Phylogenetic comparative trait and community analyses

1. Phylogenetic comparative trait and community analyses

2. Questions • Discussions: • Robbie: posting paper and questions for this week • Vania & Samoa: will be picking a paper to post for week after spring break • Reschedule Monday’s class? • 9:30-10:45 Wed in Benton 240 • Any questions?

3. Ferns Gymnosperms Angiosperms

4. Part 1: Evolutionary trees • What is systematics? • What are phylogenies? • Why are phylogenies useful? • Background information

5. What is systematics? • Systematics is the study of the diversity of organisms and the relationships among these organisms

6. Ways to examine relationships • Evolutionary systematics: Based on similarity as determined by expert (Mayr, Simpson) • Phenetics: Based on overall similarity (Rolf, Sokal, Sneath) • Cladistics: Based on shared derived characters (synapomorphies; Hennig)

7. Ways to examine relationships • Cladistics: Based on synapomorphies • Maximum Parsimony: Form the shortest possible tree (based on minimum steps) • Maximum Likelihood: Based on probability of change in character state and then calculate likelihood that a tree would lead to data (useful for molecular data) • Bayesian Inference: Based on the likelihood that the data would lead to the tree based on prior probabilities assigned using Bayes Theorem

8. Part 1: Evolutionary trees • What is systematics? • What are phylogenies? • Why are phylogenies useful? • Background information

9. a b c node 1 ch. 3 ch. 2 node 2 ch. 1 What are phylogenies? • Phylogenies are our hypotheses of evolutionary relationships among groups (taxa or taxon for singular) • Graphically represented by trees • When based on shared derived characters = cladogram

10. Part 1: Evolutionary trees • What is systematics? • What are phylogenies? • Why are phylogenies useful? • Background information

11. Why are phylogenies useful? • Useful for studying • Evolutionary relationships • Evolution of characters: Correlated (PICs vs. sister pairs), Signal, Partition variation, Ancestral state, Simulations • Types (Brownian vs. OU) and rates of evolution (Homogenous vs. heterogeneous) • Group ages (fossils, biogeography) • Diversity/Diversification: Speciation vs. Extinction? • Biogeographic history • Community phylogenetics • Phyloclimatic modeling and conservation • Assist in • Identification • Classification

12. Part 1: Evolutionary trees • What is systematics? • What are phylogenies? • Why are phylogenies useful? • Background information

13. Background information • Trees • Characters • Groups • Other

14. Trees • Tips: Living taxa • Nodes: Common ancestor • Branches: Can represent time since divergence • Root: Common ancestor to all species in study tips a b c node 1 branch node 2 root

15. a d b c Trees • Sister group: Closest relative to a taxon • c and d are sister • b = sister to c,d • a = sister to b,c,d

16. a d b c Trees • Our goal is to make bifurcating trees • But a polytomy is when we are unable to resolve which are the sister taxa (hard vs. soft)

17. Trees • Phylogenetic trees can be rotated around their nodes and not change the relationships a b c d b c a d

18. Trees • Toplogy: shape • Branch lengths: differentiation (e.g., 1 = punctuated, speciational) or time = ultrametric

19. Characters • Characters: Attribute (e.g., morphological, genetic) • Eye color • Production of flowers • Position 33 in gene X • Character state: Value of that character • Blue, green, hazel, brown • Yes, No • A, T, G, C

20. Picking Characters • Variable • Heritable • Comparable (homologous) • Independent

21. Characters • Homology: A character is homologous in > 2 taxa if found or derived from their common ancestor 1 1 1 or 1’ homologous

22. Homology • Homology is determined by: • Similar position or structures • Similar during development • Similar genetically • Evolutionary character series (transformational homology) from ancestor to descendents

23. Characters • Homoplasy: A character is homoplasious in > 2 taxa if the common ancestor did not have this character 1 1 0 analogous

24. Homoplasy • Due to • Convergent evolution: Similar character states in unrelated taxa • Reversals: A derived character state returns to the ancestral state

25. Characters • Apomorphy: Derived character • Pleisiomorphy: Ancestral character a b c ch. 2 ch. 1

26. Characters • Synapomorphy: Shared derived character • Autapomorphy: Uniquely derived character • Symplesiomorphy: Shared ancestral character 1,2,3,4 1,2,3,6 1,4,5 a b c ch. 6 ch. 4 ch. 5 node 1 chs. 2, 3 = Synapomorphies chs. 5, 6 = Autapomorphies ch. 1 = Symplesiomorphy ch. 4 = False synapomorphy ch. 4 ch. 3 ch. 2 node 2 ch. 1

