Data from: Bias in phylogenetic measurements of extinction and a case study of end-Permian tetrapods

Extinction risk in the modern world and extinction in the geological past
are often linked to aspects of life history or other facets of biology
that are phylogenetically conserved within clades. These links can result
in phylogenetic clustering of extinction, a measurement comparable across
different clades and time periods that can be made in the absence of
detailed trait data. This phylogenetic approach is particularly suitable
for vertebrate taxa, which often have fragmentary fossil records, but
robust, cladistically-inferred trees. Here we use simulations to
investigate the adequacy of measures of phylogenetic clustering of
extinction when applied to phylogenies of fossil taxa while assuming a
Brownian motion model of trait evolution. We characterize expected biases
under a variety of evolutionary and analytical scenarios. Recovery of
accurate estimates of extinction clustering depends heavily on the
sampling rate, and results can be highly variable across topologies.
Clustering is often underestimated at low sampling rates, whereas at high
sampling rates it is always overestimated. Sampling rate dictates which
cladogram timescaling method will produce the most accurate results, as
well as how much of a bias ancestor–descendant pairs introduce. We
illustrate this approach by applying two phylogenetic metrics of
extinction clustering (Fritz and Purvis's D and Moran's I) to
three tetrapod clades across an interval including the Permo-Triassic mass
extinction event. These groups consistently show phylogenetic clustering
of extinction, unrelated to change in other quantitative metrics such as
taxonomic diversity or extinction intensity.