Abstract
The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples, but much of their history is poorly understood. In particular, the genomic formation of populations that speak Uralic and Yeniseian languages today is unknown. Here, by generating genome-wide data for 180 ancient individuals spanning this region, we show that the Early-to-Mid-Holocene hunter-gatherers harboured a continuous gradient of ancestry from fully European-related in the Baltic, to fully East Asian-related in the Transbaikal. Contemporaneous groups in Northeast Siberia were off-gradient and descended from a population that was the primary source for Native Americans, which then mixed with populations of Inland East Asia and the Amur River Basin to produce two populations whose expansion coincided with the collapse of pre-Bronze Age population structure. Ancestry from the first population, Cis-Baikal Late Neolithic–Bronze Age (Cisbaikal_LNBA), is associated with Yeniseian-speaking groups and those that admixed with them, and ancestry from the second, Yakutia Late Neolithic–Bronze Age (Yakutia_LNBA), is associated with migrations of prehistoric Uralic speakers. We show that Yakutia_LNBA first dispersed westwards from the Lena River Basin around 4,000 years ago into the Altai-Sayan region and into West Siberian communities associated with Seima-Turbino metallurgy—a suite of advanced bronze casting techniques that expanded explosively from the Altai1. The 16 Seima-Turbino period individuals were diverse in their ancestry, also harbouring DNA from Indo-Iranian-associated pastoralists and from a range of hunter-gatherer groups. Thus, both cultural transmission and migration were key to the Seima-Turbino phenomenon, which was involved in the initial spread of early Uralic-speaking communities.
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Data availability
The newly reported data in this study can be obtained from the European Nucleotide Archive under accession number PRJEB86428. Bam files of aligned reads for the 180 newly published ancient individuals and 15 newly reported whole-genome sequences from a subset of these individuals can be found at secondary accession ERP169776, and the genotypes that we used for analysis can be found at secondary accession ERZ25719453. Genotype files in PLINK format for the 229 modern individuals for whom we newly report SNP array can be found at secondary accession ERZ26790638. All maps in the main text and in the Supplementary Information were created using ArcGIS 10.6.1 and QGIS 3.40.6. Figures presenting genetic data were created using Rstudio running R version 4.4.1, and further edited in Adobe Illustrator version 28. Archaeological images in Supplementary Information, section 3 were edited in Adobe Photoshop 25.12.2 and Adobe Acrobat 2025.001.20458.
References
Janhunen, J. Proto-Uralic—what, where, and when? Quasquicentennial Finno Ugrian Soc. 258, 57–78 (2009).
Tambets, K. et al. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol. 19, 139 (2018).
Lamnidis, T. C. et al. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nat. Commun. 9, 5018 (2018).
Saag, L. et al. The arrival of Siberian ancestry connecting the Eastern Baltic to Uralic speakers further east. Curr. Biol. 29, 1701–1711.e16 (2019).
Vajda, E. Dene-Yeniseian. Diachronica 35, 277–295 (2018).
Reich, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012).
Flegontov, P. et al. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 570, 236–240 (2019).
Sikora, M. et al. The population history of northeastern Siberia since the Pleistocene. Nature 570, 182–188 (2019).
Nielsen, S. V. et al. Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genet. 19, e1010410 (2023).
Flegontov, P. et al. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci. Rep. 6, 20768 (2016).
Jeong, C. et al. The genetic history of admixture across inner Eurasia. Nat Ecol. Evol. 3, 966–976 (2019).
Kidd, K. K. et al. North Asian population relationships in a global context. Sci. Rep. 12, 7214 (2022).
Svyatko, S. V. et al. Freshwater reservoir effects in archaeological contexts of Siberia and the Eurasian Steppe. Radiocarbon 64, 377–388 (2022).
Zhang, F. et al. The genomic origins of the Bronze Age Tarim Basin mummies. Nature 599, 256–261 (2021).
Kılınç, G. M. et al. Human population dynamics and Yersinia pestis in ancient northeast Asia. Sci. Adv. 7, eabc4587 (2021).
Yu, H. et al. Paleolithic to Bronze Age Siberians reveal connections with first Americans and across Eurasia. Cell 181, 1232–1245.e20 (2020).
Harney, É., Patterson, N., Reich, D. & Wakeley, J. Assessing the performance of qpAdm: a statistical tool for studying population admixture. Genetics 217, iyaa045 (2021).
