phylogenetic systematics (cladistics) uses only one evolutionary
principle for recognizing and ranking taxa: common descent.
Cladistic taxa must be monophyletic, meaning they include the
most recent common ancestor of all members of the group and all
of its descendants. Cladistic taxa do not reflect the amount of
adaptive change or the degree of similarity among organisms.
The relationship between a taxonomic group and a phylogenetic
tree or cladogram can take one of three forms: monophyly,
paraphyly, or polyphyly. Monophyly is accepted by both
evolutionary and cladistic taxonomy, while paraphyly is accepted
only by evolutionary taxonomy and polyphyly is rejected by both
theories.
Major Divisions of Life
- Major Divisions of Life are the broadest categories of biological
classification that group organisms based on their shared characteristics
and evolutionary history.

- There are different ways of defining and naming the Major Divisions of
Life, but one common system is the three-domain system, which recognizes
three domains: Bacteria, Archaea, and Eukarya.

- Eukarya are eukaryotes, which are organisms that have a nucleus and other
membrane-bound organelles in their cells. Eukarya include four kingdoms:
Protista, Fungi, Plantae, and Animalia. Protista are mostly single-celled
organisms that do not fit into the other kingdoms. Fungi are multicellular
organisms that decompose organic matter and absorb nutrients. Plantae are
multicellular organisms that produce their own food by photosynthesis.
Animalia are multicellular organisms that ingest their food and have
specialized tissues and organs.
Bacteria and Archaea are prokaryotes
which are single-celled organisms that lack a nucleus and
other membrane-bound organelles. They have diverse shapes,
sizes, metabolisms, and habitats. Bacteria and Archaea
differ in their cell wall composition, ribosomal structure,
and gene expression mechanisms.
Eukarya
Eukarya are eukaryotes, which are organisms that have a
nucleus and other membrane-bound organelles in their cells.
Eukarya include four kingdoms: Protista, Fungi, Plantae, and
Animalia. Protista are mostly single-celled organisms that
do not fit into the other kingdoms. Fungi are multicellular
organisms that decompose organic matter and absorb
nutrients. Plantae are multicellular organisms that produce
their own food by photosynthesis. Animalia are multicellular
organisms that ingest their food and have specialized
tissues and organs.
Major Subdivisions of the
Animal Kingdom
The animal kingdom is divided into two main groups: vertebrates
and invertebrates.
- Vertebrates are animals that have a backbone or spinal column.
They include mammals, birds, reptiles, amphibians and fish.
- Invertebrates are animals that lack a backbone or spinal
column. They include sponges, cnidarians, flatworms, roundworms,
annelids, mollusks, arthropods and echinoderms.
Mammals are warm-blooded vertebrates that have hair or fur and produce milk
for their young.
mammals
Birds are warm-blooded vertebrates that have feathers and
wings and lay eggs with hard shells.
Reptiles are cold-blooded vertebrates that have scales and breathe
through lungs. Most of them lay eggs with leathery shells.
Amphibians are cold-blooded vertebrates that have moist skin and
can live both on land and in water. They undergo metamorphosis
from larva to adult.
Fish are cold-blooded vertebrates that have gills and fins
and live in water. They have a variety of shapes, sizes and
colors.
Sponges are simple invertebrates that have pores and canals for
filtering water. They have no organs or tissues and can regenerate
from fragments.
Cnidarians are invertebrates that have stinging cells and a hollow
body cavity. They include jellyfish, corals, sea anemones and hydra.
Flatworms are invertebrates that have a flat body and a simple
digestive system. They include planarians, flukes and tapeworms.
 Roundworms are invertebrates that have a round body and a complete
digestive system. They include hookworms, pinworms and filarial worms.
 Annelids are invertebrates that have a segmented body and a closed
circulatory system. They include earthworms, leeches and marine worms.
Mollusks are invertebrates that have a soft body and a hard shell. They
include snails, slugs, clams, oysters, mussels, squid and octopus.
Arthropods are invertebrates that have a hard exoskeleton and jointed
appendages. They include insects, spiders, scorpions, crustaceans and centipedes.
Echinoderms are invertebrates that have a spiny skin and a radial symmetry. They
include starfish, sea urchins, sand dollars and sea cucumbers.