Rolando grande controvérsia em filogenia: a confiabilidade do BAMM [Bayesian Analysis of Macroevolutionary Mixtures]

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

Brian R. Moore a,1, Sebastian Höhna b,c, Michael R. May a, Bruce Rannala a, and John P. Huelsenbeck b

Author Affiliations

aDepartment of Evolution and Ecology, University of California, Davis, CA 95616;

bDepartment of Integrative Biology, University of California, Berkeley, CA 94720;

cDepartment of Statistics, University of California, Berkeley, CA 94720

Edited by Michael J. Donoghue, Yale University, New Haven, CT, and approved June 27, 2016 (received for review September 21, 2015)

Significance

We show that Bayesian analysis of macroevolutionary mixtures (BAMM)—a method for identifying lineage-specific diversification rates—is flawed. Exposing the problems with BAMM is important both to empiricists (to avoid making unreliable inferences using this method) and to theoreticians (to focus their efforts on solving the problems that we identify).

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.

lineage diversification rates speciation extinction macroevolution phylogeny

Footnotes

1To whom correspondence should be addressed. Email: brianmoore@ucdavis.edu.

Author contributions: B.R.M., S.H., M.R.M., B.R., and J.P.H. designed research, performed research, contributed new reagents/analytic tools, analyzed data, and wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: Data from this study have been deposited in the Dryad Digital Repository (doi: 10.5061/dryad.mb0sd).

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1518659113/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

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NOTA DESTE BLOGGER:

Um dos muitos problemas fundamentais em biologia evolucionária é detectar os padrões de variação em taxas de diversificação de linhagem e trabalhar para entender suas causas. Sugiro acompanhar a controvérsia sobre a confiabilidade do BAMM aqui:

A. Artigo de Daniel L. Rabosky: 
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

FREE PDF GRATIS: 

http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0089543.PDF

B. Artigo de Wayne P. Maddison et al

Estimating a Binary Character's Effect on Speciation and Extinction

FREE PDF GRATIS: 

http://sysbio.oxfordjournals.org/content/56/5/701.full.pdf+html

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1. Tree thinkers: 

http://treethinkers.org/prior-sensitivity-in-bamm/

2. The BAMM Project:

http://bamm-project.org/replication.html#several-theoretical-concerns-raised-by-mea-cannot-be-evaluated