Flegontova, O. et al. Performance of qpAdm-based screens for genetic admixture on graph-shaped histories and stepping-stone landscapes. Genetics 230, iyaf047 (2025).
Davidson, R. et al. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol. Ecol. Resour. 23, 1823–1840 (2023).
Grebenyuk, P. S., Fedorchenko, A. Y., Dyakonov, V. M., Lebedintsev, A. I. & Malyarchuk, B. A. in Humans in the Siberian Landscapes: Ethnocultural Dynamics and Interaction with Nature and Space (eds Bocharnikov, V. N. & Steblyanskaya, A. N.) 89–133 (Springer, 2022).
Yang, M. A. et al. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science 369, 282–288 (2020).
Mao, X. et al. The deep population history of northern East Asia from the Late Pleistocene to the Holocene. Cell 184, 3256–3266.e13 (2021).
Moreno-Mayar, J. V. et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203–207 (2018).
Mathieson, I. et al. The genomic history of southeastern Europe. Nature 555, 197–203 (2018).
Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).
Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).
de Barros Damgaard, P. et al. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science 360, eaar7711 (2018).
Saag, L. et al. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain. Sci. Adv. 7, eabd6535 (2021).
Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).
Posth, C. et al. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature 615, 117–126 (2023).
Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).
de Barros Damgaard, P. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018).
Krzewińska, M. et al. Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. Sci. Adv. 4, eaat4457 (2018).
Järve, M. et al. Shifts in the genetic landscape of the Western Eurasian Steppe associated with the beginning and end of the Scythian dominance. Curr. Biol. 29, 2430–2441.e10 (2019).
Wei, L.-H. et al. Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences. Eur. J. Hum. Genet. 26, 1687–1696 (2018).
Karmin, M. et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 25, 459–466 (2015).
YFull. ISOGG Wiki https://isogg.org/wiki/YFull (2024).
Pakendorf, B. et al. Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts. Hum. Genet. 120, 334–353 (2006).
Chernykh, E. N. & Kuz’minykh, S. V. Drevnyaya metallurgiya Severnoy Evrazii (Seiminsko-Turbinskiy fenomen) (Nauka, 1989).
Marchenko, Z. V., Svyatko, S. V., Molodin, V. I., Grishin, A. E. & Rykun, M. P. Radiocarbon chronology of complexes with Seima-Turbino type objects (Bronze Age) in Southwestern Siberia. Radiocarbon 59, 1381–1397 (2017).
Chernykh, E. N. Formation of the Eurasian ‘Steppe Belt’ of stockbreeding cultures: viewed through the prism of archaeometallurgy and radiocarbon dating. Archaeol. Ethnol. Anthropol. Eurasia 35, 36–53 (2008).
Meicun, L. & Liu, X. The origins of metallurgy in China. Antiquity 91, e6 (2017).
Chernykh, E. N. in Nomadic Cultures in the Mega-Structure of the Eurasian World (eds Savinetskaya, I & Hommel, P. N.) 234–249 (Academic Studies, 2017).
Molodin, V. I., Durakov, I. A., Mylnikova, L. N. & Nesterova, M. S. The adaptation of the Seima-Turbino tradition to the Bronze Age cultures in the south of the West Siberian plain. Archaeol. Ethnol. Anthropol. Eurasia 46, 49–58 (2018).
Ilumäe, A.-M. et al. Human Y chromosome haplogroup N: a non-trivial time-resolved phylogeography that cuts across language families. Am. J. Hum. Genet. 99, 163–173 (2016).
Kuzminykh, S. V. Seima-Turbino transcultural phenomenon: migration or diffusion of technology. In Mobility and Migration: Concepts, Methods, Results: Programme and Abstracts of the V International Scientific Symposium (eds Molodin, V. I. & Hansen, S.) 52–56 (2019).
Makarov, N. P. Khronologiya i periodizatsiya epokhi Neolita i Bronzy Krasnoyarskoy lesostepi [The chronology and periodization of the Neolithic and Bronze Krasnoyarsk forest]. Izv. Lab. Drevn. Tekhnol. 1, 149–171 (2005).
Childebayeva, A. et al. Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry. Commun. Biol. 7, 723 (2024).
Kristiansen, K. The Rise of Bronze Age Peripheries and the Expansion of International Trade 1950–1100 bc. Trade and Civilisation Cambridge (eds Kristiansen, K. et al.) 87–112 (Cambridge Univ. Press, 2018).
Powell, W. et al. Tin from Uluburun shipwreck shows small-scale commodity exchange fueled continental tin supply across Late Bronze Age Eurasia. Sci. Adv. 8, eabq3766 (2022).
Singh, M. & Glowacki, L. Human social organization during the Late Pleistocene: Beyond the nomadic-egalitarian model. Evol. Hum. Behav. 43, 418–431 (2022).
Tarasov, A. & Nordqvist, K. Made for exchange: the Russian Karelian lithic industry and hunter-fisher-gatherer exchange networks in prehistoric north-eastern Europe. Antiquity 96, 34–50 (2022).
Piezonka, H. et al. The world’s oldest-known promontory fort: Amnya and the acceleration of hunter-gatherer diversity in Siberia 8000 years ago. Antiquity 97, 1381–1401 (2023).
Holopainen, S. Indo-Iranian Borrowings in Uralic: Critical Overview of Sound Substitutions and Distribution Criterion. Doctoral thesis, Univ. of Helsinki (2019).
Grünthal, R. et al. Drastic demographic events triggered the Uralic spread. Diachronica 39, 490–524 (2022).
Gnecchi-Ruscone, G. A. et al. Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians. Sci. Adv. 7, eabe4414 (2021).
Kumar, V. et al. Genetic continuity of Bronze Age ancestry with increased Steppe-related ancestry in Late Iron Age Uzbekistan. Mol. Biol. Evol. 38, 4908–4917 (2021).
Guarino-Vignon, P., Marchi, N., Bendezu-Sarmiento, J., Heyer, E. & Bon, C. Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia. Sci. Rep. 12, 733 (2022).
Kovtun, I. V. Predystoriya Indoariyskoy Mifologii (Aziya-Print, 2013).
Häkkinen, J. in Iter Polyphonicum Multilinguae (eds Hyytiäinen, T. et al.) 91–101 (2012).
Buchhorn, M. et al. Copernicus Global Land Service: land cover 100m: collection 3: epoch 2019: Globe (V3.0.1) [Data set]. Zenodo https://doi.org/10.5281/zenodo.3939050 (2020).
Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing. Nat. Protoc. 13, 2447–2461 (2018).
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).
Briggs, A. W. & Heyn, P. in Ancient DNA. Methods in Mol. Biol. (eds Shapiro, B. & Hofreiter, M.) https://doi.org/10.1007/978-1-61779-516-9_18 (2012).
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. B 370, 20130624 (2015).
Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & M MEYER, Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).
Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).
Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5, e14004 (2010).
Speir, M. L. et al. The UCSC Genome Browser Database: 2016 update. Nucleic Acids Res. 44, D717–D725 (2016).
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
Behar, D. M. et al. A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675–684 (2012).
Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).
Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).
Lazaridis, I. et al. The genetic history of the Southern Arc: a bridge between West Asia and Europe. Science 377, eabm4247 (2022).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Maier, R., Flegontov, P., Flegontova, O., Işıldak, U., Changmai, P. & Reich, D. On the limits of fitting complex models of population history to f-statistics. eLife 12, e85492 (2023).
Kennett, D. J. et al. Archaeogenomic evidence reveals prehistoric matrilineal dynasty. Nat. Commun. 8, 14115 (2017).
Van de Loosdrecht, M. et al. Pleistocene North African genomes link near Eastern and sub-Saharan African human populations. Science 360, 548–552 (2018).
Olalde, I. et al. The genomic history of the Iberian Peninsula over the past 8000 years. Science 363, 1230–1234 (2019).
Monroy Kuhn, J. M., Jakobsson, M. & Günther, T. Estimating genetic kin relationships in prehistoric populations. PLoS ONE 13, e0195491 (2018).
