Data from: Pulled diversification rates, lineages-through-time plots and modern macroevolutionary modelling

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 understanding how ecological and evolutionary
processes shape biodiversity. Due to an increasing availability of
phylogenetic trees, a growing number of process-based methods relying on
the birth-death model have been developed in the last decade to address a
variety of questions in macroevolution. However, this methodological
progress has regularly been criticised such that one may wonder how
reliable the estimations of speciation and extinction rates are. In
particular, using lineages-through-time (LTT) plots, a recent study (Louca
& Pennell, 2020) has shown that there are an infinite number of
equally likely diversification scenarios that can generate any timetree.
This has led to questioning whether or not diversification rates should be
estimated at all. Here we summarize, clarify, and highlight technical
considerations on recent findings regarding the capacity of models to
disentangle diversification histories. Using simulations we illustrate the
characteristics of newly-proposed "pulled rates" and their
utility. We recognize that the recent findings are a step forward in
understanding the behavior of macroevolutionary modelling, but they in no
way suggest we should abandon diversification modelling altogether. On the
contrary, the study of macroevolution using phylogenetic trees has never
been more exciting and promising than today. We still face important
limitations in regard to data availability and methodological
shortcomings, but by acknowledging them we can better target our joint
efforts as a scientific community.