phyloregion: R package for biogeographic regionalization and spatial conservation (Q6692115)

Biogeographical regionalization is the classification of regions in terms of their biotas and is key to understanding biodiversity patterns across the world. Previously, it was only possible to perform analysis of biogeographic regionalization on small datasets, often using tools that are difficult to replicate. Here, we present phyloregion, a package for the analysis of biogeographic regionalization and spatial conservation in the R computing environment, tailored for mega phylogenies and macroecological datasets of ever-increasing size and complexity. Compared to available packages, phyloregion is three to four orders of magnitude faster and memory efficient for cluster analysis, determining optimal number of clusters, evolutionary distinctiveness of regions, as well as analysis of more standard conservation measures of phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness and global endangerment. A case study for zoogeographic regionalization of 9574 species of squamate reptiles (amphisbaenians, lizards, and snakes) across the globe, reveals their evolutionary affinities using visualization tools that allow rapid identification of patterns and underlying processes with user-friendly colours–for example–indicating the levels of differentiation of the taxa in different regions. Ultimately, phyloregion would facilitate rapid biogeographic analyses that accommodates the ongoing mass-production of species occurrence records and phylogenetic datasets at any scale and for any taxonomic group into completely reproducible R workflows.