mvMORPH: An R package for fitting multivariate evolutionary models to morphometric data

Methods in Ecology and Evolution

Volumn 6, Issue 11, 2015, Pages 1311-1319

  Clavel, Julien ^a,b   Escarguel, Gilles ^b   Merceron, Gildas ^c  

^a PSL RESEARCH UNIVERSITY   (France)

^b UNIVERSITÉ LYON 1   (France)

^c UNIVERSITÉ DE POITIERS   (France)

Author keywords

Brownian motion; Early Burst; Multivariate comparative methods; Ornstein Uhlenbeck; Stochastic mapping

Indexed keywords

EID: 84947815557     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12420     Document Type: Article

References (97)

1. Adams, D.C. (2013) Comparing evolutionary rates for different phenotypic traits on a phylogeny using likelihood. Systematic Biology, 62, 181-192.
2. Adams, D.C. (2014a) A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data. Systematic Biology, 63, 685-697.
3. Adams, D.C. (2014b) A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution, 68, 2675-2688.
4. Adams, D.C. (2014c) Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data. Systematic Biology, 63, 166-177.
5. Adams, D.C. & Otarola-Castillo, E. (2013) geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution, 4, 393-399.
6. Adams, D.C., Berns, C.M., Kozak, K.H. & Wiens, J.J. (2009) Are rates of species diversification correlated with rates of morphological evolution? Proceedings of the Royal Society B, 276, 2729-2738.
7. Armbruster, W.S. & Schwaegerle, K.E. (1996) Causes of covariation of phenotypic traits among populations. Journal of Evolutionary Biology, 9, 261-276.
8. Armbruster, W.S., Pélabon, C., Bolstad, G.H. & Hansen, T.F. (2014) Integrated phenotypes: understanding trait covariation in plants and animals. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 369, 1-16.
9. Arnold, S.J., Pfrender, M.E. & Jones, A.G. (2001) The adaptive landscape as a conceptual bridge between micro and macroevolution. Genetica, 112-113, 9-32.
10. Baker, R.H. & Wilkinson, G.S. (2003) Phylogenetic analysis of correlation structure in stalk-eyed flies (Diasemopsis, Diopsidae). Evolution, 57, 87-103.
11. Bartoszek, K., Pienaar, J., Mostad, P., Andersson, S. & Hansen, T.F. (2012) A phylogenetic comparative method for studying multivariate adaptation. Journal of Theoretical Biology, 314, 204-215.
12. 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, 2369-2389.
13. Blomberg, S.P., Garland, T.J. & Ives, A.R. (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717-745.
14. Boettiger, C., Coop, G. & Ralph, P. (2012) Is your phylogeny informative? Measuring the power of comparative methods. Evolution, 66, 2240-2251.
15. Bollback, J.B. (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 1-7.
16. Burnham, K.P. & Anderson, D.R. (2002) Model Selection and Multi-Model Inference: A Practical Information-Theoretic Approach. Springer-Verlag, New York, USA.
17. Butler, M.A. & King, A.A. (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. The American Naturalist, 164, 683-695.
18. Butler, M.A. & King, A.A. (2009) Multivariate comparative analysis using OUCH. Integrative Comparative Biology, 57.5, e24.
19. Cheverud, J. (1984) Quantitative genetics and developmental constraints on evolution by selection. Journal of Theoretical Biology, 110, 155-171.
20. Collar, D.C., Schulte, J.A. II & Losos, J.B. (2011) Evolution of extreme body size disparity in monitor lizards (varanus). Evolution, 65, 2664-2680.
21. 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.
22. Cooper, N. & Purvis, A. (2010) Body size evolution in mammals: complexity in tempo and mode. The American Naturalist, 175, 727-738.
23. Endler, J.A. (1995) Multiple-trait coevolution and environmental gradients in guppies. Trends in Ecology & Evolution, 10, 22-29.
24. Felsenstein, J. (1973) Maximum-likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics, 25, 471-492.
25. Felsenstein, J. (1985) Phylogenies and the comparative method. The American Naturalist, 125, 1-15.
26. Felsenstein, J. (1988) Phylogenies and quantitative characters. Annual Review of Ecology, Evolution and Systematics, 19, 445-471.
27. Felsenstein, J. (2004) Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts, USA.
28. Felsenstein, J. (2008) Comparative methods with sampling error and within-species variation: contrasts revisited and revised. The American Naturalist, 171, 712-725.
29. FitzJohn, R.G. (2012) Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution, 3, 1084-1092.
30. Freckleton, R.P. (2012) Fast likelihood calculations for comparative analyses. Methods in Ecology and Evolution, 3, 940-947.
31. Frédérich, B., Sorenson, L., Santini, F., Slater, G.J. & Alfaro, M.E. (2013) Iterative ecological radiation and convergence during the evolutionary history of damselfishes (Pomacentridae). The American Naturalist, 181, 94-113.
