Ancient genomes from eastern Kazakhstan reveal dynamic genetic legacy of Inner Eurasian hunter-gatherers

PRJEB83880 Original Paper / DOI2025-08-2621 samples (study)

AI interpretationAI-generated

Ancient DNA from eastern Kazakhstan reveals mixing between distinct hunter-gatherers and their legacy in Bronze Age herders.

This study sequenced 21 ancient individuals from the Koken site in eastern Kazakhstan: two Early Neolithic hunter-gatherers and 19 Middle-Late Bronze Age pastoralists. The two hunter-gatherers had different genetic profiles but were second-degree relatives, showing that distinct groups intermarried. They were most similar to later Neolithic people in the Irtysh River region, while contemporaneous hunter-gatherers to the west and east were genetically different, suggesting rivers shaped population structure. The Bronze Age individuals resembled other Andronovo Culture people, with two outliers showing separate admixture paths with local groups.

Two Early Neolithic hunter-gatherers from Koken were second-degree relatives but had distinct genetic profiles, proving interbreeding between different hunter-gatherer populations.
Early Neolithic hunter-gatherers in the Irtysh River region were genetically distinct from those in the Tobol-Ishim and Upper Ob regions, indicating river geography structured populations.
Middle-Late Bronze Age Koken individuals were genetically similar to other Andronovo Culture people, but two outliers reveal separate admixture trajectories with local populations.

Sample interpretation

The site yielded 19 samples with Y-chromosome data for 7 males. Y lineages include R-YP1456 (2), R-S23592, N-Y6516, R-M198, R-Y20746, and Q-F835. Mitochondrial DNA includes H2b (3), U5a1b1f (2), T1a1 (2), HV6 (2), W3a1a, and T2e2. These lineages reflect a mix of western and eastern Eurasian ancestry, consistent with the region's role as a crossroads.

For genealogy enthusiasts

For ancestry enthusiasts, this study shows that Inner Asian hunter-gatherers were not a single population but a mosaic of genetically distinct groups that interacted. The genetic legacy of these hunter-gatherers persisted into Bronze Age pastoralists, highlighting the complex population dynamics in the Steppe. It also underscores the importance of river systems in shaping ancient human migrations and interactions.

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.

Samples & Data on TheYtree

19samples on site

7Y haplogroup resolved

Paternal (Y-DNA) Haplogroups

Haplogroup	Samples
R-YP1456	2
N-Y6516	1
R-M198	1
R-Y20746	1
Q-F835	1
R-S23592	1

Maternal (mtDNA) Haplogroups

H2b · 3 HV6 · 2 U5a1b1f · 2 T1a1 · 2 T2e2 · 1 U5a2-C16294T · 1 H6a1a1 · 1 A10 · 1 U5b2a1a2 · 1 I4a · 1

Sample Highlights More samples →

Sample	Y-DNA	mtDNA	Culture / Period
KKN001	N-Y6516	A10	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists
KKN083	R-YP1456	T2e2	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists
KKN085	R-S23592	H2b	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists
KKN093	Q-F835	W3a1a	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists
KKN096	R-YP1456	HV6	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists
KKN100	R-Y20746	H6a1a1	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists
KKN102	R-M198	T1a1	· two Early Neolithic (EN) hunter-gatherers and 19 Middle-Late Bronze Age (MLBA) pastoralists