Biodiversity of the tundra vole, Alexandromys oeconomus : ancient mitogenomes and the identification of a novel European haplogroup

The palaeontological record for the tundra vole Alexandromys oeconomus indicates a reduction in geographical range and population size since the Last Pleistocene. Up to four different mitochondrial haplogroups are currently identified in modern and recent historical specimens: Central European (CE), Northern European (NE), Central Asian (CA) and Beringian (BE). Here, we generated ancient mitochondrial genomes from five Late Pleistocene palaeontological samples (mandibles) from El Mirón Cave (Cantabria, Spain), one of the last Iberian strongholds of A. oeconomus, to investigate the relationship to present-day populations. The analysis of the mitochondrial genome data obtained from the five palaeontological samples of A. oeconomus allowed the identification of a fifth novel haplogroup, currently extinct, that was present at least during the Late Pleistocene-Holocene of the Iberian Peninsula. A tentative time-calibrated phylogenetic analysis suggests that the novel haplogroup could have separated from the CE-NE haplogroups around 0.050–0.1790 Ma, probably before the separation of the CE-NE haplogroups (0.017–0.136 Ma).