Acknowledgements
We dedicate this paper to Oleg Balanovsky, who had a leading role in the collection of present-day samples newly reported in this study, and who would have been an author had he not died in 2021. The authors thank N. Adamski, R. Bernardos, N. Bradman, A. Chizhevsky, M. Ferry, E. Idrisov, J. Kidd, E. Kostyleva, S. Kuz’minykh, K. Mandl, P. Nymadawa, O. Poshekhonova, H. Ringbauer, L. Saroyants, K. Stewardson, S. Tur, Y. Yusupov and Z. Zhang for wet laboratory or bioinformatic support, providing permission to analyse samples that they shared or critical comments. We acknowledge E. Besprozvanny, T. Chikisheva, A. Chizhevskiy, O. Goryunova, E. Kostyleva, N. Kungurova, D. Maslyuzhenko, A. Polevodov, A. Shalapinin, G. Sinitsyna, Z. Trufanova and V. Zakh for providing permissions to use their previously published figures in the supplementary information. A.A.T. acknowledges support from the Russian Science Foundation (project 22-18-00470). M.Z. acknowledges support from the Collaborative Research Grants Program 091019CRP2119 to Nazarbayev University. The research of G.G.B. was conducted within the framework of the scientific research programme of the Diamond and Precious Metals Geology Institute, Siberian Branch of the Russian Academy of Science (project FUFG-2024-0005). Research by A.D.S., E.N.S. and V.M.D. was carried out within the research programme of the Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences ‘The Stone Age of Northern Asia: Cultural and Ecological context (FWZG-2025-0010). Research by D.N.E., S.N.S., S.M.S. and K.N.S. was carried out within the State Assignment FWRZ-2021–0006. A.V.F. was supported by the IHMC RAS research programme (FMZF-2025-0008). M.G.T. is supported by ERC Horizon 2020 research and innovation programme grant agreements: 951385 (COREX), 865515 (SUSTAIN), 324202 (NeoMilk), 788616 (YMPACT), and by Wellcome Senior Research Fellowship Grant 100719/Z/12/Z. G.H. was supported by BBSRC (BB/L009382/1), Wellcome Trust and Royal Society (098386/Z/12/Z, 224575/Z/21/Z). We thank the Museum of the Institute of Plant and Animal Ecology UB RAS for sharing samples. P.F. was supported by the Czech Science Foundation (project 21-27624S) and the EU Operational Program Just Transition (‘LERCO—Life Environment Research Center Ostrava’, project CZ.10.03.01/00/22_003/0000003). L.A.V. was supported by the Czech Ministry of Education, Youth and Sports (programme ERC CZ, project LL2103). P.F., R.P. and D.R. were supported by John Templeton Foundation grant 61220. P.F. and D.R. were supported by gifts from Jean-Francois Clin. D.R. was supported by National Institutes of Health grant HG012287 and by the Allen Discovery Center programme, a Paul G. Allen Frontiers Group advised programme of the Paul G. Allen Family Foundation, and is an Investigator of the Howard Hughes Medical Institute.
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T.C.Z., L.A.V., A.K. and D.R. wrote the manuscript and supplementary materials with input from all co-authors. S.M., N.R., R.P., V.M.N. and D.R. supervised different aspects of the study. T.C.Z. carried out the main genetic analyses under the supervision of P.F., R.M. and V.M.N. I.O. and I.L. contributed additional genetic analyses. M.F., P.F., V.M.N. and A.A.T. contributed to the framing and interpretation of results. L.A.V. edited archaeological information with input from D.R. and P.F. K.S. and L.A.V. contributed extensively to sample procurement. A.A.T, N.E.R., S.A.A., D.S.A., A.N.A., G.G.B., A.P.D., V.M.D., D.N.E., A.V.F., Y.V.F., S.P.G., A.A.K., K.Y.K., Y.F.K., E.P.K., P.K., I.V.K., N.P.M., V.V.M., E.N.N., M.P.R., T.M.S., M.V.S., V.S., S.N.S., O.S.S., S.M.S., K.N.S., E.N.S., A.D.S., A.A.T., A.S.V., A.V.V. and R.P. contributed anthropological remains and/or contributed to the creation of the archaeological supplement. N.E.R. wrote the ‘geophysical context’ section of the Supplementary Data. E.V.B., S.D., G.H., K.K., J.K., E.S., R.S., T.T., M.G.T. and M.Z. contributed genetic data from present-day people. A.A., M. Mah, A.M. and S.M. carried out bioinformatic data processing. K.C., O.C., D.F., D.K., F.C., L.I., A.K., K.T.Ö., F.Z. and M. Michel carried out wet laboratory work.
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Extended data figures and tables
Extended Data Fig. 1 Sites with newly-reported samples.
