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A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe
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Abstract
The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region's population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.
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TL;DR
This paper reports genome-wide data for 214 ancient individuals from Mongolia and neighboring Russia spanning ~6,000 years, revealing a dynamic population history of the Eastern Steppe. It documents a pastoralist expansion ca. 3000 BCE, a tripartite Bronze Age genetic structure, Xiongnu-era admixture, and a Mongol-period shift toward higher eastern Eurasian ancestry.
Key findings
- Pre-Bronze Age hunter-gatherers carried Ancient Northeast Asian (ANA) ancestry; Afanasievo individuals in central Mongolia (3112–2917 cal. BCE) were genetically indistinguishable from Yenisei Afanasievo, confirming Western Steppe herder expansion ~1,500 km east, but Afanasievo and Chemurchek left little enduring genetic trace in later MLBA populations.
- By the Middle/Late Bronze Age (1900–900 BCE), Mongolia was biogeographically structured into three distinct gene pools: Khövsgöl_LBA, Altai_MLBA (admixed between Khövsgöl_LBA and Sintashta-related Western Steppe ancestry), and Ulaanzuukh_SlabGrave (ANA-related, lacking ANE and WSH admixture); all practiced dairy pastoralism regardless of ancestry.
- The Xiongnu emerged from mixing these populations and surrounding regions: earlyXiongnu_west derived 92% ancestry from Chandman_IA with additional Iranian-related ancestry, while late Xiongnu showed added Sarmatian-related and Han-related gene flow and extreme genetic heterogeneity.
- Mongol-era individuals had much higher eastern Eurasian ancestry, modeled as 55%–64% Ulaanzuukh_SlabGrave, 21%–27% Han-related, and 15%–18% Western Steppe ancestry; 34 of 61 historic Mongols were genetically cladal with at least one modern Mongolic-speaking population, and lactase persistence remained at negligibly low frequency (~5%) despite widespread dairy consumption.
Methods
- New genome-wide data were generated for 214 ancient individuals from 85 Mongolian and 3 Russian sites, plus published data; 30 new AMS radiocarbon dates supplemented 74 previously published dates, totaling 98 directly dated individuals (104 dates).
- Sampling included 169 teeth and 75 petrosal bones from 225 individuals; 24 individuals were excluded for insufficient human DNA or <10,000 SNPs after capture, and 10 for >5% contamination or uncertain genetic sex; genetic sex was determined for 224 individuals (100 female, 124 male).
- Analyses included PCA projected onto 2,077 present-day Eurasians, outgroup f3 and f4 statistics, qpAdm/qpWave admixture modeling with eight outgroups, DATES admixture dating assuming 29 years per generation, uniparental haplogroup assignment, relatedness estimation, and allele-frequency estimation for five phenotypic SNPs.
Limitations
- The paper states that Early Medieval sampling is uneven (1 Xianbei/Rouran, 8 Türkic, 13 Uyghur individuals), Khitan representation is small (n = 3), and Mongol-era sampling excludes royal/regional elites and Karakorum; it also calls for further research in central and eastern Eurasia, northeastern China, the Tarim Basin, and the eastern Kazakh steppe.
- The paper states that some DATES admixture estimates should be interpreted with care because the method is designed for 2-way admixture but applied to 3-way models, and that Chemurchek source populations are distant in time or space; it also notes that ancient China, Korea, Japan, and Southeast Asia remain mostly unsampled.
- Evident from the text: nomadic camp sites are ephemeral and poorly preserved, knowledge of Mongolian prehistory is biased toward the past five millennia, radiocarbon dating reassigned many burials across periods, and sex-biased and kinship inferences are limited by sample size and context.
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168 Own result · 56 Own interpretation · 27 Sources not found · 20 Not checked yet · 18 Check pending · 12 Own method · 4 No basis given · 3 No full text of the sources
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“We identify a pastoralist expansion into Mongolia ca. 3000 BCE”
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > Abstract
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“we found that they are most closely related to contemporaneous hunter-gatherers from the western Baikal region (“Baikal_EN,” 5200–4200 BCE) and the Russian Far East (“DevilsCave_N,” ca. 5700 BCE), filling in the geographic gap in the distribution of this genetic profile”
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > Results > Pre-Bronze Age Population Structure and the Arrival of Pastoralism
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In the paper
“In Khovd province, individuals belonging to DSKC and unclassified MLBA groups (BER002 and SBG001, respectively) have a similar genetic profile that is best modeled as an equal mixture of Khövsgöl_LBA and Sintashta”
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > Results > Bronze Age Emergence of a Tripartite Genetic Structure
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In the paper
“The genetic profiles of both the Yagshiin Huduu and Dali_EBA individuals are well fitted by two-way admixture models with Botai (60%–78%) and groups with ancient Iranian-related ancestry, such as Gonur1_BA from Gonur Tepe, a key EBA site of the Bactria-Margiana Archaeological Complex (BMAC) (22%–40%; Figure 3A; Table S5B).”
