An integrative view of phylogenetic comparative methods: Connections to population genetics, community ecology, and paleobiology

Annals of the New York Academy of Sciences

Volumn 1289, Issue 1, 2013, Pages 90-105

  Pennell, Matthew W ^a,b   Harmon, Luke J ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

Author keywords

Fossils; Macroevolution; Phylogenies

Indexed keywords

ARTICLE; BIODIVERSITY; BIOLOGY; COMMUNITY ECOLOGY; EVOLUTION; FOSSIL; GEOLOGY; MATHEMATICAL MODEL; MOLECULAR PHYLOGENY; NONHUMAN; PALEOBIOLOGY; PHYLOGENETIC COMPARATIVE METHOD; PHYLOGENY; POPULATION GENETICS; QUANTITATIVE GENETICS;

EID: 84879308395     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/nyas.12157     Document Type: Article

References (206)

1. Baum, D.A. & S.D. Smith. 2012. Tree Thinking: An Introduction to Phylogenetic Biology. Greenwood Village, Colorado: Roberts and Co. Publishers.
2. Ronquist, F. & J.P. Huelsenbeck. 2003. Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
3. Drummond, A. & A. Rambaut. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
4. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
5. O'Meara, B.C. 2012. Evolutionary inferences from phylogenies: a review of methods. Annu. Rev. Ecol. Evol. Syst. 43: 267-285.
6. Alfaro, M.E., F. Santini, C. Brock, et al. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. USA 106: 13410-13414.
7. Stadler, T. 2011. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl. Acad. Sci. USA 108: 6187-6192.
8. Morlon, H., T.L. Parsons & J.B. Plotkin. 2011. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. USA 108: 16327-16332.
9. Etienne, R.S. & B. Haegeman. 2012. A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence. Am. Nat. 180: E75-E89.
10. Condamine, F.L., J. Rolland & H. Morlon. 2013. Macroevolutionary perspectives to environmental change. Ecol. Lett. 16: Issue Supplement S1: 72-85.
11. O'Meara, B.C., C. Ané, M.J. Sanderson & P.C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60: 922-933.
12. Thomas, G.H., R.P. Freckleton & T. Székely. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proc. R. Soc. B Biol. Sci. 273: 1619-1624.
13. Eastman, J.M., M.E. Alfaro, P. Joyce, et al. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65: 3578-3589.
14. Revell, L.J., D.L. Mahler, P.R. Peres-Neto & B.D. Redelings. 2012. A new phylogenetic method for identifying exceptional phenotypic diversification. Evolution 66: 135-146.
15. Beaulieu, J.M., D.C. Jhwueng, C. Boettiger & B.C. O'Meara. 2012. Modeling stabilizing selection: expanding the Ornstein-Uhlenbeck model of adaptive evolution. Evolution 66: 2369-2383.
16. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125: 1-15.
17. Grafen, A. 1989. The phylogenetic regression. Philos. Trans. R. Soc. Lond. B Biol. Sci. 326: 119-157.
18. Harvey, P.H. & M.D. Pagel. 1991. The Comparative Method in Evolutionary Biology. Oxford: Oxford University Press.
19. Nee, S., A.O. Mooers & P.H. Harvey. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. USA 89: 8322-8326.
20. Nee, S., R.M. May & P.H. Harvey. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. B Biol. Sci. 344: 305-311.
21. Hansen, T.F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51: 1341-1351.
22. Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B Biol. Sci. 255: 37-45.
23. Harmon, L.J., J.A. Schulte, A. Larson & J.B. Losos. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301: 961-964.
24. Maddison, W.P., P.E. Midford & S.P. Otto. 2007. Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56: 701-710.
25. FitzJohn, R.G. 2012. Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol. Evol. 3: 1084-1092.
26. Garland, T., P.H. Harvey & A.R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst. Biol. 41: 18-32.
27. Garland, T. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 140: 509-519.
28. Blomberg, S.P., J.G. Lefevre, J.A. Wells & M. Waterhouse. 2012. Independent contrasts and PGLS regression estimators are equivalent. Syst. Biol. 61: 382-391.
