Exploring patterns of interspecific variation in quantitative traits using sequential phylogenetic eigenvector regressions

Evolution

Volumn 66, Issue 4, 2012, Pages 1079-1090

  Felizola Diniz Filho, José Alexandre ^a   Rangel, Thiago F ^a   Santos, Thiago ^a   Mauricio Bini, Luis ^a  

^a FEDERAL UNIVERSITY OF GOIÁS   (Brazil)

Author keywords

Brownian motion; Comparative methods; K statistics; O U process; Phylogenetic eigenvector regression; Phylogeny

Indexed keywords

BROWNIAN MOTION; CORRELATION; DIVERGENCE; INTERSPECIFIC VARIATION; MATRIX; NUMERICAL MODEL; PHYLOGENETICS; PHYLOGENY; QUANTITATIVE ANALYSIS; REGRESSION ANALYSIS;

ARTICLE; BIOLOGICAL MODEL; EVOLUTION; PHENOTYPE; PHYLOGENY; QUANTITATIVE TRAIT; REGRESSION ANALYSIS; SPECIES DIFFERENCE;

BIOLOGICAL EVOLUTION; MODELS, BIOLOGICAL; PHENOTYPE; PHYLOGENY; QUANTITATIVE TRAIT, HERITABLE; REGRESSION ANALYSIS; SPECIES SPECIFICITY;

EID: 84859442021     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01499.x     Document Type: Article

References (71)

