phyloregion: R package for biogeographic regionalization and spatial conservation

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.