This map displays all the sites which are the sources of the samples in the major populations that are the focus in this paper. These include all sites 1) whose samples fall on the NEAHG cline, 2) whose samples fall in the Cisbaikal_LNBA cluster or are admixed with it, 3) whose samples fall in the Yakutia_LNBA cluster or are admixed with it, 4) whose samples are a part of the ten-population East Siberian transect described in our qpAdm modelling, and 5) whose samples are from Seima-Turbino period individuals. Each site is represented by a pie chart, whose size is proportional to the number of individuals from that site; the white fraction represents previously-published samples, and the black newly-published samples. Our sampling fills geographic and temporal lacunae.
Extended Data Fig. 2 Chronology of sites and cultures in each geographic region.
Temporal and geographic disposition of cultures from the Mesolithic to the Late Bronze and Iron Ages across Northern Eurasia. Sites whose samples are analyzed in our paper are highlighted in darker boxes, within containing boxes indicating archaeological cultures. Sites whose colors are darker are those that we believe are most securely dated (based on radiocarbon, isotopic, and archaeological evidence).
Extended Data Fig. 3 PCA with target populations projected onto ancient populations with an especially high fraction of ANE ancestry.
To illuminate the role that levels of ANE ancestry plays in generating variation among the populations we analyze, we use as a basis for another projection 71 shotgun-sequenced ancient individuals from across Eurasia, of which a large proportion are enriched in ANE ancestry and fall outside the range of present-day variation (e.g. individuals from populations like Tyumen_HG.SG or Kazakhstan_Botai.SG; for full list, see Supplementary Information section 4). The North Eurasian Hunter-Gatherer cline forms a curved arc stretching from EHG populations to present-day East Asians; the center of the arc dominated by populations rich in ANE ancestry is moved toward the positive direction in PC2. The individual furthest along the positive direction in PC2 is AG3. Clines formed by later Inner Asian populations, such as present-day Uralic, Turkic, and Mongolic speakers, as well as Late Bronze Age and Iron Age steppe populations such as Scythians and Sarmatians, are distinguished from the NEAHG cline by their much lower values along PC2, suggesting a much lower level of ANE ancestry. This PCA shows that populations along the NEAHG cline, remaining stable for many millennia, were substantially outside the range of present-day genetic variation in Northern Eurasia.
Extended Data Fig. 4 PCA focusing on East Eurasian populations.
To further uncover possible structure among the East Asian ancestries within the populations that we analyze, we constructed a third PCA, using as a basis 37 East Asian present-day populations that have minimal West Eurasian admixture, and a single West Eurasian population (Norwegian), all genotyped on the Affymetrix Human Origins array (for a full list of populations analyzed, refer to Supplementary Information section 4). We projected all other shotgun-sequenced and hybridization-captured ancient and present-day individuals onto this basis. Once again, the North Eurasian Hunter-Gatherer cline forms a curved arc stretching from West Eurasian populations to present-day East Asians, with the center of the arc deflected toward the AG3 individual. East Asian populations are now differentiated along PC2, with Southeast Asians and East Asian agriculturalists taking on especially negative values along that dimension; populations from the Amur River Basin taking on intermediate values; then populations on the Mongolian Plateau and surrounding areas. A large gap separates these populations from Yakutia_LNBA and Russia_Tatarka_BA, which take on very positive values along PC2, close to present-day Nganasans and a genetically very similar Iron-Age individual from Yakutia who clusters with Nganasans in the previous two PCAs (Yakutia_IA.SG; also see Extended Data Fig. 9). As one moves East along the NEAHG cline, their positions along PC2 tend to converge to the values found among populations of the Mongolian Plateau. In contrast, the Dzhilinda1_M_N_8.4 kya and Kolyma_M_10.1 kya individuals, and the Syalakh_Belkachi, Yakutia_LNBA and Russia_Tatarka_BA populations do not fall on the NEAHG cline and are shifted in the positive direction on PC2, toward the positions occupied by Nganasans, Beringian populations, and Native Americans. Lastly, Uralic populations possess the most positive values among PC2 when compared to Turkic, Mongolic and Tungusic populations.
Extended Data Fig. 5 PCA focusing on ancient individuals from Northern Eurasia and the Americas.
