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Phylogene)c

Trees
Chapter 8

Reading an evolu)onary tree

Werdelin, Lars, and


Lennart Olsson. "How the
leopard got its spots: a
phylogene)c view of the
evolu)on of felid coat
pa>erns." Biological
Journal of the Linnean
Society 62.3 (1997):
383-400.

There are dierent styles out there

Any tree is an hypothesis

Werdelin and Olssons tree

Texts compila)on from a couple of


subsequent papers

Clearly there is a bit of an art to this..


so, lets walk
through
this....

Clearly there is a bit of an art to this..


This is an evolu)onary
novelty, an apomorphic
character

Everyone has this feature:


plesiomorphic (shared by all,
therefore precedes the clade)

We assume:
1. We know what
the ancestral
state was.
2. New characters
evolved only
once
3. No characters
have been lost
secondarily

Clearly there is a bit of an art to this..


Unique apomorphies
dene clades consis)ng of
individual species
A clade is a taxonomic
unit that includes all
descendants of a
common ancestor and
that ancestor and is thus
monophyle8c

Clearly there is a bit of an art to this..


Shared apomorphies
(synapomorphies) dene
clades with more than one
species
In this case we have a clade
consis)ng of two sister
species

Clearly there is a bit of an art to this..


Our next clade
consists of a
grouping that
includes the
sister species
and one other
that shares the
orange mask
with them.

Some terms....

Some terms....
It is possible to make taxonomic
mistakes. Here are a couple of
common ones.

If you were to make a


grouping consis)ng of all
light-tailed birds, you will
have made a paraphyle8c
grouping.
A paraphyle8c grouping
excludes one of the
descendants of the common
ancestor

Some terms....
It is possible to make taxonomic
mistakes. Here are a couple of
common ones.
Say, pink polka dots evolved
independently in a couple of
species (homoplasy!)
If you were to make a
grouping consis)ng of all
pink do>ed birds, you will
have made a polyphyle8c
grouping.
A polyphyle8c grouping excludes more
than one group of the common ancestors
descendants and the common ancestor!

Heres some more familiar cri>ers..

We have some uncertainty here: this is a polytony

What causes uncertainty?


1.Characteris8cs of common ancestor
may not be completely known
2.Similar adapta)ons can evolve
independently (convergence or
homoplasy)
3.Evolu)onary novel)es can appear
and then subsequently be lost

Common ancestor?

The classes of mollusk diverged so


long ago that the characteris)cs of
the common ancestor is a ma>er of
some conjecture.

What causes uncertainty?


1.Characteris)cs of common ancestor
may not be completely known
2.Similar adapta8ons can evolve
independently (convergence or
homoplasy)
3.Evolu)onary novel)es can appear
and then subsequently be lost

Convergence

Convergence

A li>le less obviously


dierent...Herman
Melville classied
whales as sh!

Convergence

Ocean rocksh (top)


are not closely
related to yellow
perch (below).

What causes uncertainty?


1.Characteris)cs of common ancestor
may not be completely known
2.Similar adapta)ons can evolve
independently (convergence or
homoplasy)
3.Evolu8onary novel8es can appear
and then subsequently be lost

Loss of features

Secondary
loss of
wings in
Kiwis

What causes uncertainty?


1.Characteris8cs of common ancestor
may not be completely known
2.Similar adapta8ons can evolve
independently (convergence or
homoplasy)
3.Evolu8onary novel8es can appear
and then subsequently be lost
...given this, how do we sort things
out?

Inferring a tree using parsimony


Parsimony is one
method commonly
used. There are
others!

Here we have three ungulate


species with an unknown common
ancestor.

Inferring a tree using parsimony

The arrows represent


shared features.
Note that we dont
have the simple
situa)on that we
enjoyed with the
birds.

Inferring a tree using parsimony


The rst stage is to
dene an outgroup. A
species that will not be
part of our tree that we
can assume retains
some of the ancestral
characters. (note:
selec)ng the proper
outgroup is hard
some)mes!)
These are the
ingroup!

Inferring a tree using parsimony

We then generate all (ideally) possible groupings and ask


what needed to happen for this classica)on to be
correct?

Inferring a tree using parsimony


For example,
consider
hypothesis 1
There are a
number of
evolu8onary
transi8ons
that have to
have
occurred to
produce this
tree

Inferring a tree using parsimony

Inferring a tree using parsimony

As it turns out,
hypothesis 2 requires
the fewest transi)ons
and is therefore the
most parsimonious
tree!

Using molecular data


A strict parsimony analysis
using morphological data
indicated that whales are a
sister group to even-toed
ungulates.
However the shape of a limb
bone (the astragalus) is the key
feature dening these
ungulates. Modern whales
have lost that feature en)rely.
Oleary and Geisler (1999)

Using molecular data


If morphological evidence is not available,
molecular data can s)ll be used.

60 nucleo)des of the beta casein gene

Using molecular data


Keep in mind:
Pros:
- easy and cheap to generate a lot of sequence
data. Many more characters to use for inferring
rela)onships!
- possible to predict how dierent sequences
evolve through )me.

Cons:
- only useful for living species (or recently ex)nct).
- only 4 character states (A, C, G, and T): hard to
iden)fy homoplasies.

Using molecular data

You can use each site in the


sequence as a separate character to
look for synapomorphies

Using molecular data

Three changes required at site 166!

Using molecular data

Four changes required at site 166!

Using molecular data

The tree which places whales as a


sister group to hippos, is most
parsimonious (six changes versus
nine)

Other ways of es)ma)ng trees


1.Parsimony: tree requiring the fewest
changes
2.Maximum Likelihood: more
complicated, but tree that makes the
dataset most likely is selected
3.Neighbor Joining: connects taxa that
are most similar

Other ways of es)ma)ng trees

1) Parsimony

2) Maximum
Likelihood

3) Neighbor Joining

So, how is this useful?


Phylogene)c inference methods are used
to address a number of ques)ons

Canine
transmissable
venereal tumor:
Are tumor cells
transmissable?

So, how is this useful?

Pre-release detec8on of a biocontrol agent: combining independent and public DNA sequences to iden8fy the rst
North American record of Aulacidea pilosellae
Chandra E. Moat1* and M. Alex Smith2
1 Department of Biology, University of Bri)sh Columbia, Okanagan Campus, 3333 University Way, Kelowna, Bri)sh
Columbia, Canada, V1V 1V7 (chandra.moat@gmail.com) 506-452-6026

Mid Term next!


February 3