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Introducing a general class of species diversification models for phylogenetic trees

Author

Listed:
  • Francisco Richter
  • Bart Haegeman
  • Rampal S. Etienne
  • Ernst C. Wit

Abstract

Phylogenetic trees are types of networks that describe the temporal relationship between individuals, species, or other units that are subject to evolutionary diversification. Many phylogenetic trees are constructed from molecular data that is often only available for extant species, and hence they lack all or some of the branches that did not make it into the present. This feature makes inference on the diversification process challenging. For relatively simple diversification models, analytical or numerical methods to compute the likelihood exist, but these do not work for more realistic models in which the likelihood depends on properties of the missing lineages. In this article, we study a general class of species diversification models, and we provide an expectation‐maximization framework in combination with a uniform sampling scheme to perform maximum likelihood estimation of the parameters of the diversification process.

Suggested Citation

  • Francisco Richter & Bart Haegeman & Rampal S. Etienne & Ernst C. Wit, 2020. "Introducing a general class of species diversification models for phylogenetic trees," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 74(3), pages 261-274, August.
    • Handle: RePEc:bla:stanee:v:74:y:2020:i:3:p:261-274
    DOI: 10.1111/stan.12205
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    References listed on IDEAS

    as
    1. Ernst Wit & Edwin van den Heuvel & Jan-Willem Romeijn, 2012. "‘All models are wrong...’: an introduction to model uncertainty," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 66(3), pages 217-236, August.
    2. Sylvia. Richardson & Peter J. Green, 1997. "On Bayesian Analysis of Mixtures with an Unknown Number of Components (with discussion)," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 59(4), pages 731-792.
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