29. Rohlf, F.J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55: 2143-2160.
30. Blomberg, S.P., T. Garland & A.R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57: 717-745.
31. Harmon, L.J., J.B. Losos, T. Jonathan Davies, et al. 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64: 2385-2396.
32. Pagel, M. 1997. Inferring evolutionary processes from phylogenies. Zool. Scr. 26: 331-348.
33. Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877-884.
34. Revell, L.J. 2010. Phylogenetic signal and linear regression on species data. Methods Ecol. Evol. 1: 319-329.
35. Hansen, T.F. & K. Bartoszek. 2012. Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies. Syst. Biol. 61: 413-425.
36. Diniz-Filho, J.A.F., C.E.R. de Sant'Ana & L.M. Bini. 1998. An eigenvector method for estimating phylogenetic inertia. Evolution 52: 1247-1262.
37. Smouse, P.E., J.C. Long & R.R. Sokal. 1986. Multiple regression and correlation extensions of the mantel test of matrix correspondence. Syst. Zool. 35: 627-632.
38. Freckleton, R.P., N. Cooper & W. Jetz. 2011. Comparative methods as a statistical fix: the dangers of ignoring an evolutionary model. Am. Nat. 178: E10-E17.
39. Harmon, L.J. & R.E. Glor. 2010. Poor statistical performance of the mantel test in phylogenetic comparative analysis. Evolution 64: 2173-2178.
40. Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45: 1065-1080.
41. Housworth, E.A., E.P. Martins & M. Lynch. 2004. The phylogenetic mixed model. Am. Nat. 163: 84-96.
42. Hadfield, J.D. & S. Nakagawa. 2010. General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. J. Evol. Biol. 23: 494-508.
43. Henderson, C.R. 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32: 69-83.
44. Lynch, M. & B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates.
45. Sorensen, D. & D. Gianola. 2002. Likelihood, Bayesian and MCMC Methods in Quantitative Genetics. New York, NY: Springer-Verlag.
46. Thompson, R. 2008. Estimation of quantitative genetic parameters. Proc. R. Soc. B Biol. Sci. 275: 679-686.
47. Hadfield, J. 2010. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J. Stat. Softw. 33: 1-22.
48. Ives, A.R. & T. Garland. 2010. Phylogenetic logistic regression for binary dependent variables. Syst. Biol. 59: 9-26.
49. FitzJohn, R.G. 2010. Quantitative traits and diversification. Syst. Biol. 59: 619-633.
50. Felsenstein, J. 2012. A comparative method for both discrete and continuous characters using the threshold model. Am. Nat. 179: 145-156.
51. Freckleton, R.P. 2012. Fast likelihood calculations for comparative analyses. Methods Ecol. Evol. 3: 940-947.
52. Revell, L.J. & R. Reynolds. 2012. A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution 66: 2697-2707.
53. Hansen, T.F. & E.P. Martins. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50: 1404-1417.
54. Mooers, A.Ø., S.M. Vamosi & D. Schluter. 1999. Using phylogenies to test macroevolutionary hypotheses of trait evolution in cranes (Gruinae). Am. Nat. 154: 249-259.
55. Martins, E.P. 1994. Estimating the rate of phenotypic evolution from comparative data. Am. Nat. 144: 193-209.
56. Lewis, P.O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50: 913-925.
57. Collar, D.C., T.J. Near & P.C. Wainwright. 2005. Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes? Evolution 59: 1783-1794.
58. Green, P.J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
59. Venditti, C., A. Meade & M. Pagel. 2011. Multiple routes to mammalian diversity. Nature 479: 393-396.
60. Eastman, J.M., M.W. Pennell, G.J. Slater, et al. Geiger2: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. In preparation.
61. Beaumont, M.A. 2010. Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41: 379-406.
62. Sunnaker, M., A.G. Busetto, E. Numminen, et al. 2013. Approximate Bayesian computation. PLoS Comput. Biol. 9: e1002803.
63. Slater, G.J., L.J. Harmon, D. Wegmann, et al. 2012. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution 66: 752-762.
64. Kutsukake, N. & H. Innan. 2013. Simulation-based likelihood approach for evolutionary models of phenotypic traits on phylogeny. Evolution 67: 355-367.
