![Page 1: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/1.jpg)
or
or
or
=
ancestor
descendants
?
Down pass
Up pass (if needed)
![Page 2: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/2.jpg)
Example 1
Example 2
![Page 3: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/3.jpg)
Does it work?
Testing ancestral reconstructions in the laboratory
![Page 4: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/4.jpg)
J MR K L N Q O P
A B C D
E F
W
15 16
7 16
9 15 11 21 22 16
19 18
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
![Page 5: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/5.jpg)
Comparing actual ancestors with inferred ancestors
Parsimony got it 94% right
![Page 6: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/6.jpg)
Two cases where
parsimony got it wrong
- -- - - - - + -
- - - +
- -
-
- -- - - + + + +
- - + +
- -
-
Bgl II
Mbo I
![Page 7: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/7.jpg)
Catalytic activity
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
5
50 42 38 30 25 20 15 12 8
Time (millions of years)
Jurassic Park revisited
Recreating ancestral proteins
![Page 8: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/8.jpg)
Taxonomic sampling and missed changes
-
+ +
+
- -
--
-
-
2 changes 1 change no changes
actual reconstructed (without a taxon)
![Page 9: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/9.jpg)
Problem is acute on long branches, especially for molecular data
A
T
T T
A
G
G
GG
A
![Page 10: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/10.jpg)
Molecular trees are often imbalanced
![Page 11: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/11.jpg)
How do characters evolve?
![Page 12: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/12.jpg)
Ordered characterFused, size 1
Touching
Separate
Fused, size 2
![Page 13: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/13.jpg)
Unordered character
Fused, size 1
TouchingSeparate
Fused, size 2
![Page 14: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/14.jpg)
Dollo parsimony“once lost, complex structures are never regained”
1
0
1
0
Standard parsimony Dollo parsimony
commononce only
![Page 15: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/15.jpg)
Wing loss and gain in stick insectsWhiting M. F. et al. Nature 421, 264-267 (2003)
![Page 16: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/16.jpg)
![Page 17: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/17.jpg)
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?
![Page 18: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/18.jpg)
Swordtails and platys
![Page 19: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/19.jpg)
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.
![Page 20: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/20.jpg)
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.
?
![Page 21: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/21.jpg)
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
![Page 22: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/22.jpg)
Correlated evolution
Have two characters evolved together?
![Page 23: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/23.jpg)
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
![Page 24: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/24.jpg)
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?
![Page 25: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/25.jpg)
Prediction based on kin selection
unpalatable
gregarious
unpalatable
gregarious
![Page 26: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/26.jpg)
Results: gregariousness evolves after unpalatability
unpalatable
gregarious
unpalatable
gregarious
![Page 27: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/27.jpg)
Comparative method
Phylogeny makes cross-species comparisons non independent
![Page 28: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/28.jpg)
Species aren’t independent
A
C
B
D
E F
A B C D E F
A B C D E F
![Page 29: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/29.jpg)
Bird bills vary in size
![Page 30: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/30.jpg)
Lice are a problem for birds
QuickTime™ and aCinepak decompressor
are needed to see this picture.
![Page 31: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/31.jpg)
Independent contrasts
![Page 32: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/32.jpg)
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
![Page 33: Example 1 Example 2 Does it work? Testing ancestral reconstructions in the laboratory](https://reader036.vdocuments.mx/reader036/viewer/2022062619/5515cb1e55034689058b49f9/html5/thumbnails/33.jpg)
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