TYPES OF PHYLOGENETIC TREES

Submitted By: Arsalan Khan

Submitted To: Dr. Sara Khan

DEPARTMENT OF BIOINFORMATICS
HAZARA UNIVERSITY MANSEHRA
2021

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 TABLE OF CONTENTS
PHYLOGENETIC TREES ............................................................................................ 3

Types Of Phylogenetic Trees ......................................................................................... 3

Cladograms................................................................................................................. 5

Phylograms ................................................................................................................. 5

Phenograms ................................................................................................................ 7

References ...................................................................................................................... 8

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PHYLOGENETIC TREES

A phylogenetic tree (also phylogeny or evolutionary tree is a branching diagram or a

tree showing the evolutionary relationships among various biological species or other

entities based upon similarities and differences in their physical or genetic

characteristics. All life on Earth is part of a single phylogenetic tree, indicating

common ancestry.

In a rooted phylogenetic tree, each node with descendants represents the inferred most

recent common ancestor of those descendants, and the edge lengths in some trees may

be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes

are generally called hypothetical taxonomic units, as they cannot be directly observed.

Trees are useful in fields of biology such as bioinformatics, systematics, and

phylogenetics. Unrooted trees illustrate only the relatedness of the leaf nodes and do

not require the ancestral root to be known or inferred.

Types Of Phylogenetic Trees

This post has two motivations. First, it can serve as a future reference point if I need

to mention tree types again, and of course it can be found via search engine by

anybody who needs to look this stuff up. The second is my recent observation that

some 'evolutionary' systematists have the tendency to call all phylogenetic trees

cladograms, perhaps conflating ways of displaying evolutionary relationships with

their dubious claim that cladists do not accept the existence of ancestors. I would like

to take the opportunity to explain the different ways we can draw trees, what they

mean, and what a cladogram really is.

Phylogenetic trees are simple non-cyclical graphs connecting terminals - often species

- to show how the terminals are related. In species trees, the internal internodes are

common ancestors, and the nodes where branches meet are speciation events. In gene

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trees, they would be ancestral alleles and mutation events, respectively.

Perhaps the oldest truly phylogenetic tree was drawn by Charles Darwin in his

notebook, the famous "I think" diagram. But it was in that case an abstract model to

help him visualise for himself common descent, not yet a concrete hypothesis about

any specific organisms.

So we have a tree connecting terminals. I will further assume that the tree is outgroup-

rooted, so that it has an explicit directionality: In the following examples, the arrow of

time points from the left to the right. It could be different. All that follows would

work just as well if the trees were turned by 90 degrees and the arrow of time pointed

from bottom to top, or if the tree was circular as in the case of Darwin's sketch. What

this post is about is simply what the branch lengths on the tree diagram mean, if

anything.

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Cladograms

The least informative way of depicting a phylogenetic tree is as a cladogram. All that

it shows is how the terminals are assumed to be related, nothing else. The branch

lengths are meaningless and could be drawn with arbitrary length. But to show that

this is the case, in practice people draw them either equal length or, as in the case of

my example tree here, as all ending flush. If you are unsure if you are dealing with a

cladogram, it might be useful to check if there is a scale bar on the diagram. If there

isn't, it is probably a cladogram.However, the author may still opt to put ticks onto the

cladogram branches to illustrate where character changes took place. In that case, you

will have the same information as provided by the phylogram (see below) but without

meaningful branch lengths, so you are still dealing with a cladogram view of the tree.

If they are so uninformative, then why are cladograms used at all? As far as I can tell,

in contemporary practice it has nothing to do with cladists' supposed dogmatic

rejection of ancestors. Cladogram views are pragmatically used in phylogenetic

publications when showing true branch lengths would lead to a very untidy and

confusing looking tree or when there are no meaningful branch lengths. The latter is

the case with consensus trees summarising a number of equally parsimonious trees or

the results of bootstrapping or jackknifing. Each of the trees they are the consensus of

had branch lengths, but the consensus tree itself shows only what relationships they

agree on. It doesn't have well defined branch lengths on its own.

Phylograms

A phylogram is a phylogenetic tree whose branch lengths are proportional to how

many character changes have been inferred along the branches. If the tree you are

looking at has branches that do not end flush and a scale bar you are most likely

dealing with a phylogram.

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If the branch lengths are multiples of one, it is most parsimonious to assume that the

tree is the result of a parsimony analysis. A length of one then means that one

character change took place along the branch, two means two, and so on. If the branch

lengths are tiny fractions of one, on the order of 0.004, the tree is most likely the

result of a likelihood or Bayesian analysis. The length then means what fraction of the

characters changed along the branch. I have no idea why parsimony and model-based

phylogenies have such different conventions, but if you want to make them directly

comparable you merely have to multiply all branch lengths in the likelihood tree with

the number of characters in the original data matrix.

Note that in a phylogram view a zero length branch indicates that the common

ancestor below that branch has been reconstructed to have the same characters as the

descendant at the end of the branch. In my example tree, the common ancestor

of Planta arvensis and Planta vulgaris would have been indistinguishable

from Planta arvensis by the character set used in the analysis. An 'evolutionary'

systematist is now free to pull a "this chimpanzee over there is my ancestor" and

consider Planta arvensis to be the ancestor of Planta vulgaris. I do not think that

makes sense, but the point is this is a question of approaches to classification. It is not

a question of phylogenetic trees or cladistic analyses as such not allowing this

interpretation.

Chronograms

A chronogram is a phylogenetic tree whose branch lengths are proportional to time. If

the tree you are looking at is ultrametric, that is all branches end flush, and it has a

full-length scale bar, you may be dealing with a chronogram. If the scale bar is in

units of "Myr" or suchlike and starts with zero in the present you are definitely

dealing with a chronogram.Some chronograms may not be ultrametric because they

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contain extinct species, but the kind of fancy analysis that produces these kinds of

trees is still rarely used, not least because many groups don't have decent fossils

available anyway.

Phenograms

Another term that you may run into is phenogram, but this one is not about the

meaning of branch lengths. Many systematists do not consider clustering by similarity

to have a true phylogenetic logic whereas others disagree and consider it simply

another tool in the phylogentic toolbox. The former accordingly use phenogram to

differentiate the results of distance based, clustering, phenetic analyses from the

phylogenetic trees resulting from what they consider to be actual phylogenetic

analyses. Similarly, one would then call a group in a phenogram a cluster as opposed

to clade, reserving the latter word for phylogenetic trees.

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References

Letunic, Ivica; Bork, Peer (1 January 2007). "Interactive Tree Of Life (iTOL): an

online tool for phylogenetic tree display and annotation" (PDF).

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1367-4803. PMID 17050570. Archived (PDF) from the original on November

29, 2015. Retrieved 2015-07-21.

Ciccarelli, F. D.; Doerks, T.; Von Mering, C.; Creevey, C. J.; Snel, B.; Bork, P.

(2006). "Toward automatic reconstruction of a highly resolved tree of life"

(PDF). Science. 311 (5765): 1283–1287. Bibcode:2006Sci...311.1283C.

CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982.

S2CID 1615592.

Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.

Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette.

ISBN 978-2010035289. OCLC 461974285.

Bailly, Anatole. "Greek-french dictionary online". www.tabularium.be. Archived

from the original on April 21, 2014. Retrieved March 2, 2018.

Hodge T, Cope M (1 October 2000). "A myosin family tree". J Cell Sci. 113 (19):

3353–4. PMID 10984423. Archived from the original on 30 September 2007.