1.S: A Macroevolutionary Research Program (Summary)
Footnotes
1: This calculation gives the number of distinct tree shapes (ignoring branch lengths) that are fully bifurcating – that is, each species has two descendants - and rooted.
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2: Another difficulty is that the "tree" of life may not look much like a tree due to hybridization, introgression, and other non-branching processes. These issues are currently barely addressed by comparative methods (but see Bastide et al. 2018) , and rarely in this book as well! We leave that as a pressing future problem that has only begun to be solved.
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References
Abzhanov, A., M. Protas, B. R. Grant, P. R. Grant, and C. J. Tabin. 2004. Bmp4 and morphological variation of beaks in Darwin’s finches. Science 305:1462–1465.
Alroy, J. 1999. The fossil record of North American mammals: Evidence for a Paleocene evolutionary radiation. Syst. Biol. 48:107–118.
Bastide, P., C. Solís-Lemus, R. Kriebel, K. W. Sparks, and C. Ané. 2018. Phylogenetic comparative methods on phylogenetic networks with reticulations. Syst. Biol.
Baum, D. A., and S. D. Smith. 2012. Tree thinking: An introduction to phylogenetic biology. in Tree thinking: An introduction to phylogenetic biology.
Benton, M., and D. A. T. Harper. 2013. Introduction to paleobiology and the fossil record. John Wiley & Sons.
Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
Falconer, D. S., T. F. C. Mackay, and R. Frankham. 1996. Introduction to quantitative genetics (4th edn). Trends Genet. 12:280. [Amsterdam, The Netherlands: Elsevier Science Publishers (Biomedical Division)], c1985-.
Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Inc., Sunderland, MA.
Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1–15.
Fisher, R. A. 1930. The genetical theory of natural selection: A complete variorum edition. Oxford University Press.
Foote, M. 1997. The evolution of morphological diversity. Annu. Rev. Ecol. Syst. 28:129–152.
Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press.
Heath, T. A., J. P. Huelsenbeck, and T. Stadler. 2014. The fossilized birth–death process for coherent calibration of divergence-time estimates. Proc. Natl. Acad. Sci. U. S. A. 111:E2957–E2966. National Academy of Sciences.
Lande, R. 1976. Natural selection and random genetic drift in phenotypic evolution. Evolution 30:314–334.
Losos, J. 2009. Lizards in an evolutionary tree: Ecology and adaptive radiation of anoles. University of California Press.
Losos, J. B. 2011. Seeing the forest for the trees: The limitations of phylogenies in comparative biology. Am. Nat. 177:709–727.
Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. Am. Nat. 136:727–741.
Lynch, M., and B. Walsh. 1998. Genetics and analysis of quantitative traits. Sinauer Sunderland, MA.
Pennell, M. W., and L. J. Harmon. 2013. An integrative view of phylogenetic comparative methods: Connections to population genetics, community ecology, and paleobiology. Ann. N. Y. Acad. Sci. 1289:90–105.
Rabosky, D. L. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64:1816–1824.
Raup, D. M. 1985. Mathematical models of cladogenesis. Paleobiology 11:42–52.
Raup, D. M., S. J. Gould, T. J. M. Schopf, and D. S. Simberloff. 1973. Stochastic models of phylogeny and the evolution of diversity. J. Geol. 81:525–542.
Rice, S. H. 2004. Evolutionary theory. Sinauer, Sunderland, MA.
Rolshausen, G., G. Segelbacher, K. A. Hobson, and H. M. Schaefer. 2009. Contemporary evolution of reproductive isolation and phenotypic divergence in sympatry along a migratory divide. Curr. Biol. 19:2097–2101.
Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574.
Rosenblum, E. B., H. Römpler, T. Schöneberg, and H. E. Hoekstra. 2010. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proc. Natl. Acad. Sci. U. S. A. 107:2113–2117.
Rosindell, J., and L. J. Harmon. 2012. OneZoom: A fractal explorer for the tree of life. PLoS Biol. 10:e1001406.
Sepkoski, J. J. 1984. A kinetic model of phanerozoic taxonomic diversity. III. Post-Paleozoic families and mass extinctions. Paleobiology 10:246–267.
Slater, G. J., L. J. Harmon, and M. E. Alfaro. 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66:3931–3944.
Uyeda, J. C., T. F. Hansen, S. J. Arnold, and J. Pienaar. 2011. The million-year wait for macroevolutionary bursts. Proc. Natl. Acad. Sci. U. S. A. 108:15908–15913.
Valentine, J. W. 1996. Evolutionary paleobiology. University of Chicago Press.
Wright, S. 1984. Evolution and the genetics of populations, Volume 1: Genetic and biometric foundations. University of Chicago Press.
Yang, Z. 2006. Computational molecular evolution. Oxford University Press.