Additional analytical support for a new method to compute the likelihood of diversification models

Giovanni Laudanno*, Bart Haegeman, Rampal S Etienne

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)
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Abstract

Molecular phylogenies have been increasingly recognized as an important source of information on species diversification. For many models of macroevolution, analytical likelihood formulas have been derived to infer macroevolutionary parameters from phylogenies. A few years ago, a general framework to numerically compute such likelihood formulas was proposed, which accommodates models that allow speciation and/or extinction rates to depend on diversity. This framework calculates the likelihood as the probability of the diversification process being consistent with the phylogeny from the root to the tips. However, while some readers found the framework presented in Etienne et al. (Proc R Soc Lond B Biol Sci 279(1732):1300-1309, 2012) convincing, others still questioned it (personal communication), despite numerical evidence that for special cases the framework yields the same (i.e., within double precision) numerical value for the likelihood as analytical formulas do that were independently derived for these special cases. Here we prove analytically that the likelihoods calculated in the new framework are correct for all special cases with known analytical likelihood formula. Our results thus add substantial mathematical support for the overall coherence of the general framework.

Original languageEnglish
Article number22
Number of pages22
JournalBulletin of mathematical biology
Volume82
Issue number2
DOIs
Publication statusPublished - 22-Jan-2020

Keywords

  • Macroevolution
  • Diversification
  • Birth-death process
  • Likelihood model
  • Phylogenetic trees
  • SPECIATION

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