title: Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures.
abstract: Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM.
authors: Department of Evolution and Ecology, University of California, Davis, CA 95616; brianmoore@ucdavis.edu.
authors: Brian R
authors: BR
authors: Moore
authors: Department of Integrative Biology, University of California, Berkeley, CA 94720; Department of Statistics, University of California, Berkeley, CA 94720.
authors: Sebastian
authors: S
authors: Höhna
authors: Department of Evolution and Ecology, University of California, Davis, CA 95616;
authors: Michael R
authors: MR
authors: May
authors: Department of Evolution and Ecology, University of California, Davis, CA 95616;
authors: Bruce
authors: B
authors: Rannala
authors: Department of Integrative Biology, University of California, Berkeley, CA 94720;
authors: John P
authors: JP
authors: Huelsenbeck
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D044822:Biodiversity; D000073930:Biological Coevolution; D053476:Extinction, Biological; D049810:Genetic Speciation; D016013:Likelihood Functions; D010802:Phylogeny; D016012:Poisson Distribution; D014907:Whales / Q000145:classification* / Q000235:genetics
keywords: extinction; lineage diversification rates; macroevolution; phylogeny; speciation