Phylogenetics http://xkcd.com/287/ Brian O’Meara EEB464 Fall 2017.

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1 Phylogenetics Brian O’Meara EEB464 Fall 2017

2 Learning objectives Why bother with phylogenies
Questions we can answer using these techniques

3 © Doug Stone © Doug Stone

4 © Doug Stone © Doug Stone

5 © Doug Stone © Doug Stone

6 7 origins of agriculture
© Doug Stone 7 origins of agriculture © Doug Stone

7 7 origins of agriculture
© Doug Stone 7 origins of agriculture 8 origins of inbreeding © Doug Stone

8 7 origins of agriculture
© Doug Stone 7 origins of agriculture Angiosperm Conifer 5200 180 119 11 1500 195 8 origins of inbreeding © Doug Stone

9 Willi Hennig, Phylogenetic Systematics, 1966. p. 19

10 Willi Hennig, Phylogenetic Systematics, 1966. p. 71
This history of splitting creates a series of nestings. We typically show this as a tree, but other ways of showing this nesting are possible. Willi Hennig, Phylogenetic Systematics, p. 71

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12 2007 ecolog* 62,761 82% evolution 77,816 100% phylogen* 29,282 38% ecolog* evolution phylogen* Number of papers per year in Scopus with “phylogen*” in any field. Markers show relative frequency of “phylogen*” and “evolution”: Phylogen* up to 38% the number of evolution

13 Pull sequences from GenBank
Select clade & genes Pull sequences from GenBank Filter sequences Test and fix orthology Filter again Do subalignments Do overall alignment Smith, Beaulieu, and Donoghue. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol (2009) vol. 9 pp. 37 Infer phylogeny

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16 99% of mammal species (summary tree shown)
Bininda-Emonds et al. The delayed rise of present-day mammals. Nature (2007)

17 Pagel. Human language as a culturally transmitted replicator
Pagel. Human language as a culturally transmitted replicator. Nature Reviews Genetics (2009) vol. 10 (6) pp

18 ©2009 S. Blair Hedges & Sudhir Kumar (The TimeTree of Life)

19 13,533 species Needed 32 GB of RAM to run Smith et al. 2009

20 Number of atoms in the universe
Remember this is a log scale, so the number of trees rises faster than exponentially with the number of taxa. This becomes a problem when searching for trees. Adding two more species to the 13,533 species dataset shown earlier means increasing the search space of possible topologies by 183 million-fold. This is the same magnitude of changing the search space for an object from “around campus” (about a square mile) to “anywhere on the planet” -- and it’s just adding two species.

21 Laser printer: effectively 3600 × 4725 (can be tiled) 13,533 names
HD TV: 1920 × 1080 Laser printer: effectively 3600 × 4725 (can be tiled) 13,533 names largest computer monitors: 3280×2048 (can be tiled)

22 5 fly species Differ in body color and eye color What is history of trait evolution? The orange ones feed on oranges. Did they become orange to better feed on oranges (camouflage), or were they already that color?

23 Simple reconstruction: parsimony. Minimize changes.
(look at body color alone for example)

24 Simple reconstruction: parsimony. Minimize changes.
One possible reconstruction:

25 Simple reconstruction: parsimony. Minimize changes.
One possible reconstruction: 2 changes (both orange to purple)

26 Simple reconstruction: parsimony. Minimize changes.
One possible reconstruction: 2 changes (both orange to purple)

27 Simple reconstruction: parsimony. Minimize changes.
A different reconstruction: 1 change (purple to orange) More parsimonious

28 What is history of trait evolution?

29 5 fly species Differ in body color and eye color What is history of trait evolution? The orange ones feed on oranges. Did they become orange to better feed on oranges (camouflage), or were they already that color?

30 Did they become orange to better feed on oranges, or were they already that color?

31 Did they become orange to better feed on oranges, or were they already that color?
Want tree is calibrated to time (chronogram)

32 Want tree is calibrated to time (chronogram)
Did they become orange to better feed on oranges, or were they already that color? 10 20 30 MYA Want tree is calibrated to time (chronogram)

33 Did they become orange to better feed on oranges, or were they already that color?
10 Oranges evolve 20 30 MYA

34 Did they become orange to better feed on oranges, or were they already that color?
10 Oranges evolve 20 30 MYA Orange color evolves AFTER orange fruit does. Consistent with hypothesis.

35 If different tree, different reconstruction
10 20 30 MYA

36 If different tree, different reconstruction
10 Oranges evolve 20 30 MYA

37 If different tree, different reconstruction
10 Oranges evolve 20 30 MYA Orange color evolves BEFORE orange fruit does. Rejects hypothesis.

38 Amazing power of phylogenetics for trait evolution:
Once you have a tree... And observations of extant organisms... You can make inferences about processes happening millions of years ago.

39 First use for tree: species are not independent – tree helps you deal with that. Banal, but 1) important in getting right answer, 2) important in many fields Ackerly and Reich. Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts. Am. J. Bot. (1999) vol. 86 (9) pp

40 First use for tree: species are not independent – tree helps you deal with that. Banal, but 1) important in getting right answer, 2) important in many fields Ackerly and Reich. Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts. Am. J. Bot. (1999) vol. 86 (9) pp

41 Small, long-lived Big, short-lived
First use for tree: species are not independent – tree helps you deal with that. Banal, but 1) important in getting right answer, 2) important in many fields Ackerly and Reich. Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts. Am. J. Bot. (1999) vol. 86 (9) pp

42 Bromham and Penny. The modern molecular clock
Bromham and Penny. The modern molecular clock. Nature Reviews Genetics (2003) vol. 4 (3) pp Figure after Fleisher et al. Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar based ages of the Hawaiian islands to estimate molecular evolutionary rates. Mol Ecol (1998)

43 Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5-12% of the total genome size in the saurischian dinosaur lineage, but was 7-19% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage. Organ et al. Origin of avian genome size and structure in non-avian dinosaurs. Nature (2007) vol. 446 (7132) pp

44 Substitutions/MY Trees/shrubs Herbs Smith and Donoghue. Rates of Molecular Evolution Are Linked to Life History in Flowering Plants. Science (2008)

45 Boc et al. Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. Syst Biol (2010) vol. 59 (2) pp

46 Peter Zhang after Adams & Wendel, 2005; Cui et. al, 2006; Wolfe, 2001.

47 Young et al. Development and the evolvability of human limbs
Young et al. Development and the evolvability of human limbs. P Natl Acad Sci Usa (2010) vol. 107 (8) pp

48 Smith and Donoghue. Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales). Syst Biol (2010) vol. 59 (3) pp

49 Smith and Donoghue. Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales). Syst Biol (2010) vol. 59 (3) pp

50 Smith and Donoghue. Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales). Syst Biol (2010) vol. 59 (3) pp

51 The censored approach has been used by Dave Collar (a Losos postdoc) to investigate morphological evolution. All three fish clades have similar rates of morphological evolution in general, but sunfishes have a much higher rate of evolution of their feeding apparatus (which is interesting, as they also have a greater diet diversity). US FWS

52 Stretch tree based on these rates
Estimate rates A, B, and C Stretch tree based on these rates Estimate states on stretched tree They used Brownie to get optimal rate estimates, then used these to scale the tree and then estimate ancestral flower sizes.

53 Currie et al Nature

54 And you get these rates. Currie et al Nature

55 Smith & Wheeler 2006

56 Alfaro et al. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. P Natl Acad Sci Usa (2009) vol. 106 (32) pp

57 What questions could we address using these techniques?