65. Lande, R. 1976. Natural selection and random genetic drift in phenotypic evolution. Evolution 30: 314-334.
66. Butler, M.A. & A.A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164: 683-695.
67. Ingram, T. & D.L. Mahler. 2013. SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods Ecol. Evol. 4: 416-425.
68. Hansen, T.F., J. Pienaar & S.H. Orzack. 2008. A comparative method for studying adaptation to a randomly evolving environment. Evolution 62: 1965-1977.
69. Burbrink, F.T., X. Chen, E.A. Myers, et al. 2012. Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation. Proc. R. Soc. Lond. B Biol. Sci. 279: 4817-4826.
70. Simpson, G.G. 1953. Major Features of Evolution. New York, NY: Columbia University Press.
71. Schluter, D. 2000. The Ecology of Adaptive Radiation. Oxford University Press.
72. 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.
73. Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32: 578-601.
74. Hunt, G. 2007. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proc. Natl. Acad. Sci. USA 104: 18404-18408.
75. Slater, G.J., L.J. Harmon & M.E. Alfaro. 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66: 3931-3944.
76. Landis, M.J., J.G. Schraiber & M. Liang. 2013. Phylogenetic analysis using Lévy processes: finding jumps in the evolution of continuous traits. Syst. Biol. 62: 193-204.
77. Simpson, G.G. 1944. Tempo and Mode of Evolution. New York, NY: Columbia University Press.
78. Slowinski, J.B. & C. Guyer. 1993. Testing whether certain traits have caused amplified diversification-an improved method based on a model of random speciation and extinction. Am. Nat. 142: 1019-1024.
79. Slowinski, J.B. & C. Guyer. 1989. Testing the stochasticity of patterns of organismal diversity-an improved null model. Am. Nat. 134: 907-921.
80. Vamosi, J.C. & S.M. Vamosi. 2004. The role of diversification in causing the correlates of dioecy. Evolution 58: 723-731.
81. Sargent, R.D. 2004. Floral symmetry affects speciation rates in angiosperms. Proc. R. Soc. Lond. B Biol. Sci. 271: 603-608.
82. Blum, M.G.B. & O. Francois. 2006. Which random processes describe the tree of life? a large-scale study of phylogenetic tree imbalance. Syst. Biol. 55: 685-691.
83. Felsenstein, J. 2004. Inferring Phylogenies. Sunderland, MA: Sinauer.
84. Chan, K.M.A. & B.R. Moore. 2002. Whole-tree methods for detecting differential diversification rates. Syst. Biol. 51: 855-865.
85. Chan, K.M.A. & B.R. Moore. 2005. SYMMETREE: whole-tree analysis of differential diversification rates. Bioinformatics 21: 1709-1710.
86. Moore, B.R. & M.J. Donoghue. 2009. A Bayesian approach for evaluating the impact of historical events on rates of diversification. Proc. Natl. Acad. Sci. 106: 4307-4312.
87. Mooers, A.O. & S.B. Heard. 1997. Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72: 31-54.
88. Alroy, J. 2010. The shifting balance of diversity among major marine animal groups. Science 329: 1191-1194.
89. Harnik, P.G., H.K. Lotze, S.C. Anderson, et al. 2012. Extinctions in ancient and modern seas. Trends Ecol. Evol. 27: 608-617.
90. Raup, D.M., S.J. Gould, T.J.M. Schopf & D.S. Simberloff. 1973. Stochastic models of phylogeny and the evolution of diversity. J. Geol. 81: 525-542.
91. Raup, D.M. 1985. Mathematical models of cladogenesis. Paleobiology 11: 42-52.
92. Rabosky, D.L. & I.J. Lovette. 2008. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution 62: 1866-1875.
93. Morlon, H., M.D. Potts & J.B. Plotkin. 2010. Inferring the dynamics of diversification: a coalescent approach. PLoS Biol. 8: e1000493.
94. Rabosky, D.L. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64: 1816-1824.
95. Bokma, F. 2009. Problems detecting density-dependent diversification on phylogenies. Proc. R. Soc. B Biol. Sci. 276: 993-994.
