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BAMM at the court of false equivalency: A response to Meyer and Wiens
Author(s) -
Rabosky Daniel L.
Publication year - 2018
Publication title -
evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.84
H-Index - 199
eISSN - 1558-5646
pISSN - 0014-3820
DOI - 10.1111/evo.13566
Subject(s) - generality , estimator , biology , inference , statistics , clade , phylogenetic tree , computer science , mathematics , artificial intelligence , psychology , biochemistry , psychotherapist , gene
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.