Biology 105 - Evolution Dr. Theodore Garland, Jr. 5 Nov. 2015: "Phylogeny and Comparative Methods"

1. Biology 105 - Evolution • Dr. Theodore Garland, Jr. • 5 Nov. 2015: • "Phylogeny and Comparative Methods" Accompanies pages 167-173 in: Bergstrom, C. T., and L. A. Dugatkin. 2012. Evolution. W.W. Norton and Company.

2. More Real Examples of Comparative Studies • General take-home message: • biologists have elucidated many functional relationships by cross-species comparisons.

3. Does leg length predict maximal sprinting abilities of lizards? (after removing correlations with body size by computing residuals from least-squares linear regressions)

4. Photos by Todd Jackman and others 14 Speciesof AnolisLizards pulchellus sagrei cristatellus krugi

5. Losos, J. B. 1990. Ecomorphology, performance capability, and scaling of West Indian Anolis lizards:an evolutionary analysis. Ecological Monographs 60:369-388. Figure from Garland & Adolph (1994). Compute residuals (vertical deviations from least-squares regression line) to remove correlation with body mass ...

6. Compute residuals (vertical deviations from least-squares regression line) to remove correlation with body mass ...

7. Test for a relationship between the residuals.

8. Be cautious about influential points! Test for a relationship between the residuals.

9. This one has a lot of leverage!(term used in statistics as well as physics)

10. Relationships Within vs. Among Clades r = 0.668 P < 0.05 Consider the apparently positive relationship between two traits across 9 species. Trait B Trait A

11. Relationships Within vs. Among Clades "Grade Shifts" can “reset” mean values for traits, thus obscuring within-clade patterns. Trait B Trait A See also page 169 in Bergstrom and Dugatkin 2012

12. Independent contrasts within vs. among major lineages: 22 44 66 33 rt

13. Relationships Within vs. Among Clades ric = -0.099N.S. Analysis by phylogenetically independent contrasts (computed through the origin) indicates a much weaker relationship. Contrasts Trait B Contrasts Trait A

14. And now a real example of differences in trait relationships within vs. among clades ..

15. Mammals from the London Zoo= partially a common garden

16. Looking at the bivariate scatterplot on the previous slide to judge the relationship effectively assumes this.

17. Even if we do not know the full details of the mammalian phylogenetic tree, we could at least consider the main taxonomic groupings, which are in fact clades.

18. Considering the main clades yields a completely different conclusion! “Grade Shifts”

19. As systematists continue to work on mammals, we will eventually know the full details of the tree and could then fully apply such methods as phylogenetically independent contrasts.

20. "Well, that's fine for some traits, but it probably doesn't matter for the ones that I study …"

21. Structure of Bird Song can Vary Radically even between Closely Related Species (Nowicki et al., 2001, Animal Behaviour 62:1189-1195)

22. Structure of Bird Song Also Shows Some Similarities between Closely Related Species

23. Given that similarity may be in the eye of the beholder, we need objective ways to test for the presence of phylogenetic signal, and also to quantify how strong it is. Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. [methods for single traits] Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. Am. Nat. 160:712-726. [methods for regression equations and hence residuals]

24. For example, elephants look like elephants. "Phylogenetic Signal" =tendency for related species to resemble each other.

25. "Phylogenetic Signal" is notthe same as phylogenetic inertia or constraint. These terms imply more than is easily estimated from comparative data alone,e.g., resistance to change.

