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Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan
Open accessAbstract
Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan's Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan's immediate family or his close relatives.
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TL;DR
Ancient DNA from five Tavan Tolgoi graves attributed to Genghis Khan’s Golden family shows four bodies sharing mtDNA haplogroup D4 and male members carrying Y-haplogroup R1b-M343, while a fifth Golden-family-associated body carried CZ and had no kinship with them. The authors propose that Genghis Khan’s male lineage may have carried R1b-M343 rather than the widely discussed C3c-M48, and that the Tavan Tolgoi bodies were either mother–sons or full siblings.
Key findings
- Of 7 Tavan Tolgoi bodies, 4 suspected Golden family members (MN0104, MN0125, MN0126, MN0127) had identical mtDNA sequences and were assigned to haplogroup D4; MN0105 carried CZ and showed no kinship with the other Golden family members.
- Male Golden family bodies MN0104 and MN0126 belonged to Y-haplogroup R1b-M343 and shared identical Y-STR haplotypes; the general-public warrior MN0376 belonged to R1a1a-M17 and differed from them.
- A-STR and Kinship Index analyses indicated MN0104, MN0125, and MN0126 were related as either mother and two sons or full siblings with nearly the same probability; the probability of a parent–child relationship between MN0104 and MN0126 was 0%, and full-sibling probability was 64.2%.
- Modern Y-STR matches to MN0104 were found mainly in West/Central Eurasia, including Kalmyk, Hui, Uzbek, Russian, and Tajik individuals; the authors report R1b-M343 at 0.0% (0/101) and R1a1a-M17 at 0.99% (1/101) in modern-day Mongolians across the Mongolian plateau.
Methods
- The study analyzed ancient DNA from 7 Tavan Tolgoi skeletons plus 122 contemporary buccal samples, using physical anthropological sex/age estimation and prior radiocarbon dating of the graves to 1130–1250 AD.
- mtDNA HVR1, HVR2, and coding regions were sequenced for haplogroup assignment; male bodies were typed for 10 Y-SNP markers and 16 Y-STR loci; autosomal STRs were typed at 8 loci plus amelogenin, with repeated extractions/PCRs in two independent laboratories and contamination controls including UDG treatment.
- Modern comparisons used neighbor-joining trees with 8,478 modern mtDNA sequences, YHRD searches of up to 154,329 individuals (searched August 25, 2015), published Y-STR datasets, and a Kinship Index Calculation program.
Limitations
- Stated by the paper: MN0127 could not be analyzed for Y-SNP, Y-STR, or A-STR because of insufficient DNA/PCR failure; MN0126 had only 4 definable Y-SNP markers and 8 of 16 Y-STR loci; exact identities of the Tavan Tolgoi bodies remain ambiguous.
- Stated by the paper: no human remains from Genghis Khan’s grave were available, so the proposed R1b-M343 link to Genghis Khan and his Borjigin clan is inferential, not directly proven.
- Evident from the text: kinship conclusions rest on a small number of A-STR loci and missing data, and the broader genealogical scenarios rely on historical/geographical interpretation plus modern reference databases rather than direct ancient pedigree evidence.
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“Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Abstract
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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In the paper
“Particularly, MN0105 was more than 10 cm taller than other females of average height in the Mongolian era”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Archaeological and physical anthropological analyses of the Tavan Tolgoi bodies
plainSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“All physical anthropological parameters indicate that the skulls of the Tavan Tolgoi graves were all anthropologically Mongoloid (S2 Table).”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Archaeological and physical anthropological analyses of the Tavan Tolgoi bodies
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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In the paper
“Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup.”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Abstract
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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In the paper
“Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability.”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Abstract
plainstates an associationSingle case- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
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Claims other papers make about this one
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In the citing paper
“However, based on all available data in the literature and the results reported in this study [4][5][6][7][8][9][10], none of the donors who carried C2*-ST can trace their genealogy to Genghis Khan, and none of the self-claimed direct descendants of Genghis Khan carry C2*-ST.”
From Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan (2018) · cites this paper as [10]
In the citing paper
“As discussed by Zakharov et al. [4] some studies have opposed the connection between C2*-ST and Genghis Khan [5][6][7][8][9][10].”
From Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan (2018) · cites this paper as [10]
In the citing paper
“The signature Y-chromosome haplotype of Genghis Khan and his male-line descendants remains elusive.”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [17]
In the citing paper
“Additionally, the original R1b hypothesis suffers from methodological limitations, including reliance on limited SNP and STR markers (17), and has not been corroborated by subsequent studies.”
From Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire (2026) · cites this paper as [17]
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Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Abstract
“Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability.”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Discussion > Tavan Tolgoi bodies are members of a family with the relationship of mother-sons or full siblings
“Additional direct molecular evidence to determine his kinship with other members of Golden family could not be obtained due to failure of PCR amplification for Y-SNP, Y-STR, and A-STR.”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
“MN0126 was also positive for the same biallelic markers (R-M207 and R1b-M343) as those carried by MN0104 and negative for O-M175 and C-RPS4Y”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
“Minus (-) and del indicate failure of PCR amplification and deletion of the indicated bases, respectively.”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
“he carried R-M207, R1-M173, and R1a1a-M17 but not R1b-M343”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
“| MN0376 | TTCTC | C | G | T | T | C | G | C | G del | ND | R1a1a |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
“however, only 4 biallelic markers were definable in MN0126”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Results > Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
“| MN0126 | TTCTC | - | - | - | T | C | G | - | - | A | R1b |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Discussion > Tavan Tolgoi bodies are Golden family members from marriages between the lineage of Genghis Khan’s Borjigin clan and either the lineage of Ongud clan as guregen or the lineage of Hongirad clan as khatun
“Alaqai Beki had only one son and died approximately in her 50s”
§ Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan > Discussion > Tavan Tolgoi bodies are Golden family members from marriages between the lineage of Genghis Khan’s Borjigin clan and either the lineage of Ongud clan as guregen or the lineage of Hongirad clan as khatun
“as successors of Alaqai Beki, who had no sons.”
