Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data

Systematic Biology

Volumn 63, Issue 2, 2014, Pages 166-177

  Adams, Dean C ^a,b  

^a Evolution and Organismal Biology ^*  (United States)

^b Department of Statistics Center for Statistics and Applications in Forensic Evidence Iowa State University 2438 Osborn Dr Ames   (United States)

Author keywords

Evolutionary rates; geometric morphometrics; macroevolution; morphological evolution; phylogenetic comparative method

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; EVOLUTIONARY RATES; GEOMETRIC MORPHOMETRICS; HISTOLOGY; MACROEVOLUTION; METHODOLOGY; MORPHOLOGICAL EVOLUTION; PHENOTYPE; PHYLOGENETIC COMPARATIVE METHOD; PHYLOGENY; TIME; URODELA;

EVOLUTIONARY RATES; GEOMETRIC MORPHOMETRICS; MACROEVOLUTION; MORPHOLOGICAL EVOLUTION; PHYLOGENETIC COMPARATIVE METHOD;

ANIMALS; CLASSIFICATION; PHENOTYPE; PHYLOGENY; TIME; URODELA;

EID: 84894514976     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt105     Document Type: Article

References (84)

1. Ackerly D. 2009. Conservatism and diversification of plant functional traits: evolutionary rates versus phylogenetic signal. Proc. Natl Acad. Sci. USA 106:19699-19706.
2. Adams D.C. 2007. Organization of Plethodon salamander communities: guild-based community assembly. Ecology 88:1292-1299.
3. Adams D.C. 2010. Parallel evolution of character displacement driven by competitive selection in terrestrial salamanders. BMC Evol. Biol. 10:1-10.
4. Adams D.C. 2011. Quantitative genetics and evolution of head shape in Plethodon salamanders. Evol. Biol. 38:278-286.
5. Adams D.C. 2013. Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood. Syst. Biol. 62:181-192.
6. Adams D.C., Otárola-Castillo E. 2012. geomorph: software for geometric morphometric analyses. R package version 1.0. Available from: URL http://CRAN.R-project.org/package=geomorph.
7. Adams D.C., Otárola-Castillo E. 2013. geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods Ecol. Evol. 4:393-399.
8. Adams D.C., Rohlf F.J., Slice D.E. 2013. A field comes of age: geometric morphometrics in the 21st century. Hystrix 24:7-14.
9. Adams D.C.,West M.E., CollyerM.L. 2007. Location-specific sympatric morphological divergence as a possible response to species interactions in West Virginia Plethodon salamander communities. J. Anim. Ecol. 76:289-295.
10. Anderson M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26:32-46.
11. Anthony C.D.,Wicknick J.A., Jaeger R.G. 1997. Social interactions intwo sympatric salamanders: effectiveness of a highly aggressive strategy. Behaviour 134:71-88.
12. Arif S., Adams D.C., Wicknick J.A. 2007. Bioclimatic modelling, morphology, and behaviour reveal alternative mechanisms regulating the distributions of two parapatric salamander species Evol. Ecol. Res. 9:843-854.
13. Arnegard M.E., McIntyre P.B., Harmon L.J., Zelditch M.L., Crampton W.G.R., Davis J.K., Sullivan J.P., Lavoue S., Hopkins C.D. 2010. Sexual signal evolution outpaces ecological divergence during electric fish species radiation. Am. Nat. 176:335-356.
14. Beaulieu J.M., Jhwueng D.C., Boettiger C., O'Meara B.C. 2012. Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution 66:2369-2383.
15. Betancur-R. R., Orti G., Stein A.M., Marcenuik A.P., Pyron R.A. 2012. Apparent signal of competition limiting diversification after ecological transitions from marine to freshwater habitats. Ecol. Lett. 15:822-830.
16. Blomberg S.P., Garland T., Ives A.R. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745.
17. Boettiger C., Coop G., Ralph P. 2012. Is your phylogeny informative? Measuring the power of comparative methods. Evolution 67:2240-2251.
18. Bookstein F.L. 1991. Morphometric tools for landmark data: geometry and biology. Cambridge: Cambridge University Press.
19. Bookstein F.L. 2013.Randomwalk as a null model for high-dimensional morphometrics of fossil series: geometrical considerations. Paleobiology 39:52-74.
20. Butler M.A., King A.A. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683-695.
21. Butler M.A., Schoener T.W., Losos J.B. 2000. The relationship between sexual size dimorphism and habitat use in Greater Antillean Anolis lizards. Evolution 54:259-272.