26. A Tree and Tip Datafor 4 Species (maybe body masses of hummingbirds) 2 3 8 9 Testing for Phylogenetic Signal: Hypothetical Example

27. Phylogenetic Signal is Apparent 2 3 8 9 Relatives Resemble Each Other

28. Phylogenetic Signal is Apparent 2 3 8 9 Statistical significance canbe tested using phylogenetically independent contrasts (Felsenstein 1985)

29. Phylogenetic Signal is Apparent 2 3 8 9 Compute Standardized Contrasts

30. Low Variance of Contrasts Phylogenetic Signal is Apparent 2 3 8 9

31. No Apparent Phylogenetic Signal 2 9 3 8 High Varianceof Contrasts 18.50 Phylogenetic Signal is Apparent 2 3 8 9 Low Varianceof Contrasts 4.10

32. No Apparent Phylogenetic Signal 2 9 3 8 High Varianceof Contrasts 18.50 Phylogenetic Signal is Apparent 2 3 8 9 Test statistical significance with a simple randomization procedure. Low Varianceof Contrasts 4.10

33. Hypothetical tip data for 15 species 2 2 3 2 3 4 5 6 5 7 8 7 9 8 9 1. Calculate variance of contrasts for data in original position

34. 1. Calculate variance of contrasts for data in original position 2. Permute data (~1000 x)

35. 1. Calculate variance of contrasts for data in original position 2. Permute data (~1000 x) 3. For each, calculate variance of contrasts

36. N Variance of contrasts 1. Calculate variance of contrasts for data in original position 2. Permute data (~1000 x) 3. For each, calculate variance of contrasts 4. Construct distribution

37. Value for real data N Variance of contrasts 2 2 3 2 3 4 5 6 5 7 8 7 9 8 9 1. Calculate variance of contrasts for data in original position 2. Permute data (~1000 x) 3. For each, calculate variance of contrasts 4. Construct distribution 5. Compare with real data

38. Value for real data N Variance of contrasts 1. Calculate variance of contrasts for data in original position 2. Permute data (~1000 x) 3. For each, calculate variance of contrasts 4. Construct distribution 5. Compare with real data 6. Accept or Reject null hypothesis of no signal

39. Example with real data: Preferred Body Temperatures (oC) of 12 species of Australian skinks: P < 0.001 Phylogenetic Signal Exists Data from Huey & Bennett, 1987; phylogenetic information updatedin Garland et al., 1991

40. Example with real data: Optimal Body Temperatures for Sprinting (oC) of 12 species of Australian skinks: P = 0.167 No Statistically Significant Phylogenetic Signal Data from Huey & Bennett, 1987; phylogenetic information updatedin Garland et al., 1991

41. Power to Detect Phylogenetic Signal Power You need about 20 species to have good power (~0.80) to detect phylogenetic signal, if it exists. Number of Species Blomberg et al. 2003

42. Tests for Phylogenetic Signal in 119 Traits from 34 Studies # species P < 0.05P > 0.05 23 - 254 49 (92%)4 92% of traits with adequate sample size showed statistically significant phylogenetic signal. Blomberg et al. 2003

43. Tests for Phylogenetic Signal in 119 Traits from 34 Studies # species P < 0.05P > 0.05 23 - 254 6 - 17 49 (92%)4 27 (41%)39 With small sample sizes, signal is generally not statistically significant. Blomberg et al. 2003

44. Tests for Phylogenetic Signal in 119 Traits from 34 Studies # species P < 0.05P > 0.05 23 - 254 6 - 17 49 (92%)4 27 (41%)39 No trait showed "anti-signal" Blomberg et al. 2003

45. Take-home messages: Most traits do show phylogenetic signal. That is, related species generally do resemble each other for any particular trait that we might measure. So always consider phylogenetic information when analyzingcomparative data!

46. Removed for 2015 because running short of time

47. More Real Examples • General take-home message: • biologists have studies allometry and sexual selection by cross-species comparisons.

48. Primate Species: Allometry Testes Mass (g) Body Mass (kg)

49. Primate Species: Sexual Selection Females likely to copulate with > 1 partner per estrus Testes Mass (g) Femalesmate withonly 1 male Body Mass (kg)

50. Primate Species: Sexual Selection Sperm competition likely drove the evolution of larger testes in these species. Testes Mass (g) What was the ancestral state?You cannot tell from this graph alone -- would need to reconstruct on a phylogenetic tree. Body Mass (kg)