96. Pennell, M.W., B.A.J. Sarver & L.J. Harmon. 2012. Trees of unusual size: biased inference of early bursts from large molecular phylogenies. PLoS ONE 7: e43348.
97. Stanley, S. 1979. Macroevolution. Baltimore, Maryland: Johns Hopkins University Press.
98. Vrba, E.S. & S.J. Gould. 1986. The hierarchical expansion of sorting and selection: sorting and selection cannot be equated. Paleobiology 12: 217-228.
99. Gould, S.J. 2002. The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press.
100. Fitzjohn, R.G. 2012. What drives biological diversification? detecting traits under species selection. PhD thesis. University of British Columbia.
101. Goldberg, E.E., J.R. Kohn, R. Lande, et al. 2010. Species selection maintains self-incompatibility. Science 330: 493-495.
102. Jablonski, D. 2008. Species selection: theory and data. Annu. Rev. Ecol. Evol. Syst. 39: 501-524.
103. Rabosky, D.L. & A.R. McCune. 2010. Reinventing species selection with molecular phylogenies. Trends Ecol. Evol. 25: 68-74.
104. Maddison, W.P. 2006. Confounding asymmetries in evolution diversification and character change. Evolution 60: 1743-1746.
105. Goldberg, E.E. & B. Igic. 2008. On phylogenetic tests of irreversible evolution. Evolution 62: 2727-2741.
106. Goldberg, E.E., L.T. Lancaster & R.H. Ree. 2011. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Syst. Biol. 60: 451-465.
107. Goldberg, E.E. & B. Igić. 2012. Tempo and mode in plant breeding system evolution. Evolution 66: 3701-3709.
108. Magnuson-Ford, K. & S.P. Otto. 2012. Linking the investigations of character evolution and species diversification. Am. Nat. 180: 225-245.
109. Arnold, S.J., M.E. Pfrender & A.G. Jones. 2001. The adaptive landscape as a conceptual bridge between micro- and macroevolution. Genetica 112-113: 9-32.
110. Hendry, A.P. & M.T. Kinnison. 1999. Perspective: the pace of modern life: measuring rates of contemporary microevolution. Evolution 53: 1637-1653.
111. Kingsolver, J.G., H.E. Hoekstra, J.M. Hoekstra, et al. 2001. The strength of phenotypic selection in natural populations. Am. Nat. 157: 245-261.
112. Hereford, J., T.F. Hansen & D. Houle. 2004. Comparing strengths of directional selection: how strong is strong? Evolution 58: 2133-2143.
113. Kingsolver, J.G. & S.E. Diamond. 2011. Phenotypic selection in natural populations: what limits directional selection? Am. Nat. 177: 346-357.
114. Mousseau, T.A. & D.A. Roff. 1987. Natural selection and the heritability of fitness components. Heredity 59: 181-197.
115. Houle, D. 1992. Comparing evolvability and variability of quantitative traits. Genetics 130: 195-204.
116. Futuyma, D.J. 2010. Evolutionary constraint and ecological consequences. Evolution 64: 1865-1884.
117. Hansen, T.F., C. Pélabon & D. Houle. 2011. Heritability is not evolvability. Evol. Biol. 38: 258-277.
118. Eldredge, N. & S.J. Gould. 1972. "Punctuated equilibria: an alternative to phyletic gradualism." In Models in Paleobiology. T. Schopf, Ed.: 82-115. San Francisco, CA: Freeman, Cooper & Co.
119. Gingerich, P.D. 1983. Rates of evolution: effects of time and temporal scaling. Science 222: 159-161.
120. Hansen, T.F. & D. Houle. 2004. "Evolvability, stabilizing selection and the problem of stasis." In The Evolutionary Biology of Complex Phenotypes. M. Pigliucci & K. Preston, Eds.: 130-150. New York, NY: Oxford University Press.
121. Uyeda, J.C., T.F. Hansen, S.J. Arnold & J. Pienaar. 2011. The million-year wait for macroevolutionary bursts. Proc. Natl. Acad. Sci. 108: 15908-15913.
122. Felsenstein, J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25: 471-492.
123. Turelli, M., J.H. Gillespie & R. Lande. 1988. Rate tests for selection on quantitative characters during macroevolution and microevolution. Evolution 42: 1085-1089.
