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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.2 Phylogenies at different scales
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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.
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A trait (or character) is any observable characteristic of an
organism. Could be anatomical features, behaviors, gene sequences,
etc.
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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.
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Figure 4.4 Traits and trees
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Its 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.
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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.
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Figure 4.6 Interior nodes represent common ancestors
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Phylogenetic trees are generally drawn in either a Tree format
or a Ladder format. They convey the same information about the
relatedness of taxa
Slide 14
Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.5 Two equivalent ways of drawing a phylogeny
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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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.7 Rotating around any node leaves a phylogeny
unchanged
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.8 Rotating phylogenetic trees
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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.
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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.
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Clades are monophyletic groups
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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.
Slide 23
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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.
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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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
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 would be
fish. All of the 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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.12 Phylogenetic tree of the vertebrates
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Trees weve 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.
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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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
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.
Slide 37
Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.14 Rooted trees from unrooted trees
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E.g. Using root A (the red dot) in previous slide. (1) Draw
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).
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(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
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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.
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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. 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. 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. In these trees the branch lengths represent the amount of
evolutionary change that has occurred in that lineage.
Slide 49
Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.15 Cladograms and phylograms
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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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
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.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.22 Convergent evolution for coloration
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Figure 4.23 Convergent evolution in body forms
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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 on the next slide 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
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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.
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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). 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.
Slide 62
Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
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. 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 isnt. Instead dark coloration is an ancestral trait and the
correct phylogeny is shown in B.
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
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. 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. Some clades in tree are clearly
defined but others not so well.
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One point where relationships are unresolved. Such uncertain
branching is called a polytomy.
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If we add a 13 th trait to the data matrix we may be able to
resolve the polytomy. However, sometimes additional data doesnt
help or introduce more uncertainty.
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Absence of a lower premolar is a character shared by cats,
hyenas and otters, but that doesnt fit with our previous tree. 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. 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.
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Three equally parsimonious trees (above) Consensus tree
(below).
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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. 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 non- flying ancestral groups. Phylogenetic analysis also
reveals that birds evolved from dinosaurs.
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Velociraptor ulna with bumps resembling quill nodes in living
birds (A+B) Turkey Vulture ulna with feathers attached to quill
nodes (C-F)
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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).
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Exaptation: natural selection co-opts a trait for a new
function
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Review Question 4.1 Find the most recent common ancestor of species
3,5 and 6
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Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Review Question 4.3 What would this tree look like if it were
rotated around (i) Node A (ii) Node B (iii) both nodes A + B?
Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Review Question 4.5 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?
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(i) 5&7 (ii) 2&7 (iii) 3&5
Slide 92
Evolution, 1st Edition Copyright 2012 W.W. Norton & Company
Review Question 4.10 According to the diagram which of these five
traits do (i) sharks (ii) turtles have?
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Shark : jaws Turtle: jaws, dentary bone, lungs.
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2 3 1 4 5 6 A Rooting the tree at A draw the rooted tree for
the above unrooted tree.