
Read Chapter 4
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.


Phylogeny 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.
Figure 4.2 Phylogenies at different scales
Evolution, 1st Edition
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
A trait (or character) is any observable
characteristic of an organism.

Could 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.
Figure 4.4 Traits and trees
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
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.

Each branch tips 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.
Figure 4.6 Interior nodes represent common ancestors
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

Phylogenetic trees are generally drawn
in either a Tree format or a Ladder
format.

They convey the same information
about the relatedness of taxa
Figure 4.5 Two equivalent ways of drawing a phylogeny
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

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.
Figure 4.7 Rotating around any node leaves a phylogeny unchanged
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company
Figure 4.8 Rotating phylogenetic trees
Evolution, 1st Edition
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
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 slides 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.
Figure 4.11 Monophyletic clades of mammals
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

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. Referring to Elephants,
rhinoceroses and hippopotamuses as
“pachyderms.” Pachyderms are a
polyphyletic group because each
group evolved thick skin separately.
Elephants, rhinos and hippos would form
polyphyletic group
Evolution, 1st Edition
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
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 (four-legged
animals) are descended from lobefinned fish ancestors, but are not
considered “fish” hence “fish” is a
paraphyletic group because the
tetrapods are excluded.
Figure 4.12 Phylogenetic tree of the vertebrates
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

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.
Figure 4.13 Unrooted tree of proteobacteria
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

An unrooted tree can be rooted at any
point and depending where it is rooted
very different rooted trees will be
produced.
Figure 4.14 Rooted trees from unrooted trees
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

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
unrooted outgroup. One this 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.
Figure 4.15 Cladograms and phylograms
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

Phylogenetic trees can be used to
generate hypotheses about the
evolution of traits.

This is done by mapping the trait states
on the tree and trying to reconstruct the
simplest (most parsimonious) explanation
that accounts for the observed
distribution of traits.

Light sensitive pigments called opsins are
responsible for color vision. Humans
have three different cone opsins.

Other vertebrates have as many as four
or as few as two opsins.

By mapping the presence or absence of
different opsins onto a phylogenetic tree
of vertebrates we can attempt to
reconstruct the evolutionary history of
color vision in these vertebrates.
Figure 4.20 Evolution of tetrapod visual opsins
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company
It is clear that the ancestral trait is to
possess four opsins (as both birds and
reptiles do).
 The mammal lineage appears to have
lost two opsins (probably because the
animals were nocturnal) and one opsin
was later reevolved on the lineage
leading to old world primates and
humans.

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.

Figure 4.21 Homologous and analogous traits
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company
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.
Figure 4.22 Convergent evolution for coloration
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company
Figure 4.23 Convergent evolution in body forms
Evolution, 1st Edition
Copyright © 2012 W.W. Norton & Company

We want to avoid including analagous
traits when constructing phylogenetic
trees because they can mislead us.

An analagous trait in trees is referred to
as a homoplasy.

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.