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Dating the Tavan Tolgoi Site, Mongolia: Burials of the Nobility from Genghis Khan's Era
Youn, M., Kim, J. C., Kim, H. K., Tumen, D., Navaan, D., & Erdene, M. (2007) · Radiocarbon · doi:10.1017/s0033822200042570 · Cited by 9
Self-citationWang, Y., Liu, C., Zhang, C., Li, R., LI, Y., Ou, X., & Sun, H. (2015) · ELECTROPHORESIS · doi:10.1002/elps.201500089 · Cited by 9
Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea
Kim, A.-J., Kim, K., Choi, J., Choi, E. H., Jung, Y., Min, N. Y., Lkhagvasuren, G., Rhee, S., Kim, J. H., Noh, M., et al. (2010) · BMB Reports · doi:10.5483/bmbrep.2010.43.2.133 · Cited by 8
Self-citationSneath, D., & Kaplonski, C. (2010) · Cited by 4
(2007)
(2010)
(2004) · Dominican Scholar (Dominican University of California)
Research works printed but not linked: 6
- Z Batsaikhan, 2008, Is Tengeriin Ovoo a burial of Chinggis Khaan? Mongolian Great Khans tombs in Burkhan Khaldun Mountain, Mon J of Anthropol Archaeol and Ethnol, 4, 37
- D Tumen, 2006, Archaeology of the Mongolian period: A brief introduction, Silk Road, 4, 51
- D Navaan, 2006, Sukhbaatar aimag, Ongon Sum, Tavan Tolgoi site, grave 5 and the study of nobleman grave monuments from Mongolian period, Mon J of Anthropol Archaeol and Ethnol, 2, 10
- D Navaan, 2006, Tomb of Genghis Khan is still being found, Silk Road, 4, 55
- D Tumen, 2006, Paleoanthropology of ancient populations of Mongolia, Mon J of Anthropol Archaeol and Ethnol, 54, 90
- D Tumen, 2008, Anthropological of archaeological populations from Inner Asia, Mon J of Anthropol Archaeol and Ethnol, 4, 162
Cited by
Wei, L.-H., Yan, S., Lu, Y., Wen, S.-Q., Huang, Y.-Z., Wang, L.-X., Li, S.-L., Yang, Y.-J., Wang, X.-F., Zhang, C., et al. (2018) · European Journal of Human Genetics · doi:10.1038/s41431-017-0012-3 · Cited by 57
Keyser, C., Zvénigorosky, V., Gonzalez, A., Fausser, J., Jagorel, F., Gérard, P., Turbat, T., Duchesne, S., Crubézy, É., & Ludes, B. (2020) · Human Genetics · doi:10.1007/s00439-020-02209-4 · Cited by 33
Yu, X.-E., & Li, H. (2021) · Molecular Genetics and Genomics · doi:10.1007/s00438-021-01794-x · Cited by 31
Detecting past male-mediated expansions using the Y chromosome
Batini, C., & Jobling, M. A. (2017) · Human Genetics · doi:10.1007/s00439-017-1781-z · Cited by 29
Wen, S.-Q., Yao, H.-B., Du, P.-X., Wei, L.-H., Tong, X.-Z., Wang, L.-X., Wang, C.-C., Zhou, B.-Y., Shi, M.-S., Zhabagin, M., et al. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0618-0 · Cited by 17
Metadata
- Authors
- Lkhagvasuren, G., Shin, H., Lee, S. E., Tumen, D., Kim, J.-H., Kim, K.-Y., Kim, K., Park, A. J., Lee, H. W., Kim, M. J., Choi, J., Choi, J.-H., Min, N. Y., & Lee, K.-H.
- Affiliations
- Chung-Ang University (KR)
- National University of Mongolia (MN)
- Dong-A University (KR)
- Chung-Ang University Hospital (KR)
- Corresponding author
- Lee, Kwang-Ho
- ORCID
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2016-09-14
- Volume
- 11
- Issue
- 9
- Pages
- e0161622
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC5023095
- OpenAlex
- W2520487819
- Semantic Scholar
- f7c77a55527ab9a21f949bef301637bbdb516d57
- Cited by
- 19
- References
- 69
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 2 · 2022: 2 · 2021: 3 · 2020: 3 · 2019: 1 · 2018: 1 · 2017: 2
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- National Research Foundation
- Chung-Ang University
- National Research Foundation of Korea
- 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
- Genghis Khan, kinship analysis, Mongol khanates
- MeSH terms
- Archaeology, DNA, Mitochondrial, Family, Female, Genealogy and Heraldry, Genetics, Population, Haplotypes, Humans, Male, Molecular Biology, Mongolia, History, Medieval
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