A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios

Estimates of diversification rates at the tips of a phylogeny provide a
flexible approach for correlation analyses with multiple traits and to map
diversification rates in space, while also avoiding the uncertainty of
deep time rate reconstructions. Available methods for tip rate estimation
make different assumptions, and thus their accuracy usually depends on
characteristics of the underlying model generating the tree. Here we
introduce MiSSE, a trait-free, state-dependent speciation and extinction
approach that can be used to estimate varying speciation, extinction,
net-diversification, turnover rates, and extinction fraction at the tips
of the tree. We compare the accuracy of tip rates inferred by MiSSE
against similar methods and demonstrate that, due to certain
characteristics of the model, the error is generally low across a broad
range of speciation and extinction scenarios. MiSSE can be used alongside
regular phylogenetic comparative methods in trait related diversification
hypotheses, and we also describe a simple correction to avoid
pseudoreplication from sister tips in analyses of independent contrasts.
Finally, we demonstrate the capabilities of MiSSE, with a renewed focus on
classic comparative methods, to examine correlation between plant height
and turnover rates in eucalypts, a species-rich lineage of flowering
plants.