Chapter 4 Phylogenetics I

Report

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
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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 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.
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
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.
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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
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
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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.
 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
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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
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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.

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
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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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
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.
Figure 4.15 Cladograms and phylograms
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
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
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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 re-evolved 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
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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.


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
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.
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

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.
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,
but it isn’t it is an ancestral trait.

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.

In next slide relationships between
species 1,2,3 are unclear [this branching
arrangement is called a polytomy]
 Species 1 and 2 are dark and 3 is light.
 Species 01 and 02 are outgroups and
two cases (01 and 02 both dark and 01
and 02 both light) are shown.

Figure 4.27 Using outgroups to infer the ancestral state
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Scenario A requires only a single evolutionary change.
Scenarios B and C require two changes each.
Figure 4.28 Case 1: The outgroups help resolve the polytomy
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Scenario A and scenario B are equally likely so in this case outgroup
does not help resolve the polytomy.
Figure 4.29 Case 2: The outgroups do not help resolve the polytomy
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In next slide two characters with
ancestral states of A and C [outgroups
possess these states].
 Each of the two characters is used to
resolve a polytomy.

Figure 4.30 Synapomorphies at different levels
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
Phylogenetic trees are hypotheses about
evolutionary relationships among groups
.

When traits are mapped onto a
phylogeny the distribution of traits can
also be used to generate hypotheses
about the evolution of those traits.

A large number of very venomous
snakes possess highly developed venom
delivery systems that include large
grooved or hollow fangs, large venom
glands, and, of course, venom.
Figure 4.31 Snake fangs and venom
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
Snakes with such delivery systems belong
to the families: Viperidae (e.g. vipers and
rattlesnakes), the Elapidae (e.g. cobras
and mambas) and include some
members of the Atractaspididae (asps).
Cobra
http://img.gawkerassets.com/img/1
87dj0ekcb9kijpg/original.jpg
Gaboon Viper
http://pphotographyblog.blogspot.com/2011/11/veno
mous-gaboon-viper.html

For many years it was considered that
advanced venom delivery systems had
evolved independently in each family
and thus were analagous traits.

Researchers had assumed there would
be no venom without a delivery system.

More recent phylogenetic analysis and
more morphological studies however
have led to this idea being reevaluated.

For example, specialized oral secretory
grooves are found in many snakes and
numerous snakes have been discovered
to be able to produce salivary toxins in a
gland called Duvernoy’s gland.
Figure 4.32 Phylogeny of advanced snakes (Caenophidia)
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
Suspecting that if basic toxin production
capacity is widespread in snakes Bryan
Fry a herpetologist thought that toxin
production might be homologous in
snakes and had arisen early in the group.

If this was true, there might be many
snakes capable of producing toxic
venom among those that lacked a
sophisticated delivery system.

When Fry examined the salivary
secretions of the supposedly non
venomous rat snake he discovered that
the commonest peptide in the saliva
was a close homologue of the threefinger toxins (3FTX), potent neurotoxins,
that elapids produce.

Having discovered venom in supposedly
non-venomous snakes Fry wondered if
snake venom might be homologous with
the venom found in Gila Monsters (a
lizard) which would imply venom had
been inherited from the common
ancestor of both.

If venom evolved early, other lizard
descendents of the common ancestor
of snakes and gila monsters might also
produce venom.

Fry produced a phylogenetic tree to
identify such potentially venomous lizards
Figure 4.33 Venomousness as a homologous trait between snakes and Gila monsters
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
Fry discovered nine genes for toxins that
were shared between snakes and lizards.

Also found an Australian lizard that
produces a toxin otherwise found only in
rattlesnake venom and that some
monitor lizards produce a toxin that
reduces blood clotting and greatly
lowers blood pressure.

The significance of Fry’s work is that it
shows how the mapping of traits on
phylogentic trees may lead to
unexpected research directions and
reveal hidden characteristics of
organisms.

Vestigial traits (those with no known
current function but that were important
in the evolutionary past) are often useful
in constructing phylogenetic trees.

For example, the nictitating membrane
in birds and the plica semilunaris indicate
common descent from an ancestor that
had a nictitating membrane that
became vestigial in mammals.
Figure 4.36 The nictitating membrane
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
Vestigial traits provide a test of Darwin’s
theory of evolution by common descent.

If organisms evolved from common
ancestors via a branching process we
would expect to see vestigial traits only
in those organisms that share a common
ancestor that existed after the trait
evolved.

For example we would expect perhaps
to find vestigial limbs in some
vertebrates, but not in fish or annelid
worms.
Figure 4.38 Common ancestry predicts where we should find vestigial limbs
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Find the most recent common ancestor of species 3,5 and 6
Review Question 4.1
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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

(ii) 1, 6, 5, 4, 3, 2

(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 fraits do (i) sharks
(ii) turtles have?
Review Question 4.10
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
Shark : jaws

Turtle: jaws, dentary bone, lungs.

Do the other problems in your text!

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