AI Article Synopsis
- - Bayesian analysis of macroevolutionary mixtures (BAMM) estimates speciation and extinction rates for each branch of a phylogenetic tree and identifies shifts in diversification rates.
- - The evaluation reveals two major errors: an incorrect likelihood function for estimating model parameters and an incoherent prior model for diversification-rate shifts.
- - These errors lead to statistical issues, making posterior estimates for diversification shifts influenced by the prior and rendering the diversification-rate parameter estimates unreliable, hindering the use of BAMM for hypothesis testing on diversification patterns.
Article 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003228 | PMC |
| http://dx.doi.org/10.1073/pnas.1518659113 | DOI Listing |
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