32. Furrer, R. & Sain, S.R. (2010) Spam: A sparse matrix R package with emphasis on MCMC methods for Gaussian Markov random fields. Journal of Statistical Software, 36, 1-25.
33. Gardiner, C.W. (2004) Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences, 3rd edn. Springer, Berlin.
34. Goswami, A., Smaers, J.B., Soligo, C. & Polly, P.D. (2014) The macroevolutionary consequences of phenotypic integration: from development to deep time. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 369, 1-15.
35. Gustavson, F.G., Waśniewski, J., Dongarra, J.J. & Langou, J. (2010) Rectangular full packed format for Cholesky's algorithm: factorization, solution and inversion. ACM Transactions on Mathematical Software, 37, 1-33.
36. Hadfield, J.D. & Nakagawa, S. (2010) General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. Journal of Evolutionary Biology, 23, 494-508.
37. Hansen, T.F. (1997) Stabilizing selection and the comparative analysis of adaptation. Evolution, 51, 1341-1351.
38. Hansen, T.F. (2012) Adaptive landscape and macroevolutionary dynamics. The Adaptive Landscape in Evolutionary Biology (eds E. Svensson & R. Calsbeek), pp. 205-226. Oxford University Press, Oxford.
39. Hansen, T.F. & Bartoszek, K. (2012) Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies. Systematic Biology, 61, 413-425.
40. Hansen, T.F., Pienaar, J. & Orzack, S.H. (2008) A comparative method for studying adaptation to a randomly evolving environment. Evolution, 62, 1965-1977.
41. Harmon, L.J., Losos, J.B., Davies, J.T., Gillespie, R.G., Gittleman, J.L., Jennings, B.W. et al. (2010) Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64, 2385-2396.
42. Henderson, C.R. (1976) A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics, 32, 69-88.
43. Ho, L.S.T. & Ané, C. (2013) Asymptotic theory with hierarchical autocorrelation: Ornstein-Uhlenbeck tree models. The Annals of Statistics, 41, 957-981.
44. Ho, L.S.T. & Ané, C. (2014) A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic Biology, 63, 397-408.
45. Hohenlohe, P.A. & Arnold, S.J. (2008) MIPoD: A hypothesis-testing framework for microevolutionary inference from patterns of divergence. The American Naturalist, 171, 366-385.
46. Huelsenbeck, J.P., Nielsen, R. & Bollback, J.B. (2003) Stochastic mapping of morphological characters. Systematic Biology, 52, 131-158.
47. Hunt, G. (2012) Measuring rates of phenotypic evolution and the inseparability of tempo and mode. Paleobiology, 38, 351-373.
48. Hunt, G., Bell, M.A. & Travis, M.P. (2008) Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage. Evolution, 62, 700-710.
49. Ingram, T., Harmon, L.J. & Shurin, J.B. (2012) When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model. Journal of Evolutionary Biology, 25, 1902-1910.
50. Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise Akaike Information Criterion. Methods in Ecology and Evolution, 4, 416-425.
51. Ives, A.R., Midford, P.E. & Garland, T.J. (2007) Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology, 56, 252-270.
52. Jaffrézic, F., Thompson, R. & Pletcher, S.D. (2004) Multivariate character process models for the analysis of two or more correlated function-valued traits. Genetics, 168, 477-487.
53. Knope, M.L. & Scales, J.A. (2013) Adaptive morphological shifts to novel habitats in marine sculpin fishes. Journal of Evolutionary Biology, 26, 472-482.
54. Lande, R. (1976) Natural selection and random genetic drift in phenotypic evolution. Evolution, 30, 314-334.
55. Lande, R. (1979) Quantitative genetic analysis of multivariate evolution, applied to brain-body size allometry. Evolution, 33, 402-416.
56. Lande, R. & Arnold, S.J. (1983) The measurement of selection on correlated characters. Evolution, 37, 1210-1226.
57. Lartillot, N. (2014) A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data. Bioinformatics, 30, 488-496.
58. Mahler, D.L., Ingram, T., Revell, L.J. & Losos, J.B. (2013) Exceptional convergence on the macroevolutionary landscape in island lizard radiations. Science, 341, 292-295.
59. 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. The American Naturalist, 149, 646-667.
60. Monteiro, L.R. (2013) Morphometrics and the comparative method: studying the evolution of biological shape. Hystrix, the Italian Journal of Mammalogy, 24, 1-8.
61. O'Meara, B.C. (2012) Evolutionary inferences from phylogenies: a review of methods. Annual Review of Ecology, Evolution and Systematics, 43, 267-285.
62. O'Meara, B.C., Ané, C., Sanderson, M.J. & Wainwright, P.C. (2006) Testing for different rates of continuous trait evolution. Evolution, 60, 922-933.
63. Pagel, M.D. (1999) Inferring the historical patterns of biological evolution. Nature, 401, 877-884.
64. Pennell, M.W. & Harmon, L.J. (2013) An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences, 1289, 90-105.
65. Pinheiro, J.C. & Bates, D.M. (1996) Unconstrained parameterizations for variance-covariance matrices. Statistics and Computing, 6, 289-296.
