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Cited by 5Forensic and Genetic ResearchEurasian Exchange NetworksGenetic diversity and population structure

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Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire

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Askapuli, Ayken, Kanzawa-Kiriyama, Hideaki, Kakuda, Tsuneo, Kassenali, Aibar, Yessen, Syrym, Schamiloglu, Uli, Schrodi, Steven J., Hawks, John, Saitou, Naruya·2026·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2531003123PMC PMC12933120
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Abstract

The Golden Horde, the northwestern extension of the Mongol Empire ruled by Genghis Khan’s descendants, holds a pivotal place in the history of Central Eurasia and Eastern Europe. Consequently, understanding the genetic legacy of Genghis Khan and his lineage has long been of both academic and public interest, especially concerning the hypothesized association of his Y-chromosome with haplogroup C3*. Here, we present ancient DNA data from four archaeological individuals—three males and one female—from medieval elite mausoleums of the Golden Horde in the Ulitau region of Kazakstan. Our genomic analyses reveal that the three male individuals are paternally related and share the Y-chromosome haplogroup C3*, confirming the association between the Y-chromosome haplogroup C3* and the Mongol Empire, supporting the long-standing hypothesis about the genetic legacy of Mongols. Additionally, our findings demonstrate that the Golden Horde elites primarily derive their genomes from Ancient Northeast Asians (ANA), with an additional ancestral component from either Ancient North Eurasians (ANE) or a Berel Scythian related population, e.g., the Kipchaks. Archaeological evidence, in turn, sheds light on a medieval population undergoing religious and cultural transition, offering insights into the societal changes experienced by Mongolian conquerors. Furthermore, through constructing an Identity by Descent (IBD) network, we successfully identify medieval relatives of these individuals on the Mongolian Plateau, linking genetic data to broader population dynamics. In essence, this study provides ancient DNA evidence that advances our understanding of the genetic background of the Mongolian elites and the population dynamics in Central Eurasia.

Overview

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TL;DR

Ancient DNA from four elite medieval mausoleum burials in Ulitau, central Kazakstan, supports a Mongolian Plateau origin for Golden Horde elites and links three males to the C3* Y-chromosome lineage previously hypothesized for Genghis Khan. The study cannot confirm the identity of the individual buried in the Mausoleum of Joshi or the exact paternal lineage of Genghis Khan.

Key findings

  • The four Kenggir individuals — CKZ001 (male, Alasha Khan), CKZ002 (male, Joshi), CKZ003 (male, Ayakkamir), and CKZ004 (female, Bolghan Ana) — were dated to 1286–1398 cal AD for CKZ002/CKZ003, 1300–1369 cal AD for CKZ004, and 1726–1814 cal AD for CKZ001. The three males shared paternal lineage C2a1a3 (C3*/C2a1a3-F1918), defined by the authors as C2a1a3a6-ZQ369; mtDNA lineages were D4c2b, C4a2a1, C4a1a+195, and G2a1g, respectively.
  • Autosomal analyses showed the Kenggir individuals derived most of their genetic makeup from Ancient Northeast Asians (ANA), with a second component resembling Berel Scythians for all but CKZ001; CKZ001 was modeled with Ancient North Eurasian (ANE) ancestry. They could also be modeled as ANA plus Kipchaks, and PCA placed them near modern Altaic-speaking Siberian/northeast Asian groups.
  • Kinship analyses found no first- or second-degree relationships among the four. CKZ003 was closely related to CKZ001 and CKZ002; CKZ001 and CKZ003 shared six IBD segments totaling 121.6 cM, while CKZ001 and CKZ002 shared only one ~9 cM segment. The claim that CKZ004 was the daughter of CKZ002 was not supported.
  • A medieval IBD network connected the Kazak Steppe and Mongolian Plateau: pairs CKZ003–DA28, DA28–MRI001, CKZ002–CKZ003, and CKZ002–SHG003 shared 2–3 IBD segments, each at least 10 cM on average. CKZ001 had 9 ROH segments totaling 83.2 Mb, comparable to a Yakut individual.

Methods

  • Ancient DNA was extracted from tooth, petrous bone, talus, and fibula samples of four individuals excavated from medieval mausoleums in the Ulitau Massif, central Kazakstan; two sites were excavated in this study and two Soviet-era sites were re-excavated. Radiocarbon dating was performed by Beta Analytic, and sequencing/library preparation was done in Japan.
  • Genotypes were called at 1,240 K SNP capture sites; read depths were ~14.6× (CKZ001), ~3.9× (CKZ002), ~0.79× (CKZ003), and ~3.9× (CKZ004). The four individuals were merged with 400 AADR individuals for a 404-individual dataset, and PCA projected them onto a space calculated from 997 modern Eurasian individuals.
  • Analyses included smartPCA; outgroup f3 and f4 statistics via qp3Pop/qpDstat; qpAdm ancestry modeling with nine reference populations; Y-chromosome haplotype placement via pathPhynder; mtDNA haplotype calling via Haplogrep and RAxML-NG; kinship via READ and ancIBD; IBD analysis after GLIMPSE2 imputation; and ROH analysis via hapROH.

