Phylogentic Trees
All living organisms are related to each other having descended from common ancestors.
Understanding the evolutionary relationships between groups enables us to reconstruct the tree of life
and gain insight into history of evolutionary change.
Phylogenetics is the study of the branching relationships between populations over evolutionary time.
A phylogenetic tree is built up by analyzing the distribution of traits across populations.
A trait (or character) is any observable characteristic or feature of an organism. Traits can be
anatomical features, behaviors, gene sequences, etc. Traits are used to infer patterns of ancestry and
descent among populations. These patterns are then depicted in phylogenetic trees.
By mapping other traits onto trees it is possible to study the sequence and timing (history) of
evolutionary events.
It’s important to bear in mind that phylogenetic trees are hypotheses about the evolutionary
relationships between groups. When additional evidence is acquired it can be used to test a tree.
How to read a phylogenetic tree
Each branch tip represents a taxon (a group of related organisms). Interior nodes (where branches
meet) represent ancestral populations that are the common ancestors of the taxa at the ends of the
branches.
Phylogenetic trees are generally drawn in either a Tree format or a Ladder format. They convey the
same information about the relatedness of taxa
It is important to remember that a particular set of evolutionary relationships can be depicted in
multiple different ways in a phylogenetic tree.
Any node in a phylogenetic tree can be rotated without altering the relationships between taxa.
“Whether a phylogeny is represented as a tree (A) or ladder (B), one can rotate at any node—or any
combination of nodes—without changing the structure of the tree. Thus the leftmost tree shown in each
row is identical from a phylogenetic perspective to the trees shown to the right. The colors indicate the
nodes that were rotated in each case.” Zimmer and Emlen Evolution 2nd ed.
The purpose of building phylogenetic trees is to use them to figure out the evolutionary relationships
between taxa and to identify “natural” groupings among taxa, those that reflect their true evolutionary
relationships.
A key idea is that natural groupings called clades are monophyletic groups. Clade: a group of taxa that
share a common ancestor.
Monophyletic group: consists of an ancestor and all of the taxa that are descendants of that ancestor.
In the next images elephants, manatees and hyraxes plus their common ancestor, form a monophyletic
group. Similarly tapirs, rhinoceroses and horses plus their common ancestor form another
monophyletic group.
Polyphyletic group. A taxon is polyphyletic if it does not contain the most recent common ancestor of
all members of the group.
A polyphyletic group requires the group members to have each had an independent evolutionary origin
of some diagnostic feature. E.g. if we refer to elephants, rhinoceroses and hippopotamuses as
“pachyderms” then we have created a polyphyletic group. Pachyderms are a polyphyletic group
because each group evolved thick skin separately. (see image on previous page)
Paraphyletic group.
A taxon is paraphyletic if it includes the most recent common ancestor of a group and some but not all
of its descendents.
An example of a paraphyletic group among vertebrates would be “fish.” All of the tetrapods (fourlegged animals) are descended from lobe-finned fish ancestors, but are not considered “fish” hence
“fish” is a paraphyletic group because the tetrapods are excluded.
Rooted vs. unrooted trees
The trees we’ve seen so far have been rooted and these trees give a clear indication of the direction of
time. However, computer programs that produce phylogenetic trees often produce unrooted trees.
In an unrooted tree, branch tips are more recent than interior nodes, but you cannot tell which of
multiple interior nodes is more recent than others.
“An unrooted tree illustrates the evolutionary relationships among the proteobacteria, a large group of
bacteria including human- associated species such as E. coli and nitrogen- fixing species such as A.
tumefaciens. Here we do not have enough information to say whether, for example, interior node A
represents a more recent or less recent population than does interior node B. Adapted from Shin et al.
(1993).” Zimmer and Emlen Evolution 2nd ed.
An unrooted tree can be rooted at any point and depending where it is rooted very different rooted
trees will be produced.
How to convert an unrooted tree to a rooted tree
E.g. Use root A (the red dot) in previous picture to root the tree.
(1) Draw a vertical line leading to A and horizontal line leading to A (making a T shape). Mark A at
intersection of the T.
(2) Remember you also want the tree to bifurcate (split into two branches
(3) Looking at the unrooted tree because A is the root and splits the tree into two halves: one branch of
the rooted tree leads to species 4&5 and the other branch to species 1,2&3.
(4) Draw vertical branch that splits into two and indicate species 4&5. (that completes that side of tree).
