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LITERATURE CITED

  • Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, C. Carnevale, and L. J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Nat. Acad. Sci. 106:1341013414.
  • Blomberg, S. P., T. Garland Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Syst. Biol. 57:717745.
  • 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 62:27182726.
  • Butler, M. A., and A. A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683695.
  • Cavalli-Sforza, L. L., and A. W. F. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. Am. J. Hum. Genet. 19:233257.
  • Felsenstein, J. 1973. Maximum likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471492.
  • Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:115.
  • Freckleton, R. P., and P. H. Harvey. 2006. Detecting non-Brownian trait evolution in adaptive radiations. PLoS Biol. 4:21042111.
  • Garland, T. Jr. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. Am. Nat. 140:509519.
  • Givnish, T. J. 1997. Adaptive radiation and molecular systematics: issues and approaches. Pp. 154 in T. J. Givnish and K. J. Systma, eds. Molecular evolution and adaptive radiation. Cambridge Univ. Press, Cambridge , UK .
  • Givnish, T. J., and K. J. Systma (eds.). 1997. Molecular evolution and adaptive radiation. Cambridge Univ. Press, Cambridge , UK .
  • Glor, R. E. 2010. Phylogenetic insights on adaptive radiation. Annu. Rev. Ecol. Evol. Syst. 41:251270.
  • Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:13411351.
  • Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129131.
  • Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their application. Biometrika 57:97109.
  • Ho, S. Y. W., B. Shapiro, M. J. Phillips, A. Cooper, and A. J. Drummond. 2007. Evidence for time dependency of molecular rate estimates. Syst. Biol. 56:515522.
  • Lavoué, S., M. Miya, M. E. Arnegard, P. B. McIntyre, V. Mamonekene, and M. Nishida. 2011. Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence. Proc. R. Soc. B 278:10031008.
  • Losos, J. B., and D. B. Miles. 2002. Testing the hypothesis that a clade has adaptively radiated: iguanid lizard clades as a case study. Am. Nat. 160:147157.
  • Losos, J. B., and D. L. Mahler. 2010. Adaptive radiation: the interaction of ecological opportunity, adaptation, and speciation. Pp. 381420 in M. A. Bell, D. J. Futuyma, W. F. Eanes, and J. S. Levinton, eds. Evolution since Darwin: the first 150 years. Sinauer Associates, Sunderland , MA .
  • Maddison, W. P., P. E. Midford, and S. P. Otto. 2007. Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56:701710.
  • 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 64:27312745.
  • Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, and A. H. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:10871092.
  • McPeek, M. A. 1995. Testing hypotheses about evolutionary change on single branches of a phylogeny using evolutionary contrasts. Am. Nat. 145:686703.
  • Moore, B. R., K. M. A. Chan, and M. J. Donoghue. 2004. Detecting diversification rate variation in supertrees. Pp. 487533 in O. R. P. Bininda-Emonds, ed. Phylogenetic supertrees: combining information to reveal the tree of life. Kluwer Academic, Dordrecht , The Netherlands .
  • Olson, M. E., and A. Arroyo-Santos. 2009. Thinking in continua: beyond the “adaptive radiation” metaphor. Bioessays 31:13371346.
  • O’Meara, B. C., C. Ané, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922933.
  • Paradis, E. 2006. Analysis of phylogenetics and evolution with R. Springer, New York .
  • Paradis, E., J. Claude, and K. Strimmer. 2004. APE: snalyses of phylogenetics and evolution in R language. Bioinformatics 20:289290.
  • Plummer, M., N. Best, K. Cowles, and K. Vines. 2006. CODA: convergence diagnosis and output analysis for MCMC. R News 6:711.
  • R Development Core Team. 2010. R: a language and environment for statistical computing. R Foundation for Statistical Computing , Vienna , Austria .
  • Rabosky, D. L. 2006. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60:11521164.
  • Rambaut, A., and A. J. Drummond. 2009. Tracer: MCMC trace analysis tool v1.5.0. Available at: http://tree.bio.ed.ac.uk/software/tracer/ (accessed July 19, 2011).
  • Revell, L. J. 2008. On the analysis of evolutionary change along single branches in a phylogeny. Am. Nat. 172:140147.
  • Revell, L. J. 2011. phytools: phylogenetic tools for comparative biology (and other things). R package version 0.0–4. Available at: http://anolis.oeb.harvard.edu/~liam/R-phylogenetics
  • Revell, L. J., and D. C. Collar. 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63:10901100.
  • Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:21432160.
  • Schluter, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press, Oxford UK .
  • Slowinski, J. B., and 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. 142:10191024.
  • Simpson, G. G. 1953. The major features of evolution. Columbia Univ. Press, New York .
  • 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. B 277:30973104.
  • Stadler, T. 2011. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Nat. Acad. Sci. 108:61876192.
  • Thomas, G. H., R. P. Freckleton, and T. Székely. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proc. R. Soc. B 273:16191624.
  • Yang, Z. 2006. Computational molecular evolution. Oxford Univ. Press, Oxford , UK .