RT Journal Article
SR Electronic
T1 Additional analytical support for a new method to compute the likelihood of diversification models
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 693176
DO 10.1101/693176
A1 Giovanni Laudanno
A1 Bart Haegeman
A1 Rampal S. Etienne
YR 2019
UL http://biorxiv.org/content/early/2019/07/04/693176.abstract
AB Molecular phylogenies have been increasingly recognized as an important source of information on species diversification. For many models of macro-evolution, analytical likelihood formulas have been derived to infer macro-evolutionary 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. (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.