Abstract
Archaeogenomic studies have largely elucidated human population history in West Eurasia during the
Stone Age. However, despite being a broad geographical region of significant cultural and linguistic
diversity, little is known about the population history in North Asia. We present complete mitochondrial
genome sequences together with stable isotope data for 41 serially sampled ancient individuals from
North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron
Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed
the highest genetic affinity to present-day North Asian populations of the same geographical region
suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in
genetic diversity over time and a reduction of maternal effective population size (Ne) approximately
seven thousand years before present. Coalescent simulations were consistent with genetic continuity
between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile,
genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP
were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools
or structure within the population. These results indicate that despite some level of continuity between
ancient groups and present-day populations, the region exhibits a complex demographic history during
the Holocene.