Evolutionary history of Altai vole
Although very much sensitive to current and future environmental change, small mammals are not widely studied. Just as megafaunal species' evolutionary history was affected by climate changes during the Late Pleistocene, so were most terrestrial species. Altai grey vole (Microtus obscurus) is a rodent species present in Western Asia, Eastern Europe, and the Near East. Previous phylogeographic studies have revealed the presence of at least two main mtDNA lineages; however, there is a lack of agreement regarding the dating of divergence of these lineages and their taxonomic ranking. Additionally, the taxonomic relationship of M. obscurus with its sister species M. arvalis is a matter of ongoing debate. Our aim in this study was to further the understanding of the evolutionary history of M. obscurus. We generated mitogenomes of 5 modern and 11 ancient specimens identified as M. obscurus spanning from Russia, Ukraine, Georgia, and Türkiye to Iran, and representing all major mtDNA lineages.  We reconstructed a phylogenetic tree using 4.3 kb fragment of mtDNA, and a dataset of directly radiocarbon-dated samples to calibrate the molecular clock, estimate the divergence time of mitochondrial lineages and the age of ancient samples. We estimated the time to most recent common ancestor (TMRCA) for M. arvalis and M. obscurus to be 0.13 Mya and split of main evolutionary lines of those species to be ~100kya, which is earlier than previous estimates. Several specimens from Dzudzuana Cave, Georgia, emerged as a new, previously unknown mitochondrial lineage of M. obscurus described as Kartvelian, presumably extinct today, and replaced by South Caucasian line. Using 3 published and 3 newly generated nuclear genomes of M. obscurus we reconstructed the demographic history of the species, which, alongside PCA, revealed vast differences between two main Altai vole lineages, including bottleneck event in Sino-Russian line around ~200kya possibly surviving in Crimean refugium, and notable population expansion of Middle Eastern between ~70–20kya. Our results suggest lineage/population turnover in the Late Pleistocene, as well as highlights the importance of Crimean refugium and Ponto-Caspian zone in speciation events among microtine species.