To understand structure among NEAHG populations and non-NEAHG Siberians, we constructed two PCAs with ancient individuals including all individuals from the NEAHG cline, ancient non-NEAHG Siberians, and a selection of ancient Beringians and Native Americans. Notably, all these populations possess combinations of only WHG, EHG, ANE and East Asian ancestries. No individuals were projected in these PCAs. The first PCA (Extended Data Fig. 6a) includes all individuals in the set, and the second (Extended Data Fig. 6b) includes only individuals East of the Altai mountains. (A) In the first PCA we highlight several patterns. 1) the North Eurasian Hunter-Gatherer cline forms a curved arc stretching from West Eurasian populations to East Asian populations along PC1 and PC2. Populations rich in East Asian ancestry are differentiated along PC3, with individuals and populations within or closely related to the Cisbaikal_LNBA cluster having the most positive values, followed by those in the Transbaikal_EMN cluster and populations of the Mongolian Plateau, followed by individuals and populations in the Yakutia_LNBA cluster, followed by those from the Amur River Basin, followed by populations from the Bering Straits and the Americas. Notably, all individuals along the NEAHG cline, including individuals rich in East Asian ancestry (e.g. Cisbaikal_EN, Transbaikal_EMN, and all NEAHG individuals from the Krasnoyarsk region) form a straight line in PC3, suggesting a constant source of East Asian ancestry at the East Asian terminus of the NEAHG cline. 2) Khaiyrgas_16.7 kya occupies a central position among the other groups rich in East Asian ancestry in East Siberia, Beringia and the Americas, suggesting a lack of shared drift with later populations of the Bering region or the Americas. The situation is different for later populations: Kolyma_M_10.1 kya falls among ancient Beringian populations, while the more East Asian-admixed Ust-Kyakhta_14 kya and Dzhilinda1_M_N_8.4kya occupy a position in between Syalakh-Belkachi and ancient Bering Straits populations, with the even more East Asian-admixed Syalakh-Belkachi population showing even less of this displacement towards ancient Bering Straits populations. (B) We find a similar pattern in the second PCA, except with an opposite ordering of the clusters along PC3. Our results suggest that the distinctions we discover between groupings produced by the clustering analyses in Supplementary Information Section 6 can be recovered in PCA analyses aimed at recovering fine-scale structure, despite underlying similarities in deep ancestry in populations in East Siberia, Beringia, and the Americas—all the products of admixture between ANE and East Asian ancestry.
Extended Data Fig. 6 Graphical Summary of Genetic Changes Taking Place in Northern Eurasia.
Panel A shows the widespread distribution of individuals with Ancient Paleosiberian (APS) ancestry in Siberia before the Holocene, >10 kya. Panel B shows the formation of the NEAHG cline by ~10 kya, and the formation of the population on its eastern terminus (Transbaikal_EMN) through admixture between Amur River and Inland East Asian ancestries. Panel C shows the emergence of Cisbaikal_LNBA and Yakutia_LNBA in genetic turnovers in the Cis-Baikal and Northeastern Siberian regions in the Mid-Holocene, and the genetic diversity of Seima-Turbino period individuals ~4.0 kya. Panel D shows the genetic gradient between West Eurasian ancestry and Yakutia_LNBA formed by present-day Uralic populations, along with all locations from which present-day populations with Cisbaikal_LNBA ancestry were sampled (grey dots ringed with black), alongside the geographic locations of two late Bronze Age/early Iron Age individuals (grey dots ringed with yellow) with >90% Cisbaikal_LNBA ancestry.
Extended Data Fig. 7 Populations created by genetic grouping procedure applied over Northeast Siberians.
Details of populations created by the grouping procedure applied to individuals in Northeastern Siberia.
Extended Data Fig. 8 Statistics of the form f4(Ethiopia_4500BP.SG, Target, “Route 2” population, Cisbaikal_LNBA).
Central Siberian populations from the Yenisei Basin (including Kets and South Siberian Turks) are highlighted in brown, while Arctic North American and Asian populations on either side of the Bering Straits populations are highlighted in blue. Bering Straits populations that are heavily European-admixed (Aleut and Yukagir_forest) are colored dark blue, while Samoyedic populations (Enets, Selkup, and Nganasan) are colored violet. Despite the similarity of the APS-rich populations in this comparison (all being admixtures between APS ancestry and East Asian ancestry), present-day groups of the Bering Straits are always closer to groups with “Route 2” APS ancestry (i.e., Kolyma_M_10.1 kya → Dzhilinda1_8.4 kya → Syalakh-Belkachi → Yakutia_LNBA), while Central Siberian populations of the Yenisei Basin are always closer to Cisbaikal_LNBA. For the version including a comparison with Ust-Kyakhta, refer to Supplementary Information Section 8; Figs. S94 & S95.
Extended Data Fig. 9 ADMIXTURE results.