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > Results > Pre-Bronze Age Population Structure and the Arrival of Pastoralism
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In the paper
“Analyzing two of these individuals (Afanasievo_Mongolia, 3112–2917 cal. BCE), we find that their genetic profiles are indistinguishable from that of published Afanasievo individuals from the Yenisei region”
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > Results > Pre-Bronze Age Population Structure and the Arrival of Pastoralism
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In the citing paper
“The same dynamic characterizes the frequency of Q, which maintained dominance throughout the Early Bronze Age and Early Iron Age, but started to decline in the Late Iron Age (Hunnu period) and became minimal in the late medieval time periods.”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [19]
In the citing paper
“In contrast, the frequency of C2 increased during the same time scale and reached dominance in the late medieval period (19).”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [19]
In the citing paper
“Our analysis indicated ANE as the second genetic component of CKZ001, ZAA001, SHA001, and SHG003, although the latter three individuals were not inferred to have ANE ancestry when they were previously analyzed (19).”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [19]
In the citing paper
“This result indicated genetic continuity of some populations across various archaeological ages, despite the overall genetic heterogeneity observed in the Mongolian Plateau (19).”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [19]
In the citing paper
“In addition, CKZ002 also showed clade level genetic affinity with an individual from medieval Mongolia: MRI001 (19).”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [19]
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In the paper
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > STAR★Methods > Method Details
“three burials originally assigned to the Middle/Late Bronze Age were determined to date to the Early Iron Age (DAR001), Xiongnu (ULN004), and Late Medieval (SHU001) periods”
§ A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe > STAR★Methods > Quantification and Statistical Analysis
“four Slab Grave individuals (BOR001, DAR001, MIT001, SHU001) from eastern Mongolia”
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Self-citation
Metadata
- Authors
- Jeong, C., Wang, K., Wilkin, S., Taylor, W. T. T., Miller, B. K., Bemmann, J. H., Stahl, R., Chiovelli, C., Knolle, F., Ulziibayar, S., Khatanbaatar, D., Erdenebaatar, D., Erdenebat, U., Ochir, A., Ankhsanaa, G., Vanchigdash, C., Ochir, B., Munkhbayar, C., Tumen, D., Kovalev, A., Kradin, N., Bazarov, B. A., Miyagashev, D. A., Konovalov, P. B., Zhambaltarova, E., Miller, A. V., Haak, W., Schiffels, S., Krause, J., Boivin, N., Erdene, M., Hendy, J., & Warinner, C.
- Affiliations
- Seoul National University (KR)
- Max Planck Institute of Geoanthropology (DE)
- University of Colorado Boulder (US)
- University of Michigan (US)
- University of Bonn (DE)
- Mongolian Academy of Sciences (MN)
- Mongolian University of Science and Technology (MN)
- National University of Mongolia (MN)
- Russian Academy of Sciences (RU)
- East Siberian Academy of Culture and Arts (RU)
- Harvard University (US)
- Corresponding author
- Jeong, Choongwon
- Warinner, Christina
- ORCID
- Jeong, Choongwon
- Wang, Ke
- Wilkin, Shevan
- Taylor, William Timothy Treal
- Miller, Bryan K.
- Bemmann, Jan H.
- Stahl, Raphaela
- Ulziibayar, Sodnom
- Khatanbaatar, Dorjpurev
- Erdenebat, Ulambayar
- Munkhbayar, Chuluunbat
- Kovalev, Alexey
- Kradin, Nikolay
- Bazarov, Bilikto A.
- Miyagashev, Denis A.
- Zhambaltarova, Elena
- Miller, Alicia Ventresca
- Haak, Wolfgang
- Schiffels, Stephan
- Krause, Johannes
- Boivin, Nicole
- Hendy, Jessica
- Warinner, Christina
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-11
- Volume
- 183
- Issue
- 4
- Pages
- 890-904.e29
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7664836
- OpenAlex
- W3094811729
- Cited by
- 328
- References
- 113
- Citations by year
- 2026: 59 · 2025: 88 · 2024: 51 · 2023: 28 · 2022: 48 · 2021: 48 · 2020: 6
- FWCI
- 15.68
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (submittedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Griffith Research Online (submittedVersion, cc-by)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Cell
- Funders
- Deutsche Forschungsgemeinschaft (257731206, SFB 1167)
- Russian Foundation for Basic Research (18-59-94020)
- Ministry of Science, ICT and Future Planning (2020R1C1C1003879)
- Ministry of Education and Science of the Russian Federation
- National University of Mongolia
- Horizon 2020
- National Research Foundation of Korea
- Max-Planck-Gesellschaft
- Horizon 2020 Framework Programme
- European Research Council (804884-DAIRYCULTURES, 771234-PALEORIDER)
- National Science Foundation (BCS-1523264)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Social Sciences › Arts and Humanities › History › Eurasian Exchange Networks
- Keywords
- ancient population genetics, Xiongnu, Mongols, nomadic pastoralism, Mongolian population, population mixing, Bronze Age, Mongolian steppe
- MeSH terms
- Archaeology, Europe, Female, Gene Frequency, Gene Pool, Genetics, Population, Geography, Haplotypes, Humans, Male, Mongolia, Time Factors, Genome, Human, Genetic Heterogeneity, Principal Component Analysis, History, Ancient, Grassland
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