Fast and accurate estimation of species-specific diversification rates using data augmentation

Diversification rates vary across species as a response to various
factors, including environmental conditions and species-specific features.
Phylogenetic models that allow accounting for and quantifying this
heterogeneity in diversification rates have proven particularly useful for
understanding clades diversification. Recently, we introduced the
cladogenetic diversification rate shift model (ClaDS), which allows
inferring subtle rate variations across lineages. Here we present a new
inference technique for this model that considerably reduces computation
time through the use of data augmentation and provide an implementation of
this method in Julia. In addition to drastically reducing computation
time, this new inference approach provides a posterior distribution of the
augmented data, that is the tree with extinct and unsampled lineages as
well as associated diversification rates. In particular, this allows
extracting the distribution through time of both the mean rate and the
number of lineages. We assess the statistical performances of our approach
using simulations and illustrate its application on the entire bird
radiation.