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

BR Moore, S Höhna, MR May… - Proceedings of the …, 2016 - National Acad Sciences
Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of
lineage diversification by storm. BAMM estimates the diversification-rate parameters …

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

DL Rabosky, JS Mitchell, J Chang - Systematic biology, 2017 - academic.oup.com
Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses
reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of …

Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts

ALS Meyer, JJ Wiens - Evolution, 2018 - academic.oup.com
Estimates of diversification rates are invaluable for many macroevolutionary studies.
Recently, an approach called BAMM (Bayesian Analysis of Macro-evolutionary Mixtures) …

Likelihood methods for detecting temporal shifts in diversification rates

DL Rabosky - Evolution, 2006 - academic.oup.com
Maximum likelihood is a potentially powerful approach for investigating the tempo of
diversification using molecular phylogenetic data. Likelihood methods distinguish between …

A Bayesian approach for detecting the impact of mass‐extinction events on molecular phylogenies when rates of lineage diversification may vary

MR May, S Höhna, BR Moore - Methods in Ecology and …, 2016 - Wiley Online Library
The paleontological record chronicles numerous episodes of mass extinction that severely
culled the Tree of Life. Biologists have long sought to assess the extent to which these …

BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

DL Rabosky, M Grundler, C Anderson… - Methods in Ecology …, 2014 - Wiley Online Library
Understanding the dynamics of speciation, extinction and phenotypic evolution is a central
challenge in evolutionary biology. Here, we present BAMM tools, an r package for the …

Whole-tree methods for detecting differential diversification rates

KMA Chan, BR Moore - Systematic Biology, 2002 - academic.oup.com
Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass
extinctions are a few examples of biological phenomena that lead to differential …

Tip rates, phylogenies and diversification: what are we estimating, and how good are the estimates?

PO Title, DL Rabosky - Methods in Ecology and Evolution, 2019 - Wiley Online Library
Species‐specific diversification rates, or 'tip rates', can be computed quickly from
phylogenies and are widely used to study diversification rate variation in relation to …

Slowdowns in diversification rates from real phylogenies may not be real

N Cusimano, SS Renner - Systematic biology, 2010 - academic.oup.com
Studies of diversification patterns often find a slowing in lineage accumulation toward the
present. This seemingly pervasive pattern of rate downturns has been taken as evidence for …

Pulled diversification rates, lineages-through-time plots, and modern macroevolutionary modeling

AJ Helmstetter, S Glemin, J Käfer… - Systematic …, 2022 - academic.oup.com
Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees
of extant species (timetrees), and determining how and why they vary, is key to …