期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 113, 期 34, 页码 9569-9574出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1518659113
关键词
lineage diversification rates; speciation; extinction; macroevolution; phylogeny
资金
- National Science Foundation (NSF) Grants [DEB-0842181, DEB-0919529, DBI-1356737, DEB-1457835]
- NSF XSEDE Grants [DEB-120031, TG-DEB140025, TG-BIO140014]
- Miller Institute for Basic Research in Science
- Direct For Biological Sciences [1457835, 1356737] Funding Source: National Science Foundation
- Division Of Environmental Biology [1457835] Funding Source: National Science Foundation
- Div Of Biological Infrastructure [1356737] Funding Source: National Science Foundation
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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