1. Beltran, S., Y. Desdevises, J. Portela, and J. Boissier 2010. Mating system drives negative associations between morphological features in Schistosomatidae. BMC Evol. Biol. 10:245.
2. Bini, L. M., J. A. F. Diniz-Filho, T. F. L. V. B. Rangel, T. S. B. Akre, R. G. Albaladejo, F. S. Albuquerque, A. Aparicio, M. B. Araújo, A. Baselga, J. Beck, et al. 2009. Coefficient shifts in geographical ecology: an empirical evaluation of spatial and non-spatial regression. Ecography 32:193-204.
3. Bininda-Emonds, O. R. P., J. L. Gittleman, and A. Purvis 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol. Rev. Camb. Philos. Soc. 74:143-175.
4. Bininda-Emonds, O. R. P., M. Cardillo, K. E. Jones, R. D. E. MacPhee, R. M. D. Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman, and A. Purvis 2007. The delayed rise of present-day mammals. Nature 446:507-512.
5. Bisson, I-A., K. Safi, and R. A. Holland 2010. Evidence for repeated independent evolution of migration in the largest family of bats. PLoS One 4:E7504.
6. Blomberg, S. P., and T. Garland, Jr. 2002. Tempo and model in evolution: phylogenetic inertia, adaptation and comparative methods. J. Evol. Biol. 15:899-910.
7. 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.
8. Borcard, D., and P. Legendre 2002. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol. Model. 153:51-68.
9. Borcard, D., P. Legendre, C. Avois-Jacquet, and H. Tuomisto 2004. Dissecting the spatial structure of ecological data at multiple scales. Ecology 85:1826-1832.
10. Cheverud, J. M., M. M. Dow, and W. Leutenegger 1985. The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight in primates. Evolution 39:1335-1351.
11. Cooper, N., W. Jetz, and R. P. Freckleton 2010. Phylogenetic comparative approaches for studying niche conservatism. J. Evol. Biol. 23:2529-2539.
12. Desdevises, Y., P. Legendre, L. Azouzi, and S. Morand 2003. Quantifying phylogenetically structured environmental variation. Evolution 57:2647-2652.
13. Diniz-Filho, J. A. F. 2001. Phylogenetic autocorrelation under distinct evolutionary processes. Evolution 55:1104-1109.
14. Diniz-Filho, J. A. F., and L. M. Bini 2005. Modelling geographical patterns in species richness using eigenvector-based spatial filters. Glob. Ecol. Biogeogr. 14:177-185.
15. Diniz-Filho, J. A. F., and N. M. Tôrres 2002. Phylogenetic comparative methods and the geographic range size-body size relationship in new world terrestrial carnivora. Evol. Ecol. 16:351-367.
16. Diniz-Filho, J. A. F., C. E. R. Sant'Ana, and L. M. Bini 1998. An eigenvector method for estimating phylogenetic inertia. Evolution 52:1247-1262.
17. Diniz-Filho, J. A. F., L. M. Bini, M. A. Rodriguez, T. F. L. V. B. Rangel, and B. A. Hawkins 2007. Seeing the forest for the trees: partitioning ecological and phylogenetic components of Bergmann's rule in European Carnivora. Ecography 30:598-608.
18. Diniz-Filho, J. A. F., M. A. Rodríguez, L. M. Bini, M. A. Olalla-Tárraga, M. Cardillo, J. C. Nabout, J. Hortal, and B. A. Hawkins 2009. Climate history, human impacts and global body size of Carnivora (Mammalia: Eutheria) at multiple evolutionary scales. J. Biogeogr. 36:2222-2236.
19. Diniz-Filho J. A. F., L. C. Terribile, M. J. R. da Cruz, and L. C. G. Vieira 2010. Hidden patterns of phylogenetic non-stationarity overwhelm comparative analyses of niche conservatism and divergence. Glob. Ecol. Biogeogr. 9:916-926.
20. Diniz-Filho, J. A. F., M. V. Cianciaruso, T. F. Rangel, and L. M. Bini 2011. Eigenvector estimating of phylogenetic and functional diversity. Funct. Ecol. 25:735-744.
21. Diniz-Filho, J. A. F., L. M. Bini, T. F. Rangel, I. Morales-Castilla, M. Olalla-Tárraga, M. A. Rodriguez, and B. A. Hawkins 2012. On the selection of phylogenetic eigenvectors for ecological analysis. Ecography, doi:
22. Dray, S., P. Legendre, and P. R. Peres-Neto 2006. Spatial modeling: a comprehensive framework for principal coordinate analysis of neighbor matrices (PCNM). Ecol. Model. 196:483-493.
23. Felsenstein, J. 1985 Phylogenies and the comparative method. Am. Nat. 125:1-15.
24. Felsenstein, J. 1988. Phylogenies and quantitative characters. Annu. Rev. Ecol. Syst. 19:445-471
25. Freckleton, R. P. 2009. The seven deadly sins of comparative analysis. J. Evol. Biol. 22:1367-1375.
26. 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.
27. Freckleton, R. P., N. Cooper, and W. Jetz 2011. Comparative method as a statistical fix: the dangers of ignoring evolutionary models. Am. Nat. 178:E10-E17.
28. Gittleman, J. L., and M. Kot 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Syst. Zool. 39:227-241.
29. Grafen, A. 1989. The phylogenetic regression. Philos. Trans. R. Soc. Lond. B 326:119-157.
30. Griffith, D. A. 2003. Spatial autocorrelation and spatial filtering: gaining understanding through theory and scientific visualization. Springer-Verlag, New York
31. Griffith, D. A., and P. R. Peres-Neto 2006. Spatial modeling in ecology: the flexibility of eigenfunction spatial analyses. Ecology 87:2603-2613.
32. Hadfield, J. D., and S. Nakagawa 2009. General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. J. Evol. Biol. 23:494-508.
33. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351.
34. Hansen, T. F., and E. P. Martins 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50:1404-1417.
35. Hansen, T. F., J. Piennar, and S. H. Orzack 2008. A comparative method for studying adaptation to a randomly evolving environment. Evolution 62:1965-1977.
36. Harvey, P. H., and M. Pagel 1991. The comparative method in evolutionary biology. Oxford Univ. Press, Oxford, U.K