124. Futuyma, D.J. 1987. On the role of species in anagenesis. Am. Nat. 130: 465-473.
125. Schluter, D. 1996. Adaptive radiation along genetic lines of least resistance. Evolution 50: 1766-1774.
126. Walsh, B. & M.W. Blows. 2009. Abundant genetic variation + strong selection = multivariate genetic constraints: a geometric view of adaptation. Annu. Rev. Ecol. Evol. Syst. 40: 41-59.
127. Kingman, J.F.C. 1978. A simple model for the balance between selection and mutation. J. Appl. Probab. 15: 1-12.
128. Turelli, M. 1984. Heritable genetic variation via mutation-selection balance: Lerch's zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138-193.
129. Kimura, M. & J.F. Crow. 1964. The number of alleles that can be maintained in a finite population. Genetics 49: 725-738.
130. Estes, S. & S.J. Arnold. 2007. Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales. Am. Nat. 169: 227-244.
131. Hohenlohe, P.A. & S.J. Arnold. 2008. MIPoD: a hypothesis-testing framework for microevolutionary inference from patterns of divergence. Am. Nat. 171: 366-385.
132. Revell, L.J. & L.J. Harmon. 2008. Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evol. Ecol. Res. 10: 311-331.
133. Kolbe, J.J., L.J. Revell, B. Szekely, et al. 2011. Convergent evolution of phenotypic integration and its alignment with morphological diversification in Carribbean Anolis ecomorphs. Evolution 65: 3608-3624.
134. Bartoszek, K., J. Pienaar, P. Mostad, et al. 2012. A phylogenetic comparative method for studying multivariate adaptation. J. Theor. Biol. 314: 204-215.
135. Webb, C.O., D.D. Ackerly, M.A. McPeek & M.J. Donoghue. 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33: 475-505.
136. Cadle, J.E. & H.W. Green. 1993. Phylogenetic patterns, biogeography, and the ecological structure of Neotropical snake assemblages. In Species Diversity in Ecological Communities. R. Ricklefs & D. Schluter, Eds.: 291-293. Chicago, IL: University of Chicago Press.
137. Helmus, M.R. & A.R. Ives. 2012. Phylogenetic diversity-area curves. Ecology 93: S31-S43.
138. Peres-Neto, P.R., M.A. Leibold & S. Dray. 2012. Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics. Ecology 93: S14-S30.
139. McGill, B.J., B.J. Enquist, E. Weiher & M. Westoby. 2006. Rebuilding community ecology from functional traits. Trends Ecol. Evol. 21: 178-185.
140. Cavender-Bares, J., K.H. Kozak, P.V.A. Fine & S.W. Kembel. 2009. The merging of community ecology and phylogenetic biology. Ecol. Lett. 12: 693-715.
141. Mayfield, M.M. & J.M. Levine. 2010. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol. Lett. 13: 1085-1093.
142. Rabosky, D.L., M.A. Cowan, A.L. Talaba & I.J. Lovette. 2011. Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from arid Australia. Am. Nat. 178: 579-595.
143. Baraloto, C., O.J. Hardy, C.E.T. Paine, et al. 2012. Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities. J. Ecol. 100: 690-701.
144. Hardy, O.J. & B. Senterre. 2007. Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity. J. Ecol. 95: 493-506.
145. Ives, A.R. & M.R. Helmus. 2011. Generalized linear mixed models for phylogenetic analyses of community structure. Ecol. Monogr. 81: 511-525.
146. Revell, L.J., L.J. Harmon & D.C. Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 57: 591-601.
147. Swenson, N.G., D.L. Erickson, X. Mi, et al. 2012. Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities. Ecology 93: S112-S125.
148. Graham, C.H., J.L. Parra, B.A. Tinoco, et al. 2012. Untangling the influence of ecological and evolutionary factors on trait variation across hummingbird assemblages. Ecology 93: S99-S111.
149. Hubbell, S.P. 2001. The Unified Neutral Theory of Biodiversity and Biogeography. Princeton, NJ: Princeton University Press.
150. Cadotte, M.W., T. Jonathan Davies, J. Regetz, et al. 2010. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecol. Lett. 13: 96-105.
