Additional Analytical Support for a New Method to Compute the Likelihood of Diversification Models.
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.
['Laudanno|Giovanni|G|', 'Haegeman|Bart|B|', 'Etienne|Rampal S|RS|']
D000818:Animals D044822:Biodiversity D005075:Biological Evolution D003198:Computer Simulation D053476:Extinction, Biological D049810:Genetic Speciation D014644:Genetic Variation D016013:Likelihood Functions D055641:Mathematical Concepts D008954:Models, Biological D008957:Models, Genetic D010802:Phylogeny
Diversification Macroevolution Birth–death process Likelihood model Phylogenetic trees