RRphylogeography: A new method to find the area of origin of species and the history of past contacts between species

Abstract One of the main goals of historical biogeography is understanding where species originated, and how climate change and ecological interactions shaped their distribution. The task is complicated by both active and passive mechanisms, including habitat tracking, the separation of species into metapopulations of variably interconnected demes, and long‐distance dispersal, which may all obscure the geographic signature of species origin. Current historical biogeography tools use phylogenies to infer the area of origin (AOO). They work by discretizing the geographic range occupied by the species into distinct areas and then applying ancestral character estimation to identify the area occupied at speciation. These methods are powerful and can account for different modes of speciation. Yet, they are bound to assume that the discrete areas currently occupied by the species are faithful representation of their climatic and historic affiliation and ignore metapopulation structures. Still, most methods cannot take advantage of fossil information or work with phylogenies including extinct species. Although explicit bioclimatic modelling is now possible under some implementations, these limitations are partly unresolved, which burdens the accuracy of the AOO estimation process. We present a new tool written in R, named RRphylogeography , meant to find the AOO of species, and to locate feasible zones of contact between species throughout their history. RRphylogeography starts from the bioclimatic modelling of the species, identifies potential habitat patches occupied during speciation and finds the habitat patches most likely to represent the AOO or contact. By using virtual species simulations, we compared RRphylogeography to common historical biogeography tools. We found RRphylogeography statistically outcompetes these alternatives under all study conditions, reaching especially accurate predictions. We additionally used RRphylogeography to investigate the complex phylogeographic history of the polar bear Ursus maritimus . The method placed the origin of the species in Northern Beringia. Intriguingly, it further shows possible contact zones between polar and brown bear in northwestern Europe during the late Pleistocene and in Beringia during the Pleistocene to Holocene transition, which is in perfect agreement with the known hybridization history between the two species.