Mapping phylogenetic endemism in R using georeferenced branch extents

•Phylogenetic endemism (PE) measures range-restricted phylogenetic diversity (PD).•Previous PE implementations measured range restriction via area of occupancy (AOO).•The R functions map PE using AOO or extent of occurrence (EOO) with simple inputs.•Range sizes and PE scores are poorly correlated between AOO and EOO methods.•The functions provide new spatial information on biodiversity with R functionality.

Applications are needed to map biodiversity from large-scale species occurrence datasets whilst seamlessly integrating with existing functions in R. Phylogenetic endemism (PE) is a biodiversity measure based on range-restricted phylogenetic diversity (PD). Current implementations use area of occupancy (AOO) or frequency to estimate the spatial range of branch-length (i.e.  phylogenetic range-rarity), rather than extent of occurrence (EOO; i.e.  georeferenced phylogenetic endemism), which is known to produce different range estimates. We present R functions to map PD or PE weighted by AOO or EOO (new georeferenced implementation), taking as inputs georeferenced species occurrences and a phylogeny. Non-parametric statistics distinguish PD/PE from trivial correlates of species richness and sampling intensity.