Phylogenetic trees have become important tools to study macroevolutionary patterns and in particular, to study how diversification rates vary through both time and across lineages. Such inferences can inform us about how specific geological or climatic events might have shaped our current species diversity. They also provide insights into how specific evolutionary innovations might have lead to adaptive radiations.

In collaboration with Jim Fordyce and Ben Fitzpatrick, we developed a Parametric Rate Comparison (PRC) method to identify shifts in diversification rates in phylogenetic trees. The method explicitly compares the distribution of branch lengths in a subclade to those in remainder of the tree to identify subclades with variable diversification rates. The library for PRC is released as an R package: iteRates.


A codon model of nucleotide substitution with selection on synonymous codon usage. Kubatko et al. Mol Phylo Evol 2016

iteRates: An R package for implementing a parametric rate comparison on phylogenetic trees. Fordyce et al. Evol Bioinfo 2014

A parametric method for assessing diversification-rate variation in phylogenetic trees. Shah et al. Evolution 2013