66. Polly, P.D. (2004) On the simulation of the evolution of morphological shape: multivariate shape under selection and drift. Palaeontologia Electronica, 7.2.7A, 1-28.
67. Polly, P.D., Lawing, M.A., Fabre, A.-C. & Goswami, A. (2013) Phylogenetic principal components analysis and geometric morphometrics. Hystrix, 24, 1-9.
68. Price, S.A., Holzman, R., Near, T.J. & Wainwright, P.C. (2011) Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes. Ecology Letters, 14, 462-469.
69. Price, S.A., Tavera, J.J., Near, T.J. & Wainwright, P.C. (2013) Elevated rates of morphological and functional diversification in reef-dwelling haemulid fishes. Evolution, 67, 417-428.
70. Reitan, T., Schweder, T. & Henderiks, J. (2012) Phenotypic evolution studied by layered stochastic differential equations. The Annals of Applied Statistics, 6, 1531-1551.
71. Revell, L.J. (2009) Size-correction and principal components for interspecific comparative studies. Evolution, 63, 3258-3268.
72. Revell, L.J. (2010) Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution, 1, 319-329.
73. Revell, L.J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217-223.
74. Revell, L.J. & Collar, D.C. (2009) Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution, 63, 1090-1100.
75. Revell, L.J. & Harmon, L.J. (2008) Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evolutionary Ecology Research, 10, 311-331.
76. Revell, L.J. & Reynolds, R.G. (2012) A new bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution, 66, 2697-2707.
77. Ricklefs, R.E. (2006) Time, species, and the generation of trait variance in clades. Systematic Biology, 55, 151-159.
78. Rohlf, F.J. (2001) Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution, 55, 2143-2160.
79. Scales, J.A., King, A.A. & Butler, M.A. (2009) Running for your life or running for your dinner: what drives fiber-type evolution in lizard locomotor muscles? The American Naturalist, 173, 543-553.
80. Schluter, D. (1996) Adaptive radiation along genetic lines of least resistance. Evolution, 50, 1766-1774.
81. Shoval, O., Sheftel, H., Shinar, G., Hart, Y., Ramote, O., Mayo, A., Dekel, E., Kavanagh, K. & Alon, U. (2012) Evolutionary trade-offs, pareto optimality, and the geometry of phenotype space. Science, 336, 1157-1160.
82. Silvestro, D., Kostikova, A., Litsios, G., Pearman, P.B. & Salamin, N. (2015) Measurement errors should always be incorporated in phylogenetic comparative analysis. Methods in Ecology and Evolution, 6, 340-346.
83. Slater, G.J. (2013) Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods in Ecology and Evolution, 4, 734-744.
84. Slater, G.J. (2014) Correction to 'Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary', and a note on fitting macroevolutionary models to comparative paleontological data sets. Methods in Ecology and Evolution, 5, 714-718.
85. Slater, G.J. & Harmon, L.J. (2013) Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods in Ecology and Evolution, 4, 699-702.
86. Slater, G.J., Harmon, L.J. & Alfaro, M.E. (2012) Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution, 66, 3931-3944.
87. Slater, G.J., Price, S.A., Santini, F. & Alfaro, M.E. (2010) Diversity versus disparity and the radiation of modern cetaceans. Proceedings of the Royal Society B, 277, 3097-3104.
88. Steppan, S.J. (1997) Phylogenetic analysis of phenotypic covariance structure. II. Reconstructing matrix evolution. Evolution, 51, 587-594.
89. Steppan, S.J., Phillips, P.C. & Houle, D. (2002) Comparative quantitative genetics: evolution of the G matrix. Trends in Ecology and Evolution, 17, 320-327.
90. Sy, J.P., Taylor, J.M.G. & Cumberland, W.G. (1997) A stochastic model for the analysis of bivariate longitudinal AIDS data. Biometrics, 53, 542-555.
91. Thomas, G.H. & Freckleton, R.P. (2012) MOTMOT: models of trait macroevolution on trees. Methods in Ecology and Evolution, 3, 145-151.
92. Thomas, G.H., Freckleton, R.P. & Székely, T. (2006) Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proceedings of the Royal Society B: Biological Sciences, 273, 1619-1624.
93. Uyeda, J.C., Caetano, D.S. & Pennell, M.W. (2015) Comparative analysis of principal components can be misleading. Systematic Biology, 64, 677-689.
94. Walsh, B. (2007) Escape from flatland. Journal of Evolutionary Biology, 20, 36-38.
95. Walsh, B. & Blows, M.W. (2009) Abundant genetic variation + strong selection = multivariate genetic constraints: a geometric view of adaptation. Annual Review of Ecology, Evolution and Systematics, 40, 41-59.
96. Zeng, Z.-B. (1988) Long-term correlated response, interpopulation covariation, and interspecific allometry. Evolution, 42, 363-374.
97. Zheng, L., Ives, A.R., Garland, T.J., Larget, B.R., Yu, Y. & Cao, K. (2009) New multivariate tests for phylogenetic signal and trait correlations applied to ecophysiological phenotypes of nine Manglietia species. Functional Ecology, 23, 1059-1069.