151. Rosindell, J., S.P. Hubbell & R.S. Etienne. 2011. The unified neutral theory of biodiversity and biogeography at age ten. Trends Ecol. Evol. 26: 340-348.
152. Chave, J. 2004. Neutral theory and community ecology. Ecol. Lett. 7: 241-253.
153. Hubbell, S.P. 2006. Neutral theory and the evolution of ecological equivalence. Ecology 87: 1387-1398.
154. Kelly, C.K., M.G. Bowler, O. Pybus & P.H. Harvey. 2008. Phylogeny, niches and relative abundance in natural communities. Ecology 89: 962-970.
155. Schoener, T.W. 2011. The newest synthesis: understanding the interplay of evolutionary and ecological dynamics. Science 331: 426-429.
156. Lavorel, S. & E. Garnier. 2002. Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the holy grail. Funct. Ecol. 16: 545-556.
157. Maherali, H. & J.N. Klironomos. 2007. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316: 1746-1748.
158. Srivastava, D.S., M.W. Cadotte, A.A.M. MacDonald, et al. 2012. Phylogenetic diversity and the functioning of ecosystems. Ecol. Lett. 15: 637-648.
159. Gravel, D., T. Bell, C. Barbera, et al. 2012. Phylogenetic constraints on ecosystem functioning. Nat. Commun. 3: 1117.
160. Cadotte, M.W., R. Dinnage & D. Tilman. 2012. Phylogenetic diversity promotes ecosystem stability. Ecology 93: S223-S233.
161. Foote, M. 1993. Discordance and concordance between morphological and taxonomic diversity. Paleobiology 19: 185-204.
162. Benton, M.J. 2009. The red queen and the court jester: species diversity and the role of biotic and abiotic factors through time. Science 323: 728-732.
163. Sepkoski, J.J. 1993. Ten years in the library: new data confirm paleontological patterns. Paleobiology 19: 43-51.
164. Rabosky, D.L. 2009. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. 12: 735-743.
165. Strotz, L.C. & A.P. Allen. 2013. Assessing the role of cladogenesis in macroevolution by integrating fossil and molecular evidence. Proc. Natl. Acad. Sci. USA 110: 2904-2909.
166. Darwin, C.R. 1859. On the Origin of Species by Means of Natural Selection. London: John Murray.
167. Alroy, J., C.R. Marshall, R.K. Bambach, et al. 2001. Effects of sampling standardization on estimates of phanerozoic marine diversification. Proc. Natl. Acad. Sci. USA 98: 6261-6266.
168. Bush, A.M. & R.K. Bambach. 2004. Did alpha diversity increase during the phanerozoic? lifting the veils of taphonomic, latitudinal, and environmental biases. J. Geol. 112: 625-642.
169. Alroy, J., M. Aberhan, D.J. Bottjer, et al. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321: 97-100.
170. Hannisdal, B. & S.E. Peters. 2011. Phanerozoic earth system evolution and marine biodiversity. Science 334: 1121-1124.
171. Coyne, J.A. & H.A. Orr. 2004. Speciation. Sunderland, MA: Sinauer Associates.
172. De Queiroz, K. 2007. Species concepts and species delimitation. Syst. Biol. 56: 879-886.
173. Ezard, T.H.G., P.N. Pearson, T. Aze & A. Purvis. 2012. The meaning of birth and death (in macroevolutionary birth-death models). Biol. Lett. 8: 139-142.
174. Raup, D.M. 1976. Species diversity in the phanerozoic: a tabulation. Paleobiology 2: 279-288.
175. Janevski, G.A. & B.K. Tomasz. 2009. Evidence for extinction selectivity throughout the marine invertebrate fossil record. Paleobiology 35: 553-564.
176. Lloyd, G.T., J.R. Young & A.B. Smith. 2012. Taxonomic structure of the fossil record is shaped by sampling bias. Syst. Biol. 61: 80-89.
177. Quental, T.B. & C.R. Marshall. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol. Evol. 25: 434-441.
178. Swofford, D.L. & W.P. Maddison. 1987. Reconstructing ancestral character states under wagner parsimony. Math. Biosci. 87: 199-229.
