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

Estimates of diversification rates are invaluable for many
macroevolutionary studies. Recently, an approach called BAMM (Bayesian
Analysis of Macro-evolutionary Mixtures) has become widely used for
estimating diversification rates and rate shifts. At the same time,
several papers have concluded that estimates of net diversification rates
from the method-of-moments (MS) estimators are inaccurate. Yet, no studies
have compared the ability of these two methods to accurately estimate
clade diversification rates. Here, we use simulations to compare their
performance. We found that BAMM yielded relatively weak relationships
between true and estimated diversification rates. This occurred because
BAMM underestimated the number of rates shifts across each tree, and
assigned high rates to small clades with low rates. Errors in both
speciation and extinction rates contributed to these errors, showing that
using BAMM to estimate only speciation rates is also problematic. In
contrast, the MS estimators (particularly using stem group ages), yielded
stronger relationships between true and estimated diversification rates,
by roughly twofold. Furthermore, the MS approach remained relatively
accurate when diversification rates were heterogeneous within clades,
despite the widespread assumption that it requires constant rates within
clades. Overall, we caution that BAMM may be problematic for estimating
diversification rates and rate shifts.