Limitations

  • The paper states it could not reach an unambiguous conclusion about the true identity of the male buried in the Mausoleum of Joshi and had insufficient evidence to support or refute his descent from Genghis Khan; this would require genetic data from the 12th–13th century pedigree of Genghis Khan. It also notes that CKZ001 dated to the 18th century CE, not the Golden Horde period, and that radiocarbon dates are not infallible.
  • The paper states that Y-chromosome tree external node positions can be prone to error because ancient samples have missingness; CKZ003 had the lowest read depth, and more markers contradicted than supported the terminal branches of CKZ001 and CKZ002. It also notes qpAdm can produce equally likely ancestry models with different reference/source combinations, and that only two Kipchak samples were available and they were genetically distinct.
  • The paper states IBD cannot identify exact relationships beyond third-degree relatives. Evident from the text: the Mausoleum of Joshi may not house Joshi himself, and the Kenggir individuals might belong to a lineage other than the Altan Urug; the authors also note no consensus on Genghis Khan’s paternal lineage and that the specific Kenggir lineage proposed remains unconfirmed.

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Crossref · 10.1073/pnas.2531003123

Cites

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Statistics

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Figures

Fig. 1. Archaeological sites and radiocarbon dates. Notes: (A) Archaeological site map of the mausoleums; the orientations of the mausoleums are given as they were pictured. (B) Reconstructed image of Bolghan Ana. (C) Golden cup and its lotus motif. (D) a cloth fragment. (E) Radiocarbon dates contrasted with the lifespan of historical figures and polities. The collapse of the Great Horde in 1502 marks the end of the Golden Horde. CKZ001: male from the Mausoleum of Alasha Khan; CKZ002: male from the Mausoleum of Joshi; CKZ003: male from the Ayakkamir Mausoleum; and CKZ004: female from the Mausoleum of Bolghan Ana [could also be spelled as Bulghin or Bulgan Ana (6)].
Fig. 1. Archaeological sites and radiocarbon dates. Notes: (A) Archaeological site map of the mausoleums; the orientations of the mausoleums are given as they were pictured. (B) Reconstructed image of Bolghan Ana. (C) Golden cup and its lotus motif. (D) a cloth fragment. (E) Radiocarbon dates contrasted with the lifespan of historical figures and polities. The collapse of the Great Horde in 1502 marks the end of the Golden Horde. CKZ001: male from the Mausoleum of Alasha Khan; CKZ002: male from the Mausoleum of Joshi; CKZ003: male from the Ayakkamir Mausoleum; and CKZ004: female from the Mausoleum of Bolghan Ana [could also be spelled as Bulghin or Bulgan Ana (6)].CC BY-NC-ND · PubMed Central
Fig. 2. Modeling genetic ancestry based on autosomes and Y-chromosome. (A) Ancestral components depicted via pie charts and a bar graph. (B) A phylogenetic tree of C3* Y-chromosomes. Notes: Clades 1 and 2 are the two subbranches of C2a1a3a1-F5481, while Clade 3 corresponds to C2a1a3a6-SK1072. The numbers on the branches of ancient samples indicate variants that support or contradict the branches. For example, the branch of GoldenHorde_KLK002_GG21 was annotated with 226 to 1 (1–0), where the numbers before the parenthesis indicate the number of SNPs associated with the path before the branch and the numbers in the parenthesis indicate the SNPs that occur on this particular branch. i.e., 226 to 1 indicates that the branching was supported by 226 SNPs and contradicted by one on the path to the assigned branch; and (1–0) indicates that one SNP found on the assigned branch supports it, without any contradicting SNPs. Y-chromosome sequences are from PD18: Damgaard et al. 2018 (30); SL14: Lippold et al. (31); LW18: Wei et al. (32); GG21: Gnecchi-Ruscone et al. (33); and CJ20: Jeong et al. (19).
Fig. 2. Modeling genetic ancestry based on autosomes and Y-chromosome. (A) Ancestral components depicted via pie charts and a bar graph. (B) A phylogenetic tree of C3* Y-chromosomes. Notes: Clades 1 and 2 are the two subbranches of C2a1a3a1-F5481, while Clade 3 corresponds to C2a1a3a6-SK1072. The numbers on the branches of ancient samples indicate variants that support or contradict the branches. For example, the branch of GoldenHorde_KLK002_GG21 was annotated with 226 to 1 (1–0), where the numbers before the parenthesis indicate the number of SNPs associated with the path before the branch and the numbers in the parenthesis indicate the SNPs that occur on this particular branch. i.e., 226 to 1 indicates that the branching was supported by 226 SNPs and contradicted by one on the path to the assigned branch; and (1–0) indicates that one SNP found on the assigned branch supports it, without any contradicting SNPs. Y-chromosome sequences are from PD18: Damgaard et al. 2018 (30); SL14: Lippold et al. (31); LW18: Wei et al. (32); GG21: Gnecchi-Ruscone et al. (33); and CJ20: Jeong et al. (19).CC BY-NC-ND · PubMed Central
Fig. 3. Medieval IBD Network connecting the Kazak Steppe and the Mongolian Plateau. Notes: The network was built among individual pairs who shared at least one IBD segment that is 8 cM or longer. Kenggir sites were not labeled, and the Kenggir IBD network is given in SI Appendix, Fig. S6.
Fig. 3. Medieval IBD Network connecting the Kazak Steppe and the Mongolian Plateau. Notes: The network was built among individual pairs who shared at least one IBD segment that is 8 cM or longer. Kenggir sites were not labeled, and the Kenggir IBD network is given in SI Appendix, Fig. S6.CC BY-NC-ND · PubMed Central
Fig. 4. PCA together with ancient and modern human populations from Central Eurasia. Note: The dark red circles indicate the Kenggir individuals.
Fig. 4. PCA together with ancient and modern human populations from Central Eurasia. Note: The dark red circles indicate the Kenggir individuals.CC BY-NC-ND · PubMed Central
Fig. 5. Outgroup f3-statistic calculated with the model (CKZ002, X; Mbuti). Notes: Only modern individuals were included in the plot. The darker blue color indicates closer genetic affinity between a population and the Kenggir individuals, represented by CKZ002 in this figure.
Fig. 5. Outgroup f3-statistic calculated with the model (CKZ002, X; Mbuti). Notes: Only modern individuals were included in the plot. The darker blue color indicates closer genetic affinity between a population and the Kenggir individuals, represented by CKZ002 in this figure.CC BY-NC-ND · PubMed Central
Fig. 6. Shared IBD segments identified in two closely related Kenggir individuals (CKZ001 and CKZ003). Notes: IBD segments longer than 4 cM were used for the plot. (A) The blue color marks the physical locations of IBD segments on autosomal chromosomes. (B) the histogram depicts IBD segments, where the curved lines indicate the expected densities of various degrees of kinship.
Fig. 6. Shared IBD segments identified in two closely related Kenggir individuals (CKZ001 and CKZ003). Notes: IBD segments longer than 4 cM were used for the plot. (A) The blue color marks the physical locations of IBD segments on autosomal chromosomes. (B) the histogram depicts IBD segments, where the curved lines indicate the expected densities of various degrees of kinship.CC BY-NC-ND · PubMed Central

