4000-year-old reindeer mitogenomes from the Volga-Kama region reveal continuity among the forest reindeer in northeastern part of European Russia

Abstract There are three main ecotypes of reindeer in Eurasia: tundra reindeer, boreal forest reindeer and High Arctic reindeer. Of these, especially the forest reindeer has suff ered due to human over hunting and habitat fragmentation. Forest reindeer was still found in the Volga-Kama region at the beginning of the 20th century, but has since disappeared from the region. In order to investigate the genetic relationships of these histori-cal, southernly distributed forest reindeer populations, the authors obtained mitogenome sequences from six individuals from Pestretsy II, an archaeological site located in Tatarstan and dated to around 4000 calibrated years before the present (cal BP). The sequences reported in this study represent the fi rst published ancient reindeer mitogenomes. The authors observed genetic continuity between the historical reindeer from Tatarstan and present day wild populations from the taiga zone of northeastern part of European Russia. Interestingly, four out of the six studied individuals belong to mitochondrial control region haplogroup II, which today is a major haplogroup among the semi-domestic reindeer in Fennoscandia. Even though the haplotypes observed in Pestretsy II site are not closely related to the major haplotypes observed among the Fennoscandian semi-domestic reindeer, the results suggest that this haplogroup may have its origin east of Fennoscandia. It is also interesting to note that the size of the reindeers from the Pestretsy II site was one of the largest observed in the Holocene.Аннотация В Евразии существует три основных экотипа северного оленя: тундровый северный олень, таежный северный олень и высокоарктический северный олень. Из них лесные северные олени особенно пострадали из-за чрезмерной охоты человека и фрагментации среды обитания. Лесной северный олень еще встречался в Волго-Камском регионе в начале XX века, но с тех пор исчез из данного региона. Чтобы исследовать генетические связи этих исторических, южно-распределенных популяций лесных северных оленей, авторы получили последовательности митогенома от шести особей из Пестречинской II стоянки, археологического памятника, расположенного в Татарстане и датируемого около 4000 калиброванных лет назад (кал. л.н.). Последовательности митохондриального ДНК, описанные в этом исследовании, представляют собой первые опубликованные древние митогеномы северного оленя. Авторы выявили генетическую преемственность между историческим северным оленем из Татарстана и современными дикими популяциями из таежной зоны северо-восточной части европейской части России. Интересно, что четыре из шести исследованных особей принадлежат к гаплогруппе II, она сегодня является основной гаплогруппой среди полудомашних оленей в Фенноскандии. Несмотря на то, что гаплотипы, наблюдаемые у северных оленей из Пестречинской II стоянки, не тесно связаны с основными гаплотипами, наблюдаемыми среди полудомашних северных оленей Фенноскандии, результаты показывают, что эта гаплогруппа может иметь свое происхождение к востоку от Фенноскандии. Интересно также отметить, что размеры северных оленей из Пестречинской II стоянки были одними из самых крупных наблюдавшихся в голоцене

Over a thousand years of evolutionary history of domestic geese from Russian archaeological sites, analysed using ancient DNA

Abstract The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th–18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent

Moose genomes reveal past glacial demography and the origin of modern lineages

Abstract Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies