A Novel comparative method for identifying shifts in the rate of character evolution on trees

Evolution

Volumn 65, Issue 12, 2011, Pages 3578-3589

  Eastman, Jonathan M ^a   Alfaro, Michael E ^b   Joyce, Paul ^a   Hipp, Andrew L ^c,d   Harmon, Luke J ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MORTON ARBORETUM   (United States)

^d FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Bayesian inference; Chelonia; Comparative methods; Primates; Rate heterogeneity; Reversible jump MCMC; Trait evolution

Indexed keywords

ADAPTIVE RADIATION; BAYESIAN ANALYSIS; BODY SIZE; COMPARATIVE STUDY; DATA SET; EMPIRICAL ANALYSIS; GENETIC ANALYSIS; HETEROGENEITY; IDENTIFICATION METHOD; MARKOV CHAIN; MONTE CARLO ANALYSIS; NUMERICAL MODEL; PHYLOGENETICS; TURTLE; UNCERTAINTY ANALYSIS;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BODY SIZE; COMPARATIVE STUDY; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; TIME; VERTEBRATE;

ANIMALS; BAYES THEOREM; BODY SIZE; MARKOV CHAINS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; PHYLOGENY; TIME FACTORS; VERTEBRATES;

EMYDIDAE; PRIMATES; TESTUDINES; VERTEBRATA;

EID: 82855161365     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01401.x     Document Type: Article

References (47)

1. Bartolucci, F., L. Scaccia, and A. Mira 2006. Efficient Bayes factor estimates from the reversible jump output. Biometrika 93: 41-52.
2. Blomberg, S. P., T. Garland, and A. R. Ives 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57: 717-745.
3. Bookstein, F.L.. 1987. Random walk and the existence of evolutionary rates. Paleobiology 13: 446-464.
4. Bonett, R. M., P. T. Chippindale, P. E. Moler, R. W. Van Devender, and D. B. Wake 2009. Evolution of gigantism in amphiumid salamanders. PLoS one 4(5):e5615.
5. Butler, M. A., and A. A. King 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164: 683-695.
6. Drummond, A. J., and M. A. Suchard 2010. Bayesian random local clocks, or one rate to rule them all. BMC Biol. 8:114.
7. Ekman. S., H. L. Andersen, and M. Wedin 2008. The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota). Syst. Biol. 57: 141-156.
8. Eldredge, N., and S. M. Stanley (eds.). 1984. Living fossils. Springer Verlag: New York
9. Estes S., and S. J. Arnold 2007. Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales. Am. Nat. 169: 227-244.
10. Felsenstein, J. 1973. Maximum likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25: 471-492.
11. FitzJohn, R. G. 2010. Quantitative traits and diversification. Syst. Biol. 59: 59: 619-633.
12. Freckleton, R. P., and W. Jetz 2009. Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proc. R. Soc. Lond. B 276: 21-30.
13. Gingerich, P. D. 1983. Rates of evolution: effects of time and temporal scaling. Science 222: 159-161.
14. Goldberg, E. E., and B. Igic 2008. On phylogenetic tests of irreversible evolution. Evolution 62: 2727-2741.
15. Green, P. J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
16. Green, P. J., and D. Hastie 2009. Reversible jump MCMC. Available at;
17. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51: 1341-1351.
18. Harmon, L. J., J. A. Schulte II, A. Larson, and J. B. Losos 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301: 961-964.
19. Harmon, L. J., J. B., Losos, T. J., Davies, R. G., Gillespie, J. L., Gittleman, W. B., Jennings, K. H., Kozak, M. A., McPeek, F. Moreno-Roark, T. J. Near, et al 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64: 2385-2396.
20. Harmon, L. J., J. Weir, C. Brock, R. E. Glor, and W. Challenger 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24: 129-131.
21. Hastings, W. K. 1970. Monte-Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
22. Huelsenbeck, J. P., and F. Ronquist 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
23. Huelsenbeck, J. P., B. Larget, and M. E. Alfaro 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21: 1123-1133.
24. Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Syst. Biol. 56: 252-270.
25. Jaffe, A. L., G. J. Slater, and M. E. Alfaro 2011. The evolution of island gigantism and body size variation in tortoises and turtles. Biol. Lett. 7: 558-561.
26. Jeffreys, H. 1935. Some tests of significance, treated by the theory of probability. Proc. Cambridge Philos. Soc. 31: 203-222.
27. Kass, R. E., and A. E. Raftery 1995. Bayes factors. J. Am. Stat. Assoc. 90: 773-795.
28. Li, G., M. Steel, and L. Zhang 2008. More taxa are not necessarily better for the reconstruction of ancestral character states. Syst. Biol. 57: 647-653.
29. Martins, E. P., and T. F. Hansen 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149: 646-667.
30. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller 1953. Equation of state calculations by fast computing machines. J. Chemical Phys. 21: 1087-1092.
31. Mooers, A. Ø., S. M. Vamosi, and D. Schluter 1999. Using phylogenies to test macroevolutionary hypotheses of trait evolution in cranes (Gruinae). Am. Nat. 154:249-259.
32. O'Meara, B. C., C. Ane, M. J. Sanderson, and P. C. Wainwright 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60: 922-933.
33. Pagel, M., and A. Meade 2008. Modelling heterotachy in phylogenetic inference by reversible jump Markov chain Monte Carlo. Philos. Trans. R. Soc. Lond. B 363: 3955-3964.
34. Plummer, M., N. Best, K. Cowles, and K. Vines 2010. coda: output analysis and diagnostics for MCMC. R package version 0.14-2.
35. Redding, D. W., C. DeWolff, and A. Ø. Mooers 2010. Evolutionary distinctiveness, threat status and ecological oddity in primates. Conserv. Biol. 24: 1052-1058.
36. Revell, L. J., and D. C. Collar 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63: 1090-1100.
37. Revell, L. J., L. J. Harmon, and R. E. Glor 2005. Under parameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Syst. Biol. 54: 973-983.
38. Revell, L. J., and L. J. Harmon 2008. Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evol. Ecol. Res. 10: 311-321.
39. Revell, L. J., L. J. Harmon, and D. C. Collar 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57: 591-601.
40. Revell, L. J., L. J. Harmon, R. B. Langerhans, and J. J. Kolbe 2007. A phylogenetic approach to determining the importance of constraint on phenotypic evolution in the neotropical lizard, Anolis cristatellus. Evol. Ecol. Res. 9: 261-282.
41. Revell, L. J., D. Mahler, P. Peres-Neto, and R. Redelings A new method for identifying exceptional evolutionary diversification. Evolution: in revision.
42. Rhodin, A. G. J., P. P. van Dijk, J. B. Iverson, and H. B. Shaffer 2010. Turtles of the World, 2010 Update: annotated checklist of taxonomy, synonomy, distribution, and conservation status. Chelonian Research Monographs 5: 85-164.
43. Schluter, D., T., Price, A. Ø. Mooers, and D. Ludwig 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
44. Simpson, G. G.. 1944. Tempo and Mode in Evolution. Columbia University Press, New York
45. Simpson, G. G.. 1953. The major features of evolution. Columbia University Press, New York
46. Stadler, T. 2010. TreeSim: simulating trees under the birth-death model. R package version 1.0.
47. Vos, R. A., and A. Ø. Mooers 2006. A new dated supertree of the Primates. Chapter 5. In: Vos R.A., editor. Inferring large phylogenies: the big tree problem. [Ph.D. thesis]. Burnaby BC, Canada: Simon Fraser University