Transcript Chapter 4 Phylogenetics (in class version)

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Read Chapter 4 of Zimmer and Emlen
text
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All living organisms are descended from
a common ancestor.
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If we can construct the evolutionary
relationships between groups we can
gain insight into history of evolutionary
change.
Figure 4.2 Phylogenies at different scales
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Phylogeny is the study of the branching
relationships between populations over
evolutionary time.
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A phylogenetic tree is built up by
analyzing the distribution of traits across
populations.
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A trait (or character) is any observable
characteristic of an organism (e.g.
anatomical features, behaviors, gene
sequences)
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Traits are used to infer patterns of
ancestry and descent among
populations.
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These patterns are then depicted in
phylogenetic trees.
Mapping traits onto trees allows us to study the
sequence and timing (history) of evolutionary events.
Figure 4.4 Traits and trees
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Remember phylogenetic trees are
hypotheses about the evolutionary
relationships between groups.
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New evidence can be used to test a
tree.
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Each branch tip represents a taxon (a
group of related organisms).
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Interior nodes (where branches meet)
represent common ancestors of the taxa
at the ends of the branches.
Figure 4.6 Interior nodes represent common ancestors
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Tree format
Figure 4.5 Two equivalent ways of drawing a phylogeny
Ladder format
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
Remember there are multiple different
ways to depict relationship s in a
phylogenetic tree.
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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
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Figure 4.8 Rotating phylogenetic trees
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We build phylogenetic trees to use to
figure out evolutionary relationships
between taxa and to identify “natural”
groupings among taxa, those that reflect
their true evolutionary relationships.
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A key idea is that natural groupings
called clades are monophyletic groups.
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Clade: a group of taxa that share a
common ancestor.
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Monophyletic group: consists of an
ancestor and all of the taxa that are
descendants of that ancestor.
Clades are monophyletic groups
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In the next slides elephants, manatees
and hyraxes plus their common ancestor
form a monophyletic group.
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Similarly tapirs, rhinoceroses and horses
plus their common ancestor form
another monophyletic group.
Figure 4.11 Monophyletic clades of mammals
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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.
 “poly”
means many. Hence many
origins in this case.
E.g. Referring to Elephants,
rhinos, and hippos
as“pachyderms.”
Pachyderms are a polyphyletic
group because each group
evolved thick skin separately.
Elephants, rhinos and hippos would form
polyphyletic group
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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.
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An example of a paraphyletic group
among vertebrates is“fish.”
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All tetrapods (four-legged animals) are
descended from lobe-finned 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
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Trees we’ve seen so far have been
rooted and these trees give a clear
indication of the direction of time.
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However, computer programs that
produce phylogenetic trees often
produce unrooted trees.
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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
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
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
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
There is only one true tree of evolutionary
relationships.
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To identify that tree we must root the
tree correctly.
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Using an outgroup is the easiest way to
root a tree.
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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.
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The outgroup lets us know if a character
state within the ingroup is ancestral or
not.
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If the outgroup and some of the ingroup
possess a character state then that
character state is considered ancestral.
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Consider an unrooted tree of four
magpie species.
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To root the tree we need a group that
split off earlier from the lineage that led
to these four species of magpies.
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Azure-winged magpie is a suitable
outgroup. One this is added to the
unrooted tree we can root the tree.
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In some phylogenetic trees branches are
drawn with different lengths.
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In these trees branch lengths represent
the amount of evolutionary change that
has occurred in that lineage.
Figure 4.15 Cladograms and phylograms
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Homologous traits are 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
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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.
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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
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Figure 4.23 Convergent evolution in body forms
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When building a phylogenetic tree we
must use characters inherited from
ancestors.
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Such a character found in two or more
taxa is referred to as a shared derived
character or synapomorphy. Example B
on the next slide is a synapomorphy.
Figure 4.24 Derived traits
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
If all shared traits were shared derived
traits tree-building would be
straightforward.

However, many traits are not e.g.
analagous traits
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We want to avoid including analagous
traits when constructing phylogenetic
trees because they can mislead us.
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An analagous trait in a tree is referred to
as a homoplasy.
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Homoplasy: character state similarity not
due to common descent
› Convergent evolution: independent
evolution of similar trait
› Evolutionary reversals: reversion back to an
ancestral character state
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In the next slide (A) we do not know the
ancestral color state so we have to
represent it as unresolved (a polytomy).
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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.
Figure 4.25 An example of homoplasy
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
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.
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In the next slide, 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.
Figure 4.26 Derived traits and symplesiomorphy
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Several strategies exist to limit
homoplasies and synapomorphies.
 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.
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The mammalian order Carnivora
includes cats, dogs and other familiar
predatory mammals.
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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.
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To analyze relationships among 10
species of carnivores we construct a
data matrix of the distribution of a dozen
traits across these taxa.
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Using synapomorphies to identify clades
we can construct a phylogentic tree.
The numbers on the tree correspond to
the character states in the matrix.
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Some clades in tree are clearly defined
but others not so well.
One point where relationships are unresolved.
Such uncertain branching is called a polytomy.
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If we add a 13th trait to the data matrix
we may be able to resolve the polytomy.
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However, sometimes additional data
doesn’t help or introduces more
uncertainty.
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Absence of a lower premolar is a
character shared by cats, hyenas and
otters, but that doesn’t fit with our
previous tree.
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Most likely this is a homoplasy (and the
tooth was lost independently in different
lineages).
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In reality phylogentic analyses inevitably
involved dealing with conflicting
evidence.
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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.
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Applying the principle of phylogeny to a
larger (20 character) matrix of data reveals
three equally parsimonious phylogenetic
trees 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 can be constructed that
represents a “best estimate” of the true
tree.

Three equally parsimonious trees (above)
Consensus tree (below).
Archaeopteryx, discovered in 1860, dates to 145 mya
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Traits often change function over time.
Phylogenies allow us to track such
changes over evolutionary time.
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The oldest known fossil bird is
Archaeopteryx (145mya), which
possesses a suite of both avian and
reptilian characteristics.
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Birds today are defined by the possession
of feathers and obviously they are used
to fly, but phylogenetic analysis shows
that this was not the original function of
feathers as feathers are present in nonflying ancestral groups.

Phylogenetic analysis also reveals that
birds evolved from dinosaurs.
Velociraptor ulna with
bumps resembling quill
nodes in living birds
(A+B)
Turkey Vulture ulna with
feathers attached to
quill nodes (C-F)

Feathers must have played a different
role in dinosaurs than flight.

Most likely they served as insulation and
for display (functions they are still used
for today in birds).
Exaptation: natural selection co-opts a trait for a new function
Find the most recent common ancestor of species 3,5 and 6
Review Question 4.1
Evolution, 1st Edition
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What would this tree look like if it were rotated around
(i) Node A (ii) Node B (iii) both nodes A + B?
Review Question 4.3
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
(i) 1, 3, 2, 4, 5, 6
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(ii) 1, 6, 5, 4, 3, 2
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(iii) 1, 6, 5, 4, 2, 3
Which pairs of species are more closely related?
(i) 4&5 or 5&7?
(ii) 1&2 or 2&7?
(iii) 3&5 or 2&4?
Review Question 4.5
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(i) 5&7
 (ii) 2&7
 (iii) 3&5

According to the diagram which of these five traits do (i) sharks
(ii) turtles have?
Review Question 4.10
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
Shark : jaws
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Turtle: jaws, dentary bone, lungs.
2
3
1
A
4
5
6
Rooting the tree at A draw the rooted tree for the
above unrooted tree.
Answer
4
5
6
1
2
A
3
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Do the other problems in your text!