Skip to main content
Biology LibreTexts

12.S: Beyond Birth-Death Models (Summary)

  • Page ID
    21654
  • \( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \) \( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)\(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\) \(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\)\(\newcommand{\AA}{\unicode[.8,0]{x212B}}\)

    In this chapter I discussed models that go beyond constant rate birth-death models. We can fit models where speciation rate varies across clades or through time (or both). In some cases, very different models predict the same pattern in phylogenetic trees, warranting some caution until direct fossil data can be incorporated. I also described a model of protracted speciation, where speciation takes some time to complete. This latter model is potentially better connected to microevolutionary models of speciation, and could point towards fruitful directions for the field. We know that simple birth-death models do not capture the richness of speciation and extinction across the tree of life, so these models that range beyond birth and death are critical to the growth of comparative methods.

    Footnotes

    1: Even though this approach requires topology, Morlon et al. (2011) show that their likelihood is equivalent to other approaches, such as Nee and Maddison, that rely only on branching times and ignore topology completely. This is because trees with the same set of branching times but different topologies have identical likelihoods under this model.

    back to main text

    References

    Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L. Rabosky, G. Carnevale, and L. J. Harmon. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences 106:13410–13414. National Acad Sciences.

    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.

    Brock, C. D., L. J. Harmon, and M. E. Alfaro. 2011. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom. Syst. Biol. 60:410–419. Oxford University Press.

    Coyne, J. A., and H. A. Orr. 2004. Speciation. Sinauer, New York.

    Cusimano, N., and S. S. Renner. 2010. Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 59:458–464.

    De Queiroz, K. 2005. Ernst Mayr and the modern concept of species. Proceedings of the National Academy of Sciences 102:6600–6607. National Acad Sciences.

    Emerson, B. C., and N. Kolm. 2005. Species diversity can drive speciation. Nature 434:1015–1017.

    Etienne, R. S., and B. Haegeman. 2012. A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence. Am. Nat. 180:E75–89.

    Etienne, R. S., and 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.

    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. Biol. Sci. 279:1300–1309.

    Etienne, R. S., A. L. Pigot, and A. B. Phillimore. 2016. How reliably can we infer diversity-dependent diversification from phylogenies? Methods Ecol. Evol. 7:1092–1099.

    Höhna, S. 2014. Likelihood inference of non-constant diversification rates with incomplete taxon sampling. PLoS One 9:e84184.

    Hughes, C., and R. Eastwood. 2006. Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes. Proc. Natl. Acad. Sci. U. S. A. 103:10334–10339.

    Jetz, W., and R. A. Pyron. 2018. The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life. Nat Ecol Evol 2:850–858.

    Lambert, A., H. Morlon, and R. S. Etienne. 2015. The reconstructed tree in the lineage-based model of protracted speciation. J. Math. Biol. 70:367–397.

    Losos, J. B., and F. R. Adler. 1995. Stumped by trees? A generalized null model for patterns of organismal diversity. Am. Nat. 145:329–342.

    Losos, J. B., and D. Schluter. 2000. Analysis of an evolutionary species–area relationship. Nature 408:847. Macmillian Magazines Ltd.

    May, M. R., and B. R. Moore. 2016. How well can we detect lineage-specific diversification-rate shifts? A simulation study of sequential AIC methods. Syst. Biol. 65:1076–1084.

    Moen, D., and H. Morlon. 2014. Why does diversification slow down? Trends Ecol. Evol. 29:190–197.

    Moore, B. R., S. Höhna, M. R. May, B. Rannala, and J. P. Huelsenbeck. 2016. Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures. Proc. Natl. Acad. Sci. U. S. A. 113:9569–9574.

    Morlon, H., T. L. Parsons, and J. B. Plotkin. 2011. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. U. S. A. 108:16327–16332. National Academy of Sciences.

    Phillimore, A. B., and T. D. Price. 2008. Density-dependent cladogenesis in birds. PLoS Biol. 6:e71.

    Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. Biol. Sci. 267:2267–2272.

    Rabosky, D. L. 2014. Automatic detection of key innovations, rate shifts, anddiversity-dependence on phylogenetic trees. PLoS One 9:e89543. Public Library of Science.

    Rabosky, D. L. 2013. Diversity-Dependence, ecological speciation, and the role of competition in macroevolution. Annu. Rev. Ecol. Evol. Syst. 44:481–502. annualreviews.org.

    Rabosky, D. L. 2017. How to make any method “fail”: BAMM at the kangaroo court of false equivalency.

    Rabosky, D. L., and A. H. Hurlbert. 2015. Species richness at continental scales is dominated by ecological limits. Am. Nat. 185:572–583.

    Rabosky, D. L., and I. J. Lovette. 2008. Density-dependent diversification in North American wood warblers. Proc. Biol. Sci. 275:2363–2371.

    Rabosky, D. L., S. C. Donnellan, A. L. Talaba, and I. J. Lovette. 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia’s most diverse vertebrate clade. Proc. Biol. Sci. 274:2915–2923.

    Roelants, K., D. J. Gower, M. Wilkinson, and others. 2007. Global patterns of diversification in the history of modern amphibians. Proceedings of the. National Acad Sciences.

    Rosindell, J., S. J. Cornell, S. P. Hubbell, and R. S. Etienne. 2010. Protracted speciation revitalizes the neutral theory of biodiversity. Ecol. Lett. 13:716–727.

    Schluter, D. 2000. The ecology of adaptive radiation. Oxford University Press, Oxford.

    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., and L. J. Harmon. 2013. Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods Ecol. Evol. 4:699–702. Wiley Online Library.

    Sukumaran, J., and L. Lacey Knowles. 2017. Multispecies coalescent delimits structure, not species. Proc. Natl. Acad. Sci. U. S. A. 114:1607–1612. National Academy of Sciences.


    This page titled 12.S: Beyond Birth-Death Models (Summary) is shared under a CC BY 4.0 license and was authored, remixed, and/or curated by Luke J. Harmon via source content that was edited to the style and standards of the LibreTexts platform; a detailed edit history is available upon request.

    • Was this article helpful?