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Citations

Cites

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Research works printed but not linked: 18

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Metadata

Authors
Askapuli, A., Kanzawa-Kiriyama, H., Kakuda, T., Kassenali, A., Yessen, S., Schamiloglu, U., Schrodi, S. J., Hawks, J., & Saitou, N.
Affiliations
  • University of Wisconsin–Madison (US)
  • Department of Anthropology, National Museum of Nature and Science
  • University of Yamanashi (JP)
  • Center for the Study and Preservation of Cultural Heritage
  • Astana International University (KZ)
  • Nazarbayev University (KZ)
  • National Institute of Genetics (JP)
Corresponding author
  • Askapuli, Ayken
  • Saitou, Naruya
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2026-02-19
Volume
123
Issue
8
Pages
e2531003123-e2531003123
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.2531003123
PMC
PMC12933120
OpenAlex
W7130549537
Semantic Scholar
f03887ef5d49c722b46d4359c35b6fb16f994752
Cited by
5
References
88
Citations by year
2026: 5
FWCI
10.07
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (submittedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • Nazarbayev University Repository (Nazarbayev University) (submittedVersion)
Funders
  • Nazarbayev University (091019CRP2119)
  • National Institute of Genetics (NA)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Social Sciences › Arts and Humanities › History › Eurasian Exchange Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
Golden Horde, Mongol Empire, ancient DNA, elite burials, Kipchaks, population dynamics, Central Eurasia
MeSH terms
DNA, Ancient, East Asian People, Female, Genetics, Population, Haplotypes, Humans, Male, Mongolia, Genome, Human, Chromosomes, Human, Y

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CoChat. (2026). Citation check: Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire. https://app.cochat.ai/papers/10.1073/pnas.2531003123
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Askapuli, A., Kanzawa-Kiriyama, H., Kakuda, T., Kassenali, A., Yessen, S., Schamiloglu, U., Schrodi, S. J., Hawks, J., & Saitou, N. (2026). Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2531003123