Evolutionary history of the Altai grey vole, Microtus obscurus (Rodentia: Cricetidae), reconstructed using modern and ancient genomes

The Altai grey vole (Microtus obscurus) is a rodent species present in Western Asia, Eastern Europe, and the Near East. The taxonomic relationship of M. obscurus and its sister-species, Microtus arvalis, is a matter of ongoing debate and there is a lack of agreement regarding the date of their divergence. To further understand the evolutionary history of M. obscurus, we generated nuclear and mitochondrial data from five modern and 11 ancient specimens from Eastern Europe and the Near East. We reconstructed a tip-dated phylogeny using a 4.3-kilobase fragment of mitochondrial DNA. We estimated the time to the most recent common ancestor of M. arvalis and M. obscurus to be 130 thousand years ago (kya), correlating with the Eemian interglacial, a period characterized by the reduction of open habitats suitable for microtine species. In the Lesser Caucasus, we recorded a turnover of two lineages probably related to environmental changes at the end of the Pleistocene. Using three published and three newly generated nuclear genomes, we confirmed the general population structure and divergence times inferred from the mtDNA. We reconstructed the demographic history of the Altai grey vole, which revealed contrasting trajectories for the two main lineages.