22. Carlson B.A., Hasan S.M., Hollmann M., Miller D.B., Harmon L.J., Arnegard M.E. 2011. Brain evolution triggers increased diversification of electric fishes. Science 332:583-596.
23. Collar D.C., O'Meara B.C., Wainwright P.C., Near T.J. 2009. Piscivory limits diversification of feeding morphology in centrarchid fishes. Evolution 63:1557-1573.
24. Deitloff J., Petersen J.D., Adams D.C. 2013. Complex species interactions lead to unpredictable outcomes in Plethodon. Herpetologica 62:1-10.
25. Eastman J.M., Alfaro M.E., Joyce P., Hipp A.L., Harmon L.J. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65:3578-3589.
26. Edwards A.W.F., Cavalli-Sforza L.L. 1964. Reconstruction of evolutionary trees. In: Heywood V.H., McNeill J., editors. Phenetic and phylogenetic classification. London: Systematics Assocaition Publications. pp. 67-76.
27. Felsenstein J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471-492.
28. Felsenstein J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35:1229-1242.
29. Felsenstein J. 1985. Phylogenies and the comparativemethod. Am.Nat. 125:1-15.
30. Felsenstein J. 1988. Phylogenies and quantitative characters. Ann. Rev. Ecol. Syst. 19:445-471.
31. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
32. Foote M. 1997. Evolution of morphological diversity. Ann. Rev. Ecol. Syst. 28:129-152.
33. Garland T. Jr., Dickerman A.W., Janis C.M., Jones J.A. 1993. Phylogenetic analysis of covariance by computer simulation. Syst. Biol. 43:265-292.
34. Garland T.J. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 140:2104-2111.
35. Garland T.J., Ives A.R. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. Am. Nat. 155:346-364.
36. Gingerich P.D. 1993. Quantification and comparison of evolutionary rates. Am. J. Sci. 293A:453-478.
37. Gingerich P.D. 2009. Rates of evolution. Ann. Rev. Ecol. Evol. Syst. 40:657-675.
38. Gower J.C. 1966. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325-338.
39. Grafen A. 1989. The phylogenetic regression. Phil. Trans. Roy. Soc. London B 326:119-157.
40. Hairston N.G. 1980. Evolution under interspecific competition: field experiments on terrestrial salamanders. Evolution 34:409-420.
41. Hansen T.F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351.
42. Harmon L.J., II J.A.S., Larson A., Losos J.B. 2003. Tempo and mode of evolutionary radiation in Iguanian lizards. Science 301:961-964.
43. Harmon L.J., Losos J.B., Davies T.J., Gillespie R.G., Gittleman J.L., Jennings W.B., Kozak K.H., McPeek M.A., Moreno-Roark F., Near T.J., Purvis A., Ricklefs R. E., Schluter D., Schulte II J. A., Seehausen O., Sidlauskas B. L., Torres-Carvajal O., Weir J. T., and Mooers A.Ø. 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64:2385-2396.
44. Harmon L.J., Melville J., Larson A., Losos J.B. 2008. The role of geography and ecological opportunity in the diversification of day geckos (Phelsuma). Syst. Biol. 57:562-573.
45. Highton R. 1995. Speciation in eastern North American salamanders of the genus Plethodon. Ann. Rev. Ecol. Syst. 26:579-600.
46. Highton R. 1999. Geographic protein variation and speciation in the salamanders of the Plethodon cinereus group with the description of two new species. Herpetologica 55:43-90.
47. Highton R. 2004. A new species of woodland salamander of the Plethodon cinereus group from the Blue RidgeMountains of Virginia. Jeffersoniana: Contrib. Virg. Mus. Nat. Hist. 14:1-22.
48. Jaeger R.G. 1970. Potential extinction through competition between two species of terrestrial salamanders. Evolution 24:632-642.
49. Jaeger R.G. 1971. Competitive exclusion as a factor influencing the distributions of two species of terrestrial salamanders. Ecology 52:632-637.
50. Klingenberg C.P., Gidaszewski N.A. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst. Biol. 59:245-261.
51. Kozak K.H., Wiens J.J. 2010. Accelerated rates of climatic-niche evolution underlie rapid species diversification. Ecol. Lett. 13:1378-1389.
52. Krzanowksi W.J. 1993. Principles of multivariate analysis. Oxford: Clarendon Press.
53. Legendre P., Legendre L. 1998.Numerical ecology. 2nd ed.Amsterdam: Elsevier.
54. Mahler D.L., Revell L.J., Glor R.E., Losos J.B. 2010. Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean Anoles. Evolution 64:2731-2745.