For details, refer to Supplementary Information Section 5.
Extended Data Fig. 11 Contribution of Yakutia_LNBA and Cisbaikal_LNBA to Admixed Inner Eurasians (AIEA).
Higher-resolution version of Fig. 3, containing the group/population labels. The codes are: ATN, Altaian; ATN_C, Altaian_Chelkan; BSK, Bashkir; BSM, Besermyan; BRY, Buryat; XNB_AR, China_AR_Xianbei_IA; CVS, Chuvash; DUR, Daur; DGN, Dolgan; DGX, Dongxiang; ENT, Enets; EST, Estonian; EVN, Even; EVN_E, Evenk_FarEast; EVN_T, Evenk_Transbaikal; FIN.SG, FIN.SG; LVL, Finland_Levanluhta; SAM, Finland_Saami_Modern.SG; FIN, Finnish; HZN, Hezhen; KLM, Kalmyk; KKP, Karakalpak; KRL, Karelian; KZK, Kazakh; KZK_C, Kazakh_China; BRL, Kazakhstan_Berel_IA; SARM_C, Kazakhstan_CaspianSteppe_Sarmatian; SARM_C.SG, Kazakhstan_CaspianSteppe_Sarmatian.SG; SAKA_K, Kazakhstan_CentralKazakhSteppe_Saka; SARM_K, Kazakhstan_CentralKazakhSteppe_Sarmatian.SG; KRK, Kazakhstan_Karakhanid.SG; KLK_1, Kazakhstan_Karluk_1.SG; KLK_2, Kazakhstan_Karluk_2.SG; KMK, Kazakhstan_Kimak.SG; KPC_1, Kazakhstan_Kipchak1.SG; KPC_2, Kazakhstan_Kipchak2.SG; SAKA_TS, Kazakhstan_Kyrgystan_TianShan_Saka; BRL_P, Kazakhstan_Pazyryk_Berel; TSM, Kazakhstan_Tasmola; SARM_W, Kazakhstan_WesternKazakhSteppe_Sarmatian; KET, Ket; KKS, Khakass; KKS_K, Khakass_Kachin; KMG, Khamnegan; KHT, Khanty; KOM, Komi_Zyrian; KRG_C, Kyrgyz_China; KRG_K, Kyrgyz_Kyrgyzstan; KRG_T, Kyrgyz_Tajikistan; TUR, Kyrgyzstan_Turk.SG; MNS, Mansi; MRI, Mari.SG; SCY, Moldova_Scythian; MGL, Mongol; MGA, Mongola; XNB_M, Mongolia_IA_Xianbei; MDV, Mordovian; NNI, Nanai; NGD, Negidal; NGS, Nganasan; NVH, Nivh; NGI_A, Nogai_Astrakhan; NGI_K, Nogai_Karachay_Cherkessia; NGI_S, Nogai_Stavropol; ORQ, Oroqen; ADB, Russia_Aldy_Bel; BLS, Russia_Bolshoy; MHE_1, Russia_EarlyMedieval_Heshui_Mohe_1; MHE_2, Russia_EarlyMedieval_Heshui_Mohe_2; SARM_S, Russia_EarlySarmatian_SouthernUrals.SG; KRS_o1, Russia_Karasuk_o1.SG; KRS_o, Russia_Karasuk_oRISE.SG; KRS, Russia_Karasuk.SG; SARM_L, Russia_LateSarmatian.SG; SARM_S.SG, Russia_MiddleSarmatian_SouthernUrals.SG; SARM, Russia_Sarmatian; SARM.SG, Russia_Sarmatian.SG; TGR, Russia_Tagar.SG; SAM.DG, Saami.DG; SKP, Selkup; SHR_K, Shor_Khakassia; SHR_M, Shor_Mountain; TTR_A, Tatar_Astrakhan; TTR_I, Tatar_Irtysh_Barabinsk.SG; TTR_K, Tatar_Kazan; TTR_M, Tatar_Mishar; TTR_S, Tatar_Siberian; TTR_Z, Tatar_Siberian_Zabolotniye; TTR_T, Tatar_Tomsk.SG; TTR_V, Tatar_Volga.SG; TDZ, Todzin; TFL, Tofalar; TBL, Tubalar; TKM, Turkmen; TVN, Tuvinian; UDM, Udmurt; SCY_U, Ukraine_Scythian; ULC, Ulchi; UYG