Data from: Is BAMM flawed? Theoretical and practical concerns in the analysis of multi-rate diversification models

BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a statistical
framework that uses reversible jump MCMC to infer complex
macroevolutionary dynamics of diversification and phenotypic evolution on
phylogenetic trees. A recent article by Moore and coauthors (MEA) reported
a number of theoretical and practical concerns with BAMM. Major claims
from MEA are that (1) BAMM's likelihood function is incorrect,
because it does not account for unobserved rate shifts; (2) the posterior
distribution on the number of rate shifts is overly sensitive to the
prior; and (3) diversification rate estimates from BAMM are unreliable.
Here, we show that these and other conclusions from MEA are generally
incorrect or unjustified. We first demonstrate that MEA's numerical
assessment of the BAMM likelihood is compromised by their use of an
invalid likelihood function. We then show that “unobserved rate shifts”
appear to be irrelevant for biologically-plausible parameterizations of
the diversification process. We find that the purportedly extreme prior
sensitivity reported by MEA cannot be replicated with standard usage of
BAMM v2.5, or with any other version, when conventional Bayesian model
selection is performed. Finally, we demonstrate that BAMM performs very
well at estimating diversification rate variation across the ∼20% of
simulated trees in MEA's dataset for which it is theoretically
possible to infer rate shifts with confidence. Due to ascertainment bias,
the remaining 80% of their purportedly variable-rate phylogenies are
statistically indistinguishable from those produced by a constant-rate
birth-death process and were thus poorly-suited for the summary statistics
used in their performance assessment. We demonstrate that inferences about
diversification rates have been accurate and consistent across all major
previous releases of the BAMM software. We recognize an acute need to
address the theoretical foundations of rate-shift models for phylogenetic
trees, and we expect BAMM and other modeling frameworks to improve in
response to mathematical and computational innovations. However, we remain
optimistic that that the imperfect tools currently available to
comparative biologists have provided and will continue to provide
important insights into the diversification of life on Earth.