The newly discovered bronze age site of Koken: Merging micro-regions with major study zones in the high steppes of Kazakhstan

Abstract

Ancient genome studies are gradually revealing the diverse genetic profiles of prehistoric hunter-gatherers in the steppe and taiga regions of Eurasia, as well as their dynamic population changes over time. However, due to sparse spatial and temporal sampling coverage, the genetic history of prehistoric Inner Asian hunter-gatherers remains incomplete, especially for eastern Kazakhstan where the Eurasian Steppe meets the mountain forests of the Sayano-Altai and the Inner Asian Mountain Corridor. Here we report genome-wide data of 21 ancient individuals, consisting of two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists, from the site of Koken in the Upper Irtysh River region in eastern Kazakhstan. We find that the two EN individuals differed in their genetic profiles, and yet were also second-degree relatives, indicating that unions had formed between individuals from genetically distinct hunter-gatherer populations. They were genetically most similar to subsequent Neolithic individuals in the Irtysh River region, while contemporaneous hunter-gatherers from the more western Tobol-Ishim River region and those from the more eastern Upper Ob River region had distinct genetic profiles, suggesting that riverine geography may have played a role in structuring EN hunter-gatherer populations. The Koken MLBA individuals were genetically similar to other MLBA individuals belonging to the Andronovo Culture horizon, while two genetic outliers provide evidence of two distinct trajectories of admixture with local populations that persisted into the MLBA. These findings illuminate the dynamic population structure of Inner Asian hunter-gatherers and their genetic legacy in subsequent pastoralist populations.