A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data

Systematic Biology

Volumn 63, Issue 5, 2014, Pages 685-697

  Adams, Dean C ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Geometric morphometrics; Macroevolution; Morphological evolution; Phylogenetic comparative method

Indexed keywords

ANIMAL; ARTICLE; CLASSIFICATION; HEAD; HISTOLOGY; METHODOLOGY; MULTIVARIATE ANALYSIS; PHYLOGENY; STATISTICAL ANALYSIS; STATISTICAL MODEL; URODELA;

ANIMALS; CLASSIFICATION; DATA INTERPRETATION, STATISTICAL; HEAD; MODELS, STATISTICAL; MULTIVARIATE ANALYSIS; PHYLOGENY; URODELA;

EID: 84906267632     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu030     Document Type: Article

References (75)

1. Abouheif E. 1999. Amethod for testing the assumption of phylogenetic independence in comparative data. Evol. Ecol. Res. 1:895-909.
2. Ackerly D. 2009. Conservatism and diversification of plant functional traits: evolutionary rates versus phylogenetic signal. Proc. Natl Acad. Sci. U. S. A. 106:19699-19706.
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. 2014. Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data. Syst. Biol. 63:166-177.
6. Adams D.C., Cardini A., Monteiro L.R., O'Higgins P., Rohlf F.J. 2011. Morphometrics and phylogenetics: principal components of shape from cranial modules are neither appropriate nor effective cladistic characters. J. Hum. Evol. 60:240-243.
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., Otárola-Castillo E., Sherratt E. 2014. geomorph: Software for geometric morphometric analyses. R package version 2.0. Available from: URL http://CRAN.Rproject.org/package=geomorph.
9. Adams D.C., Rohlf F.J. 2000. Ecological character displacement in Plethodon: biomechanical differences found from a geometric morphometric study. Proc. Natl Acad. Sci. U. S. A. 97:4106-4111.
10. 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.
11. Adams D.C., Rosenberg M.S. 1998. Partial warps, phylogeny, and ontogeny: a comment on Fink and Zelditch. Syst. Biol. 47:168-173.
12. Adams D.C., West M.E., Collyer M.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.
13. Anderson M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral. Ecol. 26:32-46.
14. 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.
15. 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.
16. Blankers T., Adams D.C., Wiens J.J. 2012. Ecological radiation with limited morphological diversification in salamanders. J. Evol. Biol. 25:634-646.
17. 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.
18. Bookstein F.L. 1991. Morphometric tools for landmark data: geometry and biology. Cambridge: Cambridge University Press.
19. Cardini A., Elton S. 2008. Does the skull carry a phylogenetic signal? Evolution and modularity in the guenons. Biol. J. Linn. Soc. 93:813-834.
20. Cubo J., Ponton F., Laurin M., de Margerie E, Castanet J. 2005. Phylogenetic signal in bone microstructure of sauropsids. Syst. Biol. 54:562-574.
21. Deitloff J., Church J.O., Adams D.C., Jaeger R.G. 2009. Interspecific agonistic behaviors in a salamander community: implications for alpha-selection. Herpetologica 65:174-182.
22. Deitloff J., Petersen J.D., Adams D.C. 2013. Complex species interactions lead to unpredictable outcomes in Plethodon. Herpetologica 62:1-10.
23. 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. p. 67-76.
24. Felsenstein J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471-492.
25. Felsenstein J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35:1229-1242.
26. Felsenstein J. 1985. Phylogenies and the comparativemethod. Am.Nat. 125:1-15.
27. Felsenstein J. 1988. Phylogenies and quantitative characters. Annu.Rev. Ecol. Syst. 19:445-471.
28. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
29. Freckleton R.P., Harvey P.H., Pagel M. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. Am. Nat. 160:712-726.
30. 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.
31. Gingras B., Mohandesan E., Boko D., Fitch W.T. 2013. Phylogenetic signal in the acoustic parameters of the advertisement calls of four clades of anurans. BMC Evol. Biol. 13:1-12.
32. Gittleman J.L., Anderson C.G., Kot M., Luh H.-K. 1996. Phylogenetic lability and rates of evolution: a comparison of behavioral, morphological and life history traits. In: Martins E.P., editor. Phylogenies and the comparative method in animal behavior. Oxford: Oxford University Press. p. 166-205.
33. Gower J.C. 1966. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325-338.
34. Grafen A. 1989. The phylogenetic regression. Phil. Trans. R. Soc. Lond. B Biol. Sci. 326:119-157.
35. Hairston N.G. 1980. Evolution under interspecific competition: field experiments on terrestrial salamanders. Evolution 34:409-420.
36. Hardy O.J., Pavoine S. 2012. Assessing phylogenetic signal with measurement error: a comparison of Mantel tests, Blomberg et al.'s K, and phylogenetic distograms. Evolution 66:2614-2621.
37. Harmon L.J., Glor R.E. 2010. Poor statistical performance of theMantel test in phylogenetic comparative analyses. Evolution 64:2173-2178.