55. Martin C.H., Wainwright P.C. 2011. Trophic novelty is linked to exceptional rates of morphological diversification in two adaptive radiations of Cyprinodon pupfish. Evolution 65:2197-2212.
56. Martins E.P. 1994. Estimating the rate of phenotypic evolution from comparative data. Am. Nat. 144:193-209.
57. Martins E.P., Hansen T.F. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149:646-667.
58. McArdle B.H., Anderson M.J. 2001. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82:290-297.
59. McPeek M.A. 1995. Testing hypotheses about evolutionary change on single branches of a phylogeny using evolutionary contrasts. Am. Nat. 145:686-703.
60. McPeek M.A., Shen L., Torrey J.Z., FaridH. 2008. The tempo and mode of three-dimensional morphological evolution in male reproductive structures. Am. Nat. 171:E158-E178.
61. Millien V. 2006. Morphological evolution is accelerated among island mammals. PLoS ONE 4:1683-1688.
62. O'Meara B.C. 2012. Evolutionary inferences fromphylogenies: a review of methods. Ann. Rev. Ecol. Evol. Syst. 43:267-285.
63. O'Meara B.C., Ane C., Sanderson M.J., Wainwright P.C. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
64. Polly P.D. 2004. On the simulation of the evolution of morphological shape: multivariate shape under selection and drift. Paleaontol. Electronica 7.(2).7A:1-28.
65. Polly P.D. 2008. Adaptive zones and the pinniped ankle: a 3D quantitative analysis of carnivoran tarsal evolution. In: Sargis E., Dagosto M., editors. Mammalian evolutionary morphology: a tribute to Frederick S. Szalay. Dordrecht: Springer. pp. 165-194.
66. Price S.A., Wainwright P.C., Bellwood D.R., Kazancioglu E., Collar D.C., Near T.J. 2010. Functional innovations and morphological diversification in parrotfish. Evolution 64:3057-3068.
67. R Core Development Team. 2013. R: a language and environment for statistical computing. Version 3.0.1. Available from: URL http://cran.R-project. org. Vienna: R Foundation for Statistical Computing.
68. Rabosky D.L., Adams D.C. 2012. Rates of morphological evolution are correlated with species richness in salamanders. Evolution 66:1807-1818.
69. Rencher A.C. 1995. Methods of multivariate analysis. New York: John Wiley & Sons.
70. Revell L.J. 2008. On the analysis of evolutionary change along single branches in a phylogeny. Am. Nat. 172:140-147.
71. Revell L.J. 2012. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3:217-223.
72. Revell L.J., Collar D.C. 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63:1090-1100.
73. Revell L.J., Harmon L.J. 2008. Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evol. Ecol. Res. 10:311-331.
74. Revell L.J., Mahler D.L., Peres-Neto P.R., Redelings B.D. 2012. A new phylogenetic method for identifying exceptional phenotypic diversification. Evolution 66:135-146.
75. Rohlf F.J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:2143-2160.
76. Rohlf F.J., Slice D.E. 1990. Extensions of the Procrustes method for the optimal superimposition of landmarks. Syst. Zool. 39:40-59.
77. Sepkoski J.J.J. 1978.Akinetic model of Phanerozoic taxonomic diversity I. Analysis of marine orders. Paleobiology 4:223-251.
78. Sidlauskas B. 2008. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach. Evolution 62:3135-3156.
79. Simpson G.G. 1944. Tempo and mode in evolution. New York: Columbia University Press.
80. Sites J.W.J., Morando M., Highton R., Huber F., Jung R.E. 2004. Phylogenetic relationship of the endangered Shenandoah salamander (Plethodon shenandoah) and other salamanders of the Plethodon cinereus group (Caudata: Plethodontidae). J. Herpetol. 38:96-105.
81. Thomas G.H., Freckleton R.P., Székely T. 2006.Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proc. Roy. Soc. B 273:1619-1624.
82. Thomas G.H., Meiri S., Phillimore A.B. 2009. Body size diversification in Anolis: novel environment and island effects. Evolution 63:2017-2030.
83. Valenzuela N., Adams D.C. 2011. Chromosome number and sex determination coevolve in turtles. Evolution 65:1808-1813.
84. Wiens J.J., EngstromT.N., Chippendale P.T. 2006. Rapid diversification, incomplete isolation, and the 'speciation clock' in North American salamanders (genus: Plethodon): testing the hybrid swarm hypothesis of rapid radiation. Evolution 60:2585-2603.