example 1 example 2 does it work? testing ancestral reconstructions in the laboratory
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or
or
or
=
ancestor
descendants
?
Down pass
Up pass (if needed)
Example 1
Example 2
Does it work?
Testing ancestral reconstructions in the laboratory
J MR K L N Q O P
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7 16
9 15 11 21 22 16
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1817
34
wild-type T740 serial lysates2/3 generations per lysate
T7 bacteriophage in presence of N-methyl-N’ -n itro-N-n itroguanidine
Experimental phylogenetics
Comparing actual ancestors with inferred ancestors
Parsimony got it 94% right
Two cases where
parsimony got it wrong
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Bgl II
Mbo I
Catalytic activity
0
0.5
1
1.5
2
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50 42 38 30 25 20 15 12 8
Time (millions of years)
Jurassic Park revisited
Recreating ancestral proteins
Taxonomic sampling and missed changes
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+ +
+
- -
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2 changes 1 change no changes
actual reconstructed (without a taxon)
Problem is acute on long branches, especially for molecular data
A
T
T T
A
G
G
GG
A
Molecular trees are often imbalanced
How do characters evolve?
Ordered characterFused, size 1
Touching
Separate
Fused, size 2
Unordered character
Fused, size 1
TouchingSeparate
Fused, size 2
Dollo parsimony“once lost, complex structures are never regained”
1
0
1
0
Standard parsimony Dollo parsimony
commononce only
Wing loss and gain in stick insectsWhiting M. F. et al. Nature 421, 264-267 (2003)
Testing hypotheses
• When did a character evolve?
• Has it evolved more than once?
• Did one character evolve before another?
• Is the evolution of two (or more) characters correlated?
Swordtails and platys
Origin of swords in swordtail fishes:the “pre-existing bias hypothesis”
Idea:
Females evolve a “sensory bias” which causes them to prefer males with exaggerated features. Hence, male morphology is driven by sexual selection.
Testing this idea...
• Female choose males based on sword length. Experiments on X. helleri show females prefer males with longer
swords.
• Females of swordless species (platys) prefer males with swords. Experiments on X. maculatus confirm this.
• Absence of swords must be primitive, so that female's bias for swords predates the evolution of swords.
?
Swords are primitive!
X. couchianusX. gordoniX. meyeriX. xiphidiumX. variatusX. evelynaeX. clemenciaeX. milleriX. maculatusX. andersiX. signumX. helleriX. alvereziX. birchmanniX. pygmaeusX. montezumaeX. nezehualcoyotiX. continensX. corteziX. malincheX. nigrensisX. multilineatusP. compressP. intermediaP. olmecae
Correlated evolution
Have two characters evolved together?
Gregariousness in aposematic butterfly larvae
• Aposematic forms tend to be gregarious. R. A. Fisher suggested warning colouration evolved through kin selection.
• An individual may die during the “lesson” that teaches naïve predator not to eat brightly coloured larvae
• If predator leaves kin alone, inclusive fitness of dead larvae is positive
• Laying eggs in clutches will result in kin groups on same plant
• Prediction: aggregation evolves before colouration
Correlated character change
AB
AB
AB
ab
A
B
AB
AB
Ab
ab
A
B
Does character A always arise with character B?Does character A always precede character B?
Prediction based on kin selection
unpalatable
gregarious
unpalatable
gregarious
Results: gregariousness evolves after unpalatability
unpalatable
gregarious
unpalatable
gregarious
Comparative method
Phylogeny makes cross-species comparisons non independent
Species aren’t independent
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C
B
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E F
A B C D E F
A B C D E F
Bird bills vary in size
Lice are a problem for birds
QuickTime™ and aCinepak decompressor
are needed to see this picture.
Independent contrasts
Bird with big bills scratch more
0 0.1 0.2 0.3 0.4 0.5 0.6
Toucanet/Aracari
Woodpecker/Jacamar
Hornbill/Roller
Hummingbird/Turacos
Curlew/Ruff
Oystercatcher/Avocet
Ibis/Falcon
Stork/New Worldvulture
Pelican/penguin
Proportion of time spent grooming
Long
Short
Summary
• Given a phylogeny we can infer ancestral states
• These states can be used to test hypotheses• Comparisons between species are not
independent• The comparative method provides tools to
extract independent comparisons from a phylolgeny