38. Harvey P.H., Pagel M.D. 1991. The comparativemethod in evolutionary biology. Oxford: Oxford University Press.
39. Ivanovic A., Sotiropoulos K., Dzukic G., Kalezic M.L. 2009. Skull size and shape variation versus molecular phylogeny: a case study of alpine newts (Mesotriton alpestris, Salamandridae) from the Balkan Penninsula. Zoomorphology 128:157-167.
40. Jaeger R.G. 1971. Competitive exclusion as a factor influencing the distributions of two species of terrestrial salamanders. Ecology 52:632-637.
41. Kamilar J.M., Cooper N. 2013. Phylogenetic signal in primate behaviour, ecology and life history. Phil. Trans. R. Soc. Lond. B Biol. Sci. 368:20120341.
42. Kirkpatrick M., Heckman N. 1989. A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters. J. Math. Biol. 27:429-450.
43. Kirkpatrick M., Meyer K. 2004. Direct estimation of genetic principal components: simplified analysis of complex phenotypes. Genetics 168:2295-2306.
44. Klingenberg C.P., Gidaszewski N.A. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst. Biol. 59:245-261.
45. Krzanowksi W.J. 1993. Principles of multivariate analysis. Oxford: Clarendon Press.
46. Legendre P., Legendre L. 1998. Numerical ecology. 2nd ed.Amsterdam: Elsevier.
47. Losos J.B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11:995-1007.
48. Losos J.B. 2011. Seeing the forest for the trees: the limitations of phylogenies in comparative biology. Am. Nat. 177:709-727.
49. 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.
50. McArdle B.H., Anderson M.J. 2001. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82:290-297.
51. McPeek M.A., Shen L., Torrey J.Z., Farid H. 2008. The tempo and mode of three-dimensional morphological evolution in male reproductive structures. Am. Nat. 171:E158-E178.
52. Møller A.P., Neilsen J.T., Garamzegi L.Z. 2008. Risk taking by singing males. Behav. Ecol. 19:41-53.
53. Munkemuller T., Lavergne S., Bzeznik B., Dray S., Jombart T., Schiffers K., Thuiller W. 2012. How to measure and test phylogenetic signal. Methods Ecol. Evol. 3:743-756.
54. Myers E.M., Adams D.C. 2008. Morphology is decoupled from interspecific competition in Plethodon salamanders in the Shenandoah Mountains. Herpetologica 64:281-289.
55. Pagel M.D. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
56. Pavoine S., Ollier S., Pontier D., Chessel D. 2008. Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities. Theor. Pop. Biol. 73:79-91.
57. Pavoine S., Ricotta C. 2012. Testing for phylogenetic signal in biological traits: the ubiquity of cross-product statistics. Evolution. 67:828-840.
58. Pennell M.W., Harmon L.J. 2013. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Ann N Y Acad. Sci. 1289:90-105.
59. Perez S.I., Diniz-Filho J.A.F., Rohlf F.J., Reis S.F.D. 2009. Ecological and evolutionary factors in the morphological diversificationof South American spiny rats. Biol. J. Linn. Soc. 98:646-660.
60. Polly P.D. 2001. On morphological clocks and paleophylogeography: towards a timescale for Sorex hybrid zones. Genetica 112:339-357.
61. R Development Core Team. 2013. R: a language and environment for statistical computing. Version 3.0.1. R Vienna: Foundation for Statistical Computing. Available from: URL http://cran.Rproject.org.
62. Revell L.J. 2010. Phylogenetic signal and linear regression on species data. Methods Ecol. Evol. 1:319-329.
63. 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.
64. Revell L.J., Harmon L.J., Collar D.C. 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57:591-601.
65. Rezende E.L., Diniz-Filho J.A.F. 2012. Phylogenetic analyses: comparing species to infer adaptations and physiological mechanisms. Comp. Phys. 2:639-674.
66. Rheindt F.E., Grafe T.U., Abouheif E. 2004. Rapidly evolving traits and the comparative method: how important is testing for phylogenetic signal? Evol. Ecol. Res. 6:377-396.
67. Rohlf F.J. 1998. On applications of geometricmorphometrics to studies of ontogeny and phylogeny. Syst. Biol. 47:147-158.
68. Rohlf F.J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55: 2143-2160.
69. Rohlf F.J. 2006. A comment on the phylogenetic correction. Evolution 60:1509-1515.
70. Rohlf F.J., Slice D.E. 1990. Extensions of the Procrustes method for the optimal superimposition of landmarks. Syst. Zool. 39: 40-59.
71. Roncal J, Henderson A, Borchsenius F, Cardoso SRS, Balslev H. 2012. Can phylogenetic signal, character displacement, or random phenotypic drift explain the morphological variation in the genus Geonoma (Arecaceae)? Biol. J. Linn. Soc. 106:528-539.
72. Sidlauskas B. 2008. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach. Evolution 62:3135-3156.
73. Swenson N.G., Enquist B.J., Thompson J., Zimmerman J.K. 2007. The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities. Ecology 88:1770-1780.
74. Wiens J.J., Engstrom T.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.
75. Zheng L., Ives A.R., Garland T., Larget B.R., Yu Y., Cao K. 2009. Newmultivariate tests for phylogenetic signal and trait correlations applied to ecophysiological phenotypes of nine Manglietia species. Funct. Ecol. 23:1059-1069.