27. a d b c Monophyletic groups • Monophyletic groups: Contain the common ancestor and all of its descendents • What are the monophyletic groups? • c,d • b,c,d • a,b,c,d

28. a d b c Other groups (not recognized) • Paraphyletic groups: Contain the common ancestor and some of its descendents ch. 1 Based on sympleisiomorphic character

29. Other groups (not recognized) • Polyphyletic groups: Descendants with 2 or more ancestral sources c a d b e ch. 4 Based on false synapomorphy

30. Getting trees • From the literature, Phylomatic, Genbank, collect data yourself (may need name scrubbing tools: Phylomatic, TaxonScrubber) • Methods for assembly: Supertree, Supermatrix, Megatree, Zip them together • Getting the topology vs. getting branch lengths? • Discord among trees based on different characters? Gene trees vs. species trees

31. Storing trees • Newick: ((b:1, c:1), a:1):1; • Nexus (output of Paup) • Pagel • Distance matrix a b c

32. Part 2: Hypothesis Testing Using Evolutionary Trees

33. Part 2: Hypothesis testing http://treetapper.org/, http://cran.r-project.org/web/views/Phylogenetics.html • What sort of hypotheses can we test? • Phylogeography • Evolutionary dating • Phylogenetic community structure • Coevolution/Cospeciation • Mapping characters • Types of characters • Correlated Change • Dependent Change • Phylogenetic Signal

34. When do we need to use phylogenies? • Is it always necessary in ecological questions? • Yes, taxa are not independent points so we must “correct for” phylogeny • Sometimes, it is interesting to “incorporate” phylogenetic hypotheses to see how they influence our analyses • No, evolutionary questions can be asked by incorporating phylogenies but each species represents a separate successful event and should be analyzed with that in mind

35. Part 2: Hypothesis testing • What sort of hypotheses can we test? • Phylogenetic community structure • Mapping characters • Types of characters • Correlated Change • Dependent Change • Phylogenetic Signal

36. Phylogenetic Community Structure • Webb (2000) tested the alternate hypotheses that co-occurring species are (1) more or (2) less closely related than a random assembly of species • He examined the phylogenetic structure in 28 plots in 150 ha of Bornean forest

38. Phylogenetic Community Structure • He found species were more closely related than a random distribution

39. Phylogenetic Community Structure • Recent development of metrics: • NRI, NTI, PSV, PSC • Do you use abundance or presence/absence? • What regional pool do you compare to? • What null models should you use?

40. Part 2: Hypothesis testing • What sort of hypotheses can we test? • Phylogenetic community structure • Mapping characters • Types of characters • Correlated Change • Dependent Change • Phylogenetic Signal

41. Mapping Characters • Once we have a known phylogeny, we can map on characters of interest to test hypotheses • The phylogeny must be built on characters independent of those of interest

42. Types of Characters • If we have a character that appears in a number of taxa, we may • Test the alternate hypotheses that it is (1) analogous or (2) homologous • Test hypotheses as to which state is ancestral and derived • We can map the character onto the phylogeny to test these hypotheses

43. Homologous vs. Analogous Characters

44. Part 2: Hypothesis testing • What sort of hypotheses can we test? • Phylogenetic community structure • Mapping characters • Types of characters • Correlated Change • Dependent Change • Phylogenetic Signal

45. Branch size Correlated Change • Comparative biologists often try to test hypotheses about the relationships between two or more characters by taking measurements across many species • Seed size and seedling size • Body mass and surface area • Fruit size and branch size Fruit size

46. Correlated Change • We might want to ask whether the correlation between traits is due to repeated coordinated evolutionary divergences • We might expect closely related species to resemble one another

47. Branch size Correlated Change • If our phylogeny looked something like this • Then all of the change is really the result of one evolutionary event Fruit size

48. Correlated Change • To incorporate phylogeny into comparative analyses, looking for correlated change, we can use • Sister pairs analyses • Felsenstein’s Independent Contrasts • Grafen’s Phylogenetic regression (ML and Bayesian approaches too) • Pagel’s Discrete and Multistate (Change in character state)

49. Sign test: 32 of 45 are negative (p < 0.01) Strychnos 3 2 1 Hamelia 0 Miconia -1 trees & lianas shrubs

50. Correlated Change • To incorporate phylogeny into comparative analyses, looking for correlated change, we can use • Sister pairs analyses • Felsenstein’s Independent Contrasts (Brownian) • Grafen’s Phylogenetic regression (Other models) • ML and Bayesian approaches too • Pagel’s Discrete and Multistate (Change in character state)