BAMM at the court of false equivalency A response to Meyer and Wiens

The software program BAMM has been widely used to study rates of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common macroevolutionary rate dynamics and to estimate parameters. A recent...

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Vydáno v:Evolution Ročník 72; číslo 10; s. 2246 - 2256
Hlavní autor: Rabosky, Daniel L.
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Wiley 01.10.2018
Oxford University Press
Témata:
Biodiversity
Biological evolution
Clustering
Computer simulation
Empirical analysis
Equivalence
Estimators
Evolution & development
Genetic Speciation
Parameter estimation
Phylogeny
Software
Speciation
TECHNICAL COMMENT
ISSN:0014-3820, 1558-5646, 1558-5646
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Shrnutí:The software program BAMM has been widely used to study rates of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common macroevolutionary rate dynamics and to estimate parameters. A recent simulation study by Meyer and Wiens (M & W) argued that (1) a simple inference framework (MS) performs much better than BAMM, and (2) evolutionary rates inferred with BAMM are poorly correlated with true rates. I address two statistical concerns with their assessment that affect the generality of their conclusions. These considerations are not specific to BAMM and apply to other methods for estimating parameters from empirical data where the true grouping structure of the data is unknown. M & W constrain roughly half of the parameters in their MS analyses to their true values, but BAMM is given no such information and must estimate all parameters from the data. This information disparity results in a substantial degrees of freedom advantage for the MS estimators. When both methods are given equivalent information, BAMM outperforms the MS estimators.
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ISSN:0014-3820
1558-5646
1558-5646
DOI:10.1111/evo.13566