Data from: A robust semi-parametric test for detecting trait-dependent diversification

Rates of species diversification vary widely across the tree of life and
there is considerable interest in identifying organismal traits that
correlate with rates of speciation and extinction. However, it has been
challenging to develop methodological frameworks for testing hypotheses
about trait-dependent diversification that are robust to phylogenetic
pseudoreplication and to directionally biased rates of character change.
We describe a semi-parametric test for trait-dependent diversification
that explicitly requires replicated associations between character states
and diversification rates in order to detect effects. To use the method,
diversification rates are reconstructed across a phylogenetic tree with no
consideration of character states. A test statistic is then computed to
measure the association between species-level traits and the corresponding
diversification rate estimates at the tips of the tree. The empirical
value of the test statistic is compared to a null distribution that is
generated by structured permutations of evolutionary rates across the
phylogeny. The test is applicable to binary discrete characters as well as
continuous-valued traits and can accommodate extremely sparse sampling of
character states at the tips of the tree. We apply the test to several
empirical datasets and demonstrate that the method has acceptable Type I
error rates.