Integrating fossils with molecular phylogenies improves inference of trait evolution

Evolution

Volumn 66, Issue 12, 2012, Pages 3931-3944

  Slater, Graham J ^a   Harmon, Luke J ^b   Alfaro, Michael E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF IDAHO   (United States)

Author keywords

Ancestral states; Brownian motion; Caniformia; Model selection; Phylogenetic comparative methods

Indexed keywords

BODY SIZE; CLADISTICS; COMPARATIVE STUDY; DATA SET; FOSSIL RECORD; INFORMATION MANAGEMENT; MACROECOLOGY; MOLECULAR ECOLOGY; NUMERICAL MODEL; PHYLOGENY; QUANTITATIVE ANALYSIS; SIMULATION;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BODY SIZE; CARNIVORA; EVOLUTION; FOSSIL; PHYLOGENY;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; BODY SIZE; CARNIVORA; FOSSILS; MODELS, GENETIC; PHYLOGENY;

CANIFORMIA;

EID: 84870542995     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2012.01723.x     Document Type: Article

References (111)

1. Albert, J. S., D. M. Johnson, and J. H. Knouft. 2009. Fossils provide better estimates of ancestral body size than do extant taxa in fishes. Acta Zool. 90:357-384.
2. Alroy, J. 1998. Cope's rule and the dynamics of body mass evolution in North American fossil mammals. Science 280:731-734.
3. Alroy, J. 2000. Understanding the dynamics of trends within evolving lineages. Paleobiology 26:319-329.
4. Aze, T, T. H. G. Ezard, A. Purvis, H. K. Coxall, D. R. M. Stewart, B. S. Wade, and P. N. Pearson. 2011. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol. Rev. 86:900-927.
5. Baele, G., P. Lemey, T. Bedford, A. Rambaut, M. A. Suchard, and A. V. Alekseyenko. In press Improving the accuracy of demographic and molecular clock model comparison wihle accommodating phylogenetic uncertainty. Mol. Biol. Evol. doi:10.1093/molbev/mss084.
6. Bardeleben, C., R. L. Moore, and R. K. Wayne. 2005. A molecular phylogeny of the Canidae based on six nuclear loci. Mol. Phylogenet. Evol. 37:815-831.
7. Beaulieu, J. M., D. C. Jhwueng, C. Boettiger, and B. C. O'Meara. In press Modeling stabilizing selection: Expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution, doi:10.1111/j.1558-5646.2012.01619.x.
8. 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.
9. 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.
10. Boettiger, C., G. Coop, and P. Ralph. 2012. Is your phylogeny informative? Measuring the power of comparative methods. Evolution 66:2240-2251.
11. Bokma, F. 2008. Detection of "punctuated equilibrium" by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution 62:2718-2726.
12. Burbrink, F. T. and R. A. Pyron. 2010. How does ecological opportunity influence rates of speciation, extinction, and morphological diversification in new world ratsnakes (tribe Lampropeltini)? Evolution 64:934-943.
13. Burnham, K. P. and D. R. Anderson. 2002. Model selection and multimodel inference: a practical information theoretic approach. 2nd ed. Springer, New York.
14. Butler, M. A. and A. A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683-695.
15. Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis models and estimation procedures. Am. J. Hum. Genet. 19:233-257.
16. Deméré, T. A. 1994. The family Odobenidae: a phylogenetic analysis of fossil and living taxa. Proc. San Diego Soc. Nat. Hist. 29:99-123.
17. Donoghue, M. J., J. A. Doyle, J. Gauthier, A. G. Kluge, and T. Rowe. 1989. The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20:431-460.
18. Dornburg, A., B. Sidlauskas, F. Santini, L. Sorenson, T. J. Near, and M. E. Alfaro. 2011. The influence of an innovative locomotor strategy on the phenotypic diversification of trigegerfish (Family: Balistidae). Evolution 65:1912-1926.
19. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian Evolutionary Analysis By Sampling Trees. BMC Evol. Biol. 7:214.
20. Eastman, J. M., M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65:3578-3589.
21. Eizirik, E., W. J. Murphy, K.-P. Koepfli, W. E. Johnson, J. W. Dragoo, R. K. Wayne, and S. J. O'Brien. 2010. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol. Phylogenet. Evol. 56:49-63.
