‘treesliceR': a package for slicing phylogenies and inferring phylogenetic patterns over evolutionary time

Abstract

Phylogenetic indexes summarize the evolutionary information within a given assemblage pool based on the topology and branch lengths of a hypothesized phylogenetic tree. However, different historical contingencies experienced by these assemblages can unevenly distribute evolutionary information through time and over the phylogeny. ‘treesliceR' is an R package containing tools to flexibly cut phylogenies at different depths, and also has built‐in functions to assess spatially explicit phylogenetic patterns over time. ‘treesliceR' can slice phylogenies in any temporal orientation (‘rootwardly' or ‘tipwardly'), using different criteria (million years or phylogenetic diversity). Moreover, ‘treesliceR' contains functions to assess the rates of accumulation of any phylogenetic information (e.g. α and β diversities) through time. These functions are unique to the package and provide outputs that are ready‐to‐use in graphing functions. We demonstrated the main uses of ‘treesliceR' by investigating areas of paleo‐endemism and neo‐endemism of Passeriformes in Australia. Finally, we mapped rates of accumulation of phylogenetic β‐diversity (Cpβrate) across Australia. ‘treesliceR' is an open‐source R package under continuous progress, designed to decompose temporally any phylogenetic information.