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Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia
Open accessAbstract
Mongolia is located in a strategic position at the eastern edge of the Eurasian Steppe. Nomadic populations moved across this wide area for millennia before developing more sedentary communities, extended empires, and complex trading networks, which connected western Eurasia and eastern Asia until the late Medieval period. We provided a fine-grained portrait of the mitochondrial DNA (mtDNA) variation observed in present-day Mongolians and capable of revealing gene flows and other demographic processes that took place in Inner Asia, as well as in western Eurasia. The analyses of a novel dataset (N = 2,420) of mtDNAs highlighted a clear matrilineal differentiation within the country due to a mixture of haplotypes with eastern Asian (EAs) and western Eurasian (WEu) origins, which were differentially lost and preserved. In a wider genetic context, the prevalent EAs contribution, larger in eastern and central Mongolian regions, revealed continuous connections with neighboring Asian populations until recent times, as attested by the geographically restricted haplotype-sharing likely facilitated by the Genghis Khan’s so-called Pax Mongolica. The genetic history beyond the WEu haplogroups, notably detectable on both sides of Mongolia, was more difficult to explain. For this reason, we moved to the analysis of entire mitogenomes (N = 147). Although it was not completely possible to identify specific lineages that evolved in situ, two major changes in the effective (female) population size were reconstructed. The more recent one, which began during the late Pleistocene glacial period and became steeper in the early Holocene, was probably the outcome of demographic events connected to western Eurasia. The Neolithic growth could be easily explained by the diffusion of dairy pastoralism, as already proposed, while the late glacial increase indicates, for the first time, a genetic connection with western Eurasian refuges, as supported by the unusual high frequency and internal sub-structure in Mongolia of haplogroup H1, a well-known post-glacial marker in Europe. Bronze Age events, without a significant demographic impact, might explain the age of some mtDNA haplogroups. Finally, a diachronic comparison with available ancient mtDNAs made it possible to link six mitochondrial lineages of present-day Mongolians to the timeframe and geographic path of the Silk Route.
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TL;DR
This study analyzes mtDNA control-region sequences from 2,420 present-day Mongolians and 147 complete mitogenomes to characterize eastern and western Eurasian maternal ancestry and demographic history. It finds strong regional differentiation, with eastern Asian lineages predominating overall and western Eurasian lineages concentrated in western Mongolia, and links some western Eurasian lineages to post-glacial expansions and later Silk Route-era movements.
Key findings
- Of 2,420 Mongolian mtDNAs, 1,987 (82.1%) belong to eastern Asian haplogroups, with C at 19.6% and D4 at 19.8%; western Eurasian haplogroups reach 21.7% in western Mongolia and decrease eastwards, with H the most represented western Eurasian haplogroup at 6.5%.
- The 2,420 mtDNAs were classified into 413 lineages grouped into 18 macro-haplogroups; PCA separates the westernmost regions Bayan-Ölgii, Khovd, and Uvs due to JT, N2, R0, and X, while northern regions cluster together and southern regions are separated by eastern Asian lineages.
- Complete mitogenomes (N = 147; 121 western Eurasian and 26 eastern Asian) revealed two novel sub-branches, HV13b1 and U5b1c2; haplogroup H1 was present at about 3%, three times higher than reported for Inner Asia, with sub-clades H1b, H1c, and H1j.
- Bayesian analyses reconstructed two major increases in effective population size: one beginning in the late glacial period around 18–15 kya and a steeper early Holocene increase; some lineages coalesced around 5 kya during the Bronze Age without a significant demographic impact, and six sub-lineages matched the timeframe and geographic path of the Silk Route.
Methods
- Collected 2,420 unrelated subjects with a Mongolian terminal maternal ancestor from 20 of 21 provinces using mouthwash; sequenced the mtDNA control region (2,133 full control-region haplotypes and 2,335 HVS1 haplotypes), classified haplogroups with PhyloTree build 17, and analyzed diversity, PCA, MDS, and haplotype sharing.
- Sequenced 147 complete mitogenomes using the Ion Torrent Personal Genome Machine, built a most parsimonious tree and Bayesian BEAST analyses with an L3 outgroup, and compared results with 693 published ancient mitogenomes, including 25 excavated in Mongolia.
