Inferring phylogenies:

1
Tracing evolutionary history

• Inferring phylogenies
• closely related species should have traits in
  common
• inherited from their common ancestor (homology)
• informative traits are shared derived traits
• (homologies that are not the ancestral state)
• identifying shared derived traits requires
  determining
• homologies
• ancestral vs. derived states (direction of
  change)

2
outgroup provides information about
ancestral state roots the tree
Which traits are ancestral? Which traits are
derived?
3
3 possible trees what changes are implied?
which traits are informative? which tree is
best?
parsimony
4
Use parsimony to build a phylogeny
outgroup? homologies?
ancestral vs. derived states? shared derived
traits?
5
Tracing evolutionary history

• Inferring phylogenies
• closely related species should have traits in
  common
• inherited from their common ancestor (homology)
• informative traits are shared derived traits
• (homologies that are not the ancestral state)
• complications arise when traits are shared for
  other reasons

6
convergence
7
Shared traits
1) Homology
8
Shared traits
1) Homology 2) Convergent evolution
9

• long head?
• hair?
• smile?
• ears?
• nose?

H shared derived trait H convergence
10
Same pattern can reflect different evolutionary
histories
convergent evolution of hair
reversal to hairless
H
H
OR
LH
LH
SM
N
SM
N
E
E
11
Phylogenetic analysis of molecular data
12 A T T T T
12
What are phylogenies good for?

• Tracing evolutionary relationships
• e.g. disease transmission (problem set 4)
• coevolution (in text)
• tree of life
• adaptive radiation

13
Evolutionary relationships the tree of life
14
Evolutionary relationships the tree of life
15
Evolutionary relationships the tree of life
16
Evolutionary relationships adaptive radiation
on islands
17
What are phylogenies good for?

• Tracing evolutionary relationships
• e.g. disease transmission (problem set 4)
• coevolution (in text)
• tree of life
• adaptive radiation
• Studying trait evolution
• requires independent data
• e.g. origin of whales (in text)
• evolution of viviparity

map morphological traits onto molecular phylogeny
18
Trait evolution origin of whales
19
Trait evolution evolution of viviparity in
Sceloporus
Sceloporus (a lizard genus) some
populations lay eggs, others bear live young