22. Etienne, R. S., and M. E. F. Apol. 2009. Estimating speciation and extinction rates from diversity data and the fossil record. Evolution 63:244-255.
23. Etienne, R. S., B. Haegeman, T. Stadler, T. Aze, P. N. Pearson, A. Purvis, and A. B. Phillimore. 2012. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. R. Soc. Lond. B. 279:1300-1309.
24. Ezard, T. H. G., T. Aze, P. N. Pearson, and A. Purvis. 2011. Interplay between changing climate and species' ecology drives macroevolutionary dynamics. Science 332:349-351.
25. Felsenstein, J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471-492.
26. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
27. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
28. Felsenstein, J. 1988. Phylogenies and quantitative characters. Annu. Rev. Ecol. Syst. 19:445-471.
29. Felsenstein, J. 2002. Quantitative characters, phylogenies, and morphometrics. Pp. 27-44 in N. MacLeod and P. L. Forey, eds. Morphology, shape and phylogeny. Taylor and Francis, London, U.K.
30. Figueirido, B., F. J. Serrano-Alarcon, G. J. Slater, and P. Palmqvist. 2010. Shape at the cross-roads: homoplasy and history in the evolution of the carnivoran skull towards herbivory. J. Evol. Biol. 23:2579-2594.
31. Finarelli, J. A., and J. J. Flynn. 2006. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Syst. Biol. 55:301-313.
32. FitzJohn, R. G. 2010. Quantitative traits and diversification. Syst. Biol. 59:619-633.
33. FitzJohn, R. G., W. P. Maddison, and S. P. Otto. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58:595-611.
34. Flynn, J. J., J. A. Finarelli, S. Zehr, J. Hsu, and M. A. Nedbal. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54:317-337.
35. Foote, M. 1996. Evolutionary patterns in the fossil record. Evolution 50:1-11.
36. Fulton, T. L., and C. Strobeck. 2010a. Multiple fossil calibrations, nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae, Pinnipedia). J. Biogeogr. 37:814-829.
37. Fulton, T. L., and C. Strobeck. 2010b. Multiple markers and multiple individuals refine true seal phylogeny and bring molecules and morphology back in line. Proc. R. Soc. Lond. B 277:1065-1070.
38. Gauthier, J., A. Kluge, and T. Rowe. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
39. Gavrilets, S., and J. B. Losos. 2009. Adaptive radiation: contrasting theory with data. Science 323:732-737.
40. Gingerich, P. D. 1987. Evolution and the fossil record: patterns, rates and processes. Can. J. Zool. 65:1053-1060.
41. Gould, S. J. 1988. Trends as changes in variance: a new slant on progress and directionality in evolution. J. Paleontol. 62:319-329.
42. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351.
43. 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.
44. Harmon, L. J., J. A. Schulte, A. Larson, and J. B. Losos. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301:961-964.
45. Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008. Geiger: investigating evolutionary radiations. Bioinformatics 24:129-131.
46. 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.
47. Hastings, W. K. 1970. Monte carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
48. Hone, D. W. E., T. M. Keesey, D. Pisani, and A. Purvis. 2005. Macroevolutionary trends in the Dinosauria: Cope's rule. J. Evol. Biol. 18:587-595.
49. Huelsenbeck, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis? Syst. Biol. 40:458-469.
50. Hulbert, R. C., Jr. 1993. Taxonomic evolution in North American Neogene horses (subfamily Equinae): the rise and fall of an adaptive radiation. Paleobiology 19:216-234.
51. Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578-601.
52. Hunt, G. 2007a. Evolutionary divergence in directions of high phenotypic variance in the ostracode genus Poseidonamicus. Evolution 61:1560-1576.
53. Hunt, G. 2007b. The relative importance of directional change, random walks and stasis in the evoluton of fossil lineages. Proc. Natl. Acad. Sci. USA 104:18404-18408.
54. Hunt, G. 2008. Gradual or pulsed evoluton: when should punctional explanations be preferred? Paleobiology 34:360-377.