Limitations
- Stated: provinces or macro-areas with fewer than 30 individuals were excluded from intra-Mongolia analyses; sample bias in the Khangai Mountains (N = 12) cannot be excluded; it was not completely possible to identify specific lineages that evolved in situ; and recent events younger than 3 kya cannot be accurately described through coalescent estimates because mitogenomes accumulate about one mutation in more than two thousand years on average.
- Evident from the text: sampling is uneven across provinces, and 348 individuals lacked province information and were assigned to an “unspecified” group, which may affect regional comparisons; control-region-only analyses also have lower resolution than complete mitogenomes.
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“The macro-haplogroup distribution across the country clearly shows a differential contribution of haplogroups with two distinct geographic origins”
§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Results > The Mitochondrial DNA Variation Within Mongolia
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“The PC2 separates the westernmost regions, Bayan-Ölgii, Khovd and Uvs, due to the high contribution of the typical WEu lineages JT, N2, R0 and X.”
§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Results > The Mitochondrial DNA Variation Within Mongolia
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“When we tried to differentiate eastern and western contributions, the legacy of WEu haplogroups was less marked and more widespread.”
§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Results > The Mitochondrial DNA Variation of Mongolia in the Eurasian Context
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“This genetic diversity is heterogeneously distributed within Mongolia (Figure 1A).”
§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Results > The Mitochondrial DNA Variation Within Mongolia
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“The map based on haplotype sharing shows a greater proximity to surrounding Asian populations.”
§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Results > The Mitochondrial DNA Variation of Mongolia in the Eurasian Context
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§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Materials and Methods > Sample Collection and DNA Extraction
“The samples were collected in 20 (out of 21) Mongolian provinces:”
§ Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia > Introduction
“21 provinces (aimags) and one provincial municipality (Ulaanbaatar)”
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In the paper
“Lan, 2019, MtDNA Polymorphism Analyses in the Chinese Mongolian Group: Efficiency Evaluation and Further Matrilineal Genetic Structure Exploration, Mol. Genet. Genomic Med., 7, e00934, 10.1002/mgg3.934”
Cited work 10.1002/mgg3.934 · retracted 2024-02-12 · notice 10.1002/mgg3.2366 · this paper published 2022-01-06
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Self-citationFifteen millennia of human mitogenome evolution in Sicily
Tommasi, A., Agostini, R. B., Villani, G., Migliore, N. R., Vizzari, M. T., Cardinali, I., Gerlando, R. D., Nicolini, V., Sorasio, G., Santos, P., et al. (2025) · Science Advances · doi:10.1126/sciadv.ady1674 · Cited by 6
Self-citationBodner, M., Amory, C., Olivieri, A., Gandini, F., Cardinali, I., Lancioni, H., Huber, G. E., Xavier, C., Pala, M., Fichera, A., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23126725 · Cited by 6
Self-citationCrisà, A., Cardinali, I., Giontella, A., Silvestrelli, M., Lancioni, H., & Buttazzoni, L. (2024) · Biology · doi:10.3390/biology13121087 · Cited by 5
Self-citation
Metadata
- Authors
- Cardinali, I., Bodner, M., Capodiferro, M. R., Amory, C., Rambaldi Migliore, N., Gomez, E. J., Myagmar, E., Dashzeveg, T., Carano, F., Woodward, S. R., Parson, W., Perego, U. A., Lancioni, H., & Achilli, A.
- Affiliations
- University of Perugia (IT)
- Innsbruck Medical University (AT)
- University of Pavia (IT)
- National University of Mongolia (MN)
- University of Bologna (IT)
- Pennsylvania State University (US)
- Southeastern Community College - Iowa (US)
- Corresponding author
- Cardinali, Irene
- Achilli, Alessandro
- ORCID
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2022-01-06
- Volume
- 12
- Pages
- 819337-819337
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC8773455
- OpenAlex
- W4206652868
- Cited by
- 8
- References
- 58
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 3 · 2022: 2
- FWCI
- 0.86
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Geographic Society
- Ministero dell’Istruzione, dell’Università e della Ricerca
- Dipartimenti di Eccellenza
- Università degli Studi di Pavia
- Ministry of Education, Culture, Sports, Science and Technology
- Russian Foundation for Basic Research
- National University of Mongolia
- 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 › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- mitochondrial DNA, Inner Asia, Eurasian steppe, gene flow, haplotype sharing, Pax Mongolica, Genghis Khan, effective population size, Bronze Age, Silk Road, ancient DNA, nomadic populations
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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