Data from: Estimating age-dependent extinction: contrasting evidence from fossils and phylogenies

The estimation of diversification rates is one of the most vividly debated
topics in modern systematics, with considerable controversy surrounding
the power of phylogenetic and fossil-based approaches in estimating
extinction. Van Valen’s seminal work from 1973 proposed the “Law of
constant extinction” which states that the probability of extinction of
taxa is not dependent on their age. This assumption of age-independent
extinction has prevailed for decades with its assessment based on
survivorship curves, which, however, do not directly account for the
incompleteness of the fossil record, and have rarely been applied at the
species level. Here, we present a Bayesian framework to estimate
extinction rates from the fossil record accounting for age-dependent
extinction (ADE). Our approach, unlike previous implementations,
explicitly models unobserved species and accounts for the effects of
fossil preservation on the observed longevity of sampled lineages. We
assess the performance and robustness of our method through extensive
simulations and apply it to a fossil data set of terrestrial Carnivora
spanning the past 40 Myr. We find strong evidence of ADE, as we detect the
extinction rate to be highest in young species and declining with
increasing species age. For comparison, we apply a recently developed
analogous ADE model to a dated phylogeny of extant Carnivora. Although the
phylogeny-based analysis also infers age-dependent extinction, it
indicates that the extinction rate, instead, increases with increasing
taxon age. The estimated mean species longevity also differs
substantially, with the fossil-based analyses estimating 2.0 Myr, in
contrast to 9.8 Myr derived from the phylogeny-based inference.
Scrutinizing these discrepancies, we find that both fossil and
phylogeny-based ADE models are prone to high error rates when speciation
and extinction rates increase or decrease through time. However, analyses
of simulated and empirical data show that fossil-based inferences are more
robust. This study shows that an accurate estimation of ADE from
incomplete fossil data is possible when the effects of preservation are
jointly modeled, thus allowing for a reassessment of Van Valen’s model as
a general rule in macroevolution.