55. Hunt, R. M., Jr. 1998. Amphicyonidae. Pp. 196-221 in C. M. Janis, K. M. Scott, and L. J. Jacobs, eds. Evolution of tertiary mammals of North America. Cambridge Univ. Press, Cambridge, U.K.
56. Jones, K. E., J. Bielby, M. Cardillo, S. A. Fritz, J. O'Dell, C. D. L. Orme, K. Safi, W. Sechrest, E. H. Boakes, C. Carbone, et al. 2009. Pantheria: A Species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.
57. Kass, R. E. and A. E. Raftery. 1995. Bayes factors. J. Am. Stat. Assoc. 90:773-795.
58. Koepfli, K.-P., M. E. Gompper, E. Eizirik, C. C. Ho, L. Linden, J. E. Maldonado, and R. K. Wayne. 2007. Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange. Mol. Phylogenet. Evol. 43:1076-1095.
59. Koepfli, K.-P., K. A. Deere, G. J. Slater, C. Begg, K. Begg, L. Grassman, M. Lucherini, G. Veron, and R. K. Wayne. 2008. Multigene phylogeny of the Mustelidae: resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation. BMC Biol. 6:10.
60. Krause, J., T. Unger, A. Nocon, A. S. Malaspinas, S. O. Kolokotronis, M. Stiller, L. Soibelzon, H. Spriggs, P. H. Dear, A. W. Briggs, et al. 2008. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol. Biol. 8:220.
61. Lartillot, N., and H. Phillipe. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195-207.
62. Liow, L. H., T. B. Quental, and C. R. Marshall. 2010. When can decreasing diversification rates be detected with molecular phylogenies and the fossil record? Syst. Biol. 59:646-659.
63. Liow, L. H., T. B. Quental, and C. R. Marshall. 2011. Seeing the forest for the trees: the limitations of phylogenies in comparative biology. Am. Nat. 177:709-727.
64. Maddison, W. P. 1991. Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Syst. Zool. 40:304-314.
65. Maddison, W. P., P. E. Midford, and S. P. Otto. 2007. Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56:701-710.
66. Mahler, D. L., L. J. Revell, R. E. Glor, and J. B. Losos. 2010. Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. Evolution 64:2731-2745.
67. Meredith, R. W., J. E. Janecka, J. Gatesy, O. A. Ryder, C. A. Fisher, E. C. Teeling, A. Goodbla, E. Eizirik, T. L. L. Simao, T. Stadler, et al. 2011. Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334:521-524.
68. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
69. Morlo, M., and S. Peigné. 2010. Molecular and morphological evidence for Ailuridae and a review of its genera. Pp. 92-140 in A. Goswami and A. R. Friscia, eds. Carnivoran evolution: new views on phylogeny, form and function. Cambridge Univ. Press, Cambridge, U.K.
70. Morlon, H., T. L. Parsons, and J. B. Plotkin. 2011. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. USA 108:16327-16332.
71. Newton, M. A., and A. E. Raftery. 1994. Approximate Bayesian-inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B Met. 56:3-48.
72. Oakley, T. H., and C. W. Cunningham. 2000. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54:397-405.
73. 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.
74. Pagel, M. 1994. Detecting correlated evolution on phylogenies-a general-method for the comparative-analysis of discrete characters. Proc. R. Soc. Lond. B 255:37-45.
75. Pagel, M. 1997. Inferring evolutionary processes from phylogenies. Zool. Scr. 26:331-348.
76. Purvis, A., and C. D. L. Orme. 2005. Evolutionary trends in body size. Pp. 1-18 in J. C. Carel, P. A. Kelly, and Y. Christen, eds. Deciphering growth. Springer, Berlin, Heidelberg.
77. Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267:2267-2272.
78. Pyron, R. A. 2011. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60:466-481.
79. Quental, T. B., and C. R. Marshall. 2009. Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution 63:3158-3167.
80. Quental, T. B., and C. R. Marshall. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol. Evol. 25:434-441.
81. R Development Core Team. 2011. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at http://www.R-project.org/.
82. Rabosky, D. L. 2009. Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils. Syst. Biol. 58:629-640.
83. Rabosky, D. L., and I. J. Lovette. 2008a. Density-dependent diversification in North American wood warblers. Proc. R. Soc. Lond. B 275: 2363-2371.
