Species limits and hybridization in Andean leaf-eared mice (Phyllotis)

Abstract

ABSTRACTLeaf-eared mice (genusPhyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation inPhyllotismice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification ofPhyllotisoccurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification ofPhyllotislargely coincided with climatically induced environmental changes in the mid- to late Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of ongoing hybridization between the sister speciesPhyllotis limatusandP. vaccarumand suggest that the contemporary zone of range overlap between the two species may represent an active hybrid zone.