(5) looking at the left side of the unrooted tree we can see it splits into two branches. One branch leads
to species 3 and the other branch leads to species 1&2.
(6) Draw a bifurcation (or split) where one branch tip is labelled 3 and the other branch leads to a
second split which are labeled 1&2
Obviously, there is only one true tree of evolutionary relationships and we would like to identify that
tree. To do that we need to root the tree correctly. One of the easiest ways to root a tree is to use an
outgroup to root it.
An outgroup is a close relative of the members of the ingroup (the various species being studied) that
provides a basis for comparison with the others.
The outgroup lets us know if a character state within the ingroup is ancestral or not.
If the outgroup and some of the ingroup possess a character state then that character state is
considered ancestral.
Consider an unrooted tree of four magpie species.
To root the tree we need a group that split off earlier from the lineage that led to these four
species of magpies. Azure-winged magpie is a suitable outgroup. One this is added to the
unrooted tree we can root the tree.
In some phylogenetic trees branches are drawn with different lengths.
In these trees the branch lengths represent the amount of evolutionary change that has occurred in that
lineage.
Building a phylogenetic tree--Homologous and analagous traits
Homologous traits are those derived from a common ancestor. E.g. all mammals possess hair. This is a
homologous trait all mammals share because they inherited it from a common ancestor.
Analagous traits are shared by different species not because they were inherited from a common
ancestor but because they evolved independently.
Divergent evolution occurs when closely related populations diverge from each other because selection
operates differently on them.
Such new species will possess many homologous traits in common.
Analagous traits are the result of a process of convergent evolution whereby the same or similar
solution to an evolutionary problem is converged upon by different organisms independently of each
other.
When building a phylogenetic tree we want to use characters inherited from ancestors. Such a
character found in two or more taxa is referred to as a shared derived character or synapomorphy.
Example B below is a synapomorphy.
If all shared traits were shared derived traits tree-building would be straightforward. However, many
traits are not e.g. analagous traits. We want to avoid including analagous traits when constructing
phylogenetic trees because they can mislead us.
An analagous trait in a tree is referred to as a homoplasy. Homoplasy: character state similarity not due
to common descent. Other causes of similarity are:
Convergent evolution: independent evolution of similar trait.
Evolutionary reversals: reversion back to an ancestral character state.
In the next image (A) we do not know the ancestral color state so we have to represent it as unresolved
(a polytomy). If we know that our phylogenetic tree (B) correctly indicates the relationships between
taxa then we know that dark coloration is a homoplasy having evolved independently twice.
Another way in which we could be mistaken is if a new trait arises in a lineage and is not shared with
other taxa. This is called a symplesiomorphy.
In the next image, light coloration has recently arisen in taxon 3. If we thought dark coloration was a
shared derived character we would group species 1+2, (as in A) but it isn’t. Instead dark coloration is an
ancestral trait and the correct phylogeny is shown in B.
Several strategies exist to limit homoplasies and synapomorphies when constructing a phylogenetic
tree.
1. use traits that change relatively slowly in evolutionary time
2. use many traits to build the tree
3. use multiple outgroups to help identify ancestral values of traits.
In reality phylogentic analyses inevitably involved dealing with conflicting evidence. The most
commonly applied rule to resolve conflict is the principle of parsimony – choosing the simplest
explanation i.e., the phylogeny that requires the fewest trait changes to construct it.
The mammalian order Carnivora includes cats, dogs and other familiar predatory mammals.
Building a phylogeny of Carnivora
Certain synapomorphies such as carnassial teeth (enlarged side teeth used to shear meat) unite the
group, but there has been debate about relationships within the group.
To analyze relationships among 10 species of carnivores we construct a data matrix of the distribution of
a dozen traits across these taxa.
 Using synapomorphies to identify clades we can construct a phylogentic tree. The numbers on
the tree correspond to the character states in the matrix.
 Some clades in tree are clearly defined but others not so well.
One point in the figure above where relationships are unresolved is where the line from raccoons, the
line from dogs and the line from the large group including seals, walrus, sea lions, bears and otters all
come together. Such uncertain branching is called a polytomy.
One good strategy toresolve polytomys is to increase the amount of data being analysed.
Applying the principle of phylogeny to a larger (20 character) matrix of data reveals three equally
parsimonious phylogenetic trees (A on next page) that differ somewhat from each other. Notice,
however, that certain portions of the tree are consistent across all three trees. Using some
mathematical analysis a consensus tree (B) can be constructed that represents a “best estimate” of the
true tree.