37. Hill, S. B., and P. M. Kotanen 2011. Phylogenetic structure predicts capitular damage to Asteraceae better than origin or phylogenetic distance to natives. Oecologia 166:843-851.
38. Hof, C., C. Rahbek, and M. B. Araújo 2010. Phylogenetic signals in the climatic niches of world's amphibians. Ecography 33:242-250.
39. Housworth, E. A., E. P. Martins, and M. Lynch 2004. The phylogenetic mixed model. Am. Nat. 163:84-96.
40. Kozak, K. H., and J. J. Wiens 2010. Niche conservatism drives elevational diversity patterns in Appalachian salamanders. Am. Nat. 176:40-54.
41. Kuhn, I., M. P. Nobis, and W. Durka 2009. Combining spatial and phylogenetic eigenvector filtering in trait analysis. Glob. Ecol. Biogeogr. 18:745-758.
42. Laurin, M. 2010. Assessment of the relative methods of a few methods to detect evolutionary trends. Syst. Biol. 59:689-704.
43. Legendre P., and L. Legendre 1998. Numerical ecology, 3rd ed. Elsevier, Amsterdam
44. Losos, J. B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 11:995-1003.
45. Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45:1065-1080.
46. Martins, E. P. 1996. Phylogenies, spatial autoregression and the comparative method: a computer simulation test. Evolution 50:1750-1765.
47. Martins, E. P. and T. Garland, Jr. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45:534-557.
48. Martins, E. P., and T. F. Hansen 1996. A microevolutionary link between phylogenies and comparative data. Pp. 273-288 in P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee, eds. Oxford Univ. Press, Oxford, U.K
49. Martins, E. P., and T. F. Hansen 1997. Phylogenies and the comparative method: a general approach to incorporate phylogenetic information into the analysis of interspecific data. Am. Nat. 149:646-667.
50. Martins, E. P., J. A. F. Diniz-Filho, and E. A. Housworth 2002. Adaptive constraints and the phylogenetic comparative method: a computer simulation test. Evolution 56:1-13.
51. Monteiro, L. R., and A. S. Abe 1999. Functional and historical determinants of shape in the scapula of Xenarthran mammals: evolution of a complex morphological structure. J. Morphol. 241:251-263.
52. Morales, E. 2000. Estimating phylogenetic inertia in Tithonia (Asteraceae): a comparative approach. Evolution 54:475-484.
53. Olalla-Tárraga M. Á., L. M. Bini, J. A. F. Diniz-Filho, and M. A. Rodríguez 2010. Cross-species and assemblage-based approaches to Bergmann's rule and the biogeography of body size in Plethodon salamanders of Eastern North America. Ecography 33:362-368.
54. Ollier, S., P. Couteron, and D. Chessel 2006. Orthonormal transform to decompose the variance of a life-history trait across a phylogenetic tree. Biometrics 62:471-477.
55. Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:977-984.
56. Pavoine, S., S. Ollier, D. Pontier, and D. Chessel 2007. Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities. Theor. Popul. Biol. 73:79-91.
57. Peres-Neto, P. R. 2006. A unified strategy for estimating and controlling spatial, temporal and phylogenetic autocorrelation in ecological models. Oecologia Brasiliensis 10:105-119.
58. Peres-Neto, P. R., and P. Legendre 2010. Estimating and controlling for spatial autocorrelation in the study of ecological communities. Glob. Ecol. Biogeogr. 19:174-184.
59. Pillar, V. D., and L. D. S. Duarte 2010. A framework for metacommunity analysis of phylogenetic structure. Ecol. Lett. 13:587-596.
60. R Development Core Team. 2010. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria Available at
61. Ramirez, L., J. A. F. Diniz-Filho, and B. A. Hawkins 2008. Partitioning phylogenetic and adaptive components of the geographical body-size pattern of New World birds. Glob. Ecol. Biogeogr. 17:100-110.
62. Revell, L. J., L. J. Harmon, and D. C. Collar 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57:591-601.
63. Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:2143-2160.
64. Rohlf, F. J., W. S. Chang, R. R. Sokal, and J. Kim 1990. Accuracy of estimated phylogenies: effects of tree topology and evolutionary models. Evolution 44:1671-1684.
65. Safi, K., and N. Pettorelli 2010. Phylogenetic, spatial and environmental components of extinction risk in carnivores. Glob. Ecol. Biogeogr. 19:352-362.
66. Sakamoto, M, G. T. Lloyd, and M. J. Benton 2010. Phylogenetically structured variance in felid bite force: the role of phylogeny in the evolution of biting performance. J. Evol. Biol. 23:463-478.
67. Staggemeier, V. G., J. A. F. Diniz-Filho, and L. P. C. Morellato 2010. The shared influence of ecology and phylogeny on the reproductive patterns of Myrtaea (Myrtaceae). J. Ecol. 98:1409-1421.
68. Stone, G. N., S. Nee, and J. Felsenstein 2011. Controlling for non-independence in comparative analysis of patterns across populations within species. Philos. Trans. R. Soc. Lond. B. 366:1410-1424.
69. Terribile, L. C., M. A. Olalla-Tárraga, J. A. F. Diniz-Filho, and M. Á. Rodríguez 2009. Ecological and evolutionary components of body size: geographic variation of venomous snakes at the global scale. Biol. J. Linn. Soc. 98:94-109.
70. Tiefelsdorf, M., and D. Griffith 2007. Semi-parametric filtering of spatial autocorrelation: the eigenvector approach. Environ. Plann. A 39:1193-1221.
71. Wiens, J. J., D. D. Ackerly, A. P. Allen, B. L. Anacker, L. B. Buckley, H. V. Cornell, E. I. Damschen, R. Davies, T. J. J. A. Grytnes, S. P. Harrison, et al. 2010. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol. Lett. 13:1310-1324