Phylogenetics
We’re now moving into the realm of macroevolution: relationships among
divergent species…
Monophyletic
Paraphyletic group
Phylogeny (=tree): graphical representation of the historical relationships
among species or higher taxonomic groups
A
B
D
A
C
B
speciation
C
speciation
A and B are sister group to
C and D: diverged from
shared common ancestor
D
speciation
These phylogenies show the same relationship.
Reptiles are paraphyletic
Vertebrate phylogeny:
Monophyletic: group derived from one common ancestor and that
represents all descendents of that common ancestor (= clade).
Paraphyletic: group derived from one common ancestor and that
represents some but not all descendents of that common
ancestor.
Polyphyletic: group does not share a single common ancestor in the time
frame under consideration.
Basic idea of phylogenetic inference: traits (=characters) that
are more similar reflect more recent common ancestry
Homology: trait similarity reflecting shared common ancestry
ray finned fish
lungfish
e.g.,
salamanders
Same underlying skeletal elements
Mammalian forelimb
Synapomorphy:
shared, derived form
of a trait
frogs
lizards
(e.g., human/cat:
forelimb bone ratio)
snakes
turtles
Reptiles
crocodiles
birds
mammals
human
cat
whale
bat
Autapomorphy:
derived form of a
trait unique to a
group (e.g., bat
phalanges)
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Nested synapomorphies define a phylogeny
For a homologous gene, mutations define synapomorphies:
e.g., portion of Cytochrome c gene sequence…
Synapomorphy: shared, derived form of a trait
Autapomorphy: derived form of a trait unique to a group
(not phylogenetically informative)
Other birds
Species 1
Species 2
Species 3
Perching birds (passerines)
Finches
T at position 7:
synapomorphy for
species 2/3
12 tail feathers, thick beak: finch synapomorphy
3 front toes, 1 back toe: passerine synapomorphy
Phylogeny defined solely by synapomorphies: cladogram
Synapomorphy: shared, derived trait…
We’ve already seen an example of outgroup rooting:
Q: For a variable trait, how do you know which form is derived?
Outgroup comparison demonstrates that female preference predates long tails.
A: Outgroup comparison: compare those species of interest
(=ingroup) to closely related species (=outgroup)
Female preference for long tails (P+) is a
synapomorphy that groups species 1 and 2.
The outgroup roots the tree: indicates polarity (direction) of change:
ingroup
a*
a*
a
Intersexual selection: sensory bias explanation for female choice
outgroup
a
Species 1
a
Species 2
a  a*
Polytomy
(unresolved branch)
a
Outgroup tells us that a* is derived, so a* species are a monophyletic group.
P+: females prefer long tails
T+: males possess long tails
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Homology vs. Homoplasy
Homoplasy: trait similarity that does not reflect common ancestry
Homoplasy: trait similarity that does not reflect common ancestry:
Can arise by evolutionary convergence or evolutionary reversal
1) Evolutionary reversal back to the ancestral form:
Fish eye
Arises by:
Octopus eye
Homoplasy: trait similarity that does not reflect common ancestry:
DNA sequences: only 4 variants, so homoplasy easily obscures
divergence.
Especially for mutational hotspots: repeated evolution at the same sites
Arises by:
2) Evolutionary convergence: independent evolution of a derived trait
% divergence
ATTGCTATTC ATTGCTTTTC ATTGCTCTTC ATTGCTTTTC
T to C
ATTGCTCTTC
T to C
# nucleotide changes
To
sp. 1
sp. 2
ATCGATGCAC
TTCGATGCAG
20%
2
T1
sp. 1
sp. 2
ATCGATGCAC
GTCGATGCAC
10%
2+2=4
At time To: 2 substitutions = 20% divergence
At time T1: there have been 2 more substitutions, but now
there is only 10% divergence
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DNA sequences: multiple hits (mutations) over enough time will
ultimately obscure any phylogenetic signal.
% sequence divergence
II
e.g., Dog-like mammalian carnivores
Marsupial:
Varies by gene, depending on mutation rate
I
Analagous features arise through evolutionary convergence
Placental:
III
75%
Time since divergence from common ancestor
Multiple mutations
will ultimately
randomize
sequences: for 4
nucleotides, expect
25% similarity by
chance alone
Tasmanian wolf
(Thylacinus cynocephalus)
Dingo (Canis lupis)
Placental
mammals
I. Divergence obeys molecular clock: phylogenetic inference straightforward
II. Need statistical correction for multiple hits
III. Saturation: no phylogenetic information
Evolutionary convergence in beak shape: distantly related
nectar feeding birds
Marsupials
Evolutionary convergence in plant form: cool tropics
Colombia
South Africa
Hawaii
Tasmania
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Evolutionary convergence in plant form: arid climate
Avoiding erroneous inferences caused by homoplasy…
1. Examine traits at more than one developmental stage.
e.g., As adults, limpets and barnacles are superficially similar, but larval
anatomy reveals true phylogenetic relationship
barnacle (crustacean)
limpet (mollusk)
Milkweed family
Spurge family
Cactus family
(Asclepiadaceae)
(Euphorbiaceae)
(Cactaceae)
crab (crustacean)
Mollusks
Traits evolving under strong
natural selection may be
most likely to show
evolutionary convergence
crabs
barnacle
(plus convergence to look/smell like carrion)
Avoiding erroneous inferences caused by homoplasy…
2. Look at many traits (=characters). Phylogenetic signal
from homologous traits will drown out ‘noise’ from homoplasy
Looking at multiple characters…
Methodology for distinguishing homology from homoplasy:
The key:
Synapomorphies reflecting homology require only 1 change on a
phylogeny, whereas homoplasies require 2 or more changes.
e.g., for a known phylogeny:
if nucleotide position 1: G to A is a synapomorphy reflecting homology
Fish eye
Octopus eye
Sp. 1
Sp. 2
A
A
Sp. 3
G
Sp. 4
G
Outgroup
G
G to A
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Methodology for distinguishing homology from homoplasy:
Synapomorphies reflecting homology require only 1 change on a
phylogeny, whereas homoplasies require 2 or more changes.
So…
If we look at many characters, the phylogeny that requires the
fewest number of changes (=steps) is the most probable true
phylogeny.
= ‘Maximum parsimony’ criterion (principle of Occam’s razor)
e.g., for a known phylogeny:
if nucleotide position 1: G to A is a synapomorphy reflecting homology
and position 2: T to C is a homoplasy
Sp. 1
AT
Sp. 2
Sp. 3
AC GT
T to C
Sp. 4
GC
e.g., for three species (ingroup),
3 possible trees:
Outgroup
GT
outgroups (=OG)
T to C
1
G to A
2
3
4
5
1
3
2
(4
OG
5)
OG
2
3
1
(4
5)
Homoplasies require more steps (changes) on a tree than
homologous characters .
If we’re looking at 7 variable nucleotide positions (a-g)…
Tree 1 requires 8 changes (steps): tree length, L= 8
Tree 2 requires 9 changes (steps): tree length = 9
Consistency Index (CI): min. no. possible steps/ number of steps on tree
Here, CI = 7/8 = 0.88
(for CI= 1, no homoplasy)
Consistency Index, CI = 7/9 = 0.78
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Tree 3 requires 10 changes (steps): tree length = 10
So tree 1 is most parsimonious (8 steps, CI = 0.88)
Consistency Index, CI = 7/10 = 0.70
Grouping whales with fish based on the presence of dorsal fins
is less parsimonious than true phylogeny:
CI = 9/17 = 0.53
CI = 9/10 = 0.90
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