84. Rabosky, D. L., and I. J. Lovette. 2008b. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution 62:1866-1875.
85. Raftery, A. E. 1996. Approximate Bayes factors and accounting for model uncertainty in generalised linear models. Biometrika 83:251-266.
86. Raftery, A. E., M. Newton, J. Satagopan, P. Krivitsky. 2007. Estimating the integrated likelihood via posterior simulation using the harmonic mean identity. Pp. 1-45 in J. M. Bernardo, M. J. Bayarri, and J. O. Berger, eds. Bayesian statistics. Oxford Univ. Press. Oxford, U.K.
87. Revell, L. J., L. J. Harmon, and D. C. Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57:591-601.
88. Revell, L. J., D. L. Mahler, P. R. Peres-Neto, and B. D. Redelings. 2012. A new phylogenetic method for identifying exceptional phenotypic diversification. Evolution 66:135-146.
89. Ricklefs, R. E. 2007. Estimating diversification rates from phylogenetic information. Trends Ecol. Evol. 22:601-610.
90. Rosenblum, E. B., B. A. J. Sarver, J. W. Brown, S. Des Roches, K. M. Hardwick, T. D. Hether, J. M. Eastman, M. W. Pennell, and L. J. Harmon 2012. Goldilocks meets Santa Rosalia: an ephemeral speciation model explains patterns of diversification across time scales. Evol. Biol 39:255-261.
91. Schluter, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press, Oxford, U.K.
92. Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
93. Simpson, G. G. 1944. Tempo and mode in evolution. Columbia biological series; no. 15. Columbia Univ. Press, New York.
94. Simpson, G. G. 1953. The major features of evolution. Columbia biological series, no. 17. Columbia Univ. Press, New York.
95. Simpson, C., W. Kiessling, H. Mewis, R. C. Baron-Szabo, and J. Muller. 2011. Evolutionary diversification of reef corals: a comparison of the molecular and fossil records. Evolution 65:3274-3284.
96. Slater, G. J., S. A. Price, F. Santini, and M. E. Alfaro. 2010. Diversity versus disparity and the radiation of modern cetaceans. Proc. R. Soc. Lond. B 277:3097-3104.
97. Slater, G. J., L. J. Harmon, D. Wegmann, P. Joyce, L. J. Revell, and M. E. Alfaro. 2012. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution 66:752-762.
98. Stanley, S. M. 1973. An explanation for Cope's rule. Evolution 27:1-26.
99. Thomas, G. H., R. P. Freckleton, and T. Szekely. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proc. R. Soc. Lond. B 273:1619-1624.
100. Thomas, G. H., S. Meiri, and A. B. Phillimore. 2009. Body size diversification in Anolis: novel environment and island effects. Evolution 63:2017-2030.
101. Tracy, C. R. 1977. Minimum size of mammalian homeotherms-role of thermal environment. Science 198:1034-1035.
102. Van Valkenburgh, B. 1990. Skeletal and dental predictors of body mass in carnivores. Pp. 181-205 in J. Damuth and B. McFadden, eds. Body Size in mammalian paleobiology. Cambridge Univ. Press, Cambridge, UK.
103. Van Valkenburgh, B. 1999. Major patterns in the history of carnivorous mammals. Annu. Rev. Earth Pl. Sc. 27:463-493.
104. Van Valkenburgh, B., X. Wang, and J. Damuth. 2004. Cope's rule, hypercarnivory, and extinction in North American canids. Science 306:101-104.
105. Wagner, P. J. 1996. Contrasting the underlying patterns of active trends in morphologic evolution. Evolution 50:990-1007.
106. Wagner, P. J. 2000. The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Syst. Biol. 49:65-86.
107. Wang, X. 1994. Phylogenetic systematics of the Hesperocyoninae (Carnivora: Canidae). Bull. Am. Mus. Nat. Hist. 221:1-207.
108. Wang, X., R. H. Tedford, and B. E. Taylor. 1999. Phylogenetic systematics of the Borophaginae (Carnivora: Canidae). Bull. Am. Mus. Nat. Hist. 243:1-391.
109. Webster, A. J., J. L. Gittleman, and A. Purvis. 2004. The life history legacy of evolutionary body size change in carnivores. J. Evol. Biol. 17:396-407.
110. West, G. B., W. H. Woodruff, and J. H. Brown. 2002.Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals. Proc. Natl. Acad. Sci. USA 99:2473-2478.
111. Xie, W., P. O. Lewis, Y. Fan, L. Kuo, and M.-H. Chen. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60:150-160.