179. Cunningham, C.W., K.E. Omland & T.H. Oakley. 1998. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13: 361-366.
180. Oakley, T.H. & C.W. Cunningham. 2000. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54: 397-405.
181. Finarelli, J.A. & 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.
182. Losos, J.B. 2010. Adaptive radiation, ecological opportunity, and evolutionary determinism. Am. Nat. 175: 623-639.
183. Höhna, S., T. Stadler, F. Ronquist & T. Britton. 2011. Inferring speciation and extinction rates under different sampling schemes. Mol. Biol. Evol. 28: 2577-2589.
184. Stadler, T. 2013. How can we improve accuracy of macroevolutionary rate estimates? Syst. Biol. 62: 321-329.
185. Ezard, T.H.G., T. Aze, P.N. Pearson & A. Purvis. 2011. Interplay between changing climate and species' ecology drives macroevolutionary dynamics. Science 332: 349-351.
186. Etienne, R.S. & J. Rosindell. 2012. Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification. Syst. Biol. 61: 204-213.
187. Pyron, R.A. 2011. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60: 466-481.
188. Ronquist, F., S. Klopfstein, L. Vilhelmsen, et al. 2012. A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera. Syst. Biol. 61: 973-999.
189. Nakagawa, S. & R.P. Freckleton. 2008. Missing inaction: the dangers of ignoring missing data. Trends Ecol. Evol. 23: 592-596.
190. Garamszegi, L.Z. & A.P. Moller. 2011. Nonrandom variation in within-species sample size and missing data in phylogenetic comparative studies. Syst. Biol. 60: 876-880.
191. Foote, M., J.P. Hunter, C.M. Janis & J.J. Sepkoski. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283: 1310-1314.
192. Tavaré, S., C.R. Marshall, O. Will, et al. 2002. Using the fossil record to estimate the age of the last common ancestor of primates. Nature 416: 726-729.
193. Stadler, T. 2010. Sampling-through-time in birth-death trees. J. Theor. Biol. 267: 396-404.
194. Didier, G., M. Royer-Carenzi & M. Laurin. 2012. The reconstructed evolutionary process with the fossil record. J. Theor. Biol. 315: 26-37.
195. Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23: 278-300.
196. Wagner, P.J. 1995. Diversity patterns among early gastropods: contrasting taxonomic and phylogenetic descriptions. Paleobiology 21: 410-439.
197. Brusatte, S.L., M.J. Benton, M. Ruta & G.T. Lloyd. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321: 1485-1488.
198. Roy, K., G. Hunt & D. Jablonski. 2009. Phylogenetic conservatism of extinctions in marine bivalves. Science 325: 733-737.
199. Hunt, G. & M. Carrano. 2010. "Models and methods for analyzing phenotypic evolution in lineages and clades." In Quantitative Methods in Paleobiology. J. Alroy & G. Hunt, Eds.: 245-269. Boulder, CO: The Paleontological Society.
200. Sallan, L.C. & M. Friedman. 2012. Heads or tails: staged diversification in vertebrate evolutionary radiations. Proc. R. Soc. B Biol. Sci. 279: 2025-2032.
201. Benson, R.B.J., M. Evans & P.S. Druckenmiller. 2012. High diversity, low disparity and small body size in plesiosaurs (Reptilia, Sauropterygia) from the Triassic-Jurassic boundary. PLoS ONE 7: e31838.
202. Hunt, G. 2012. Measuring rates of phenotypic evolution and the inseparability of tempo and mode. Paleobiology 38: 351-373.
203. Pol, D. & M.A. Norell. 2006. Uncertainty in the age of fossils and the stratigraphic fit to phylogenies. Syst. Biol. 55: 512-521.
204. Lloyd, G.T., S.C. Wang & S.L. Brusatte. 2012. Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (sarcopterygii: Dipnoi). Evolution 66: 330-348.
205. Bapst, D.W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods Ecol. Evol. 3: 803-807.
206. Simpson, C., W. Kiessling, H. Mewis, et al. 2011. Evolutionary diversification of reef corals: a comparison of the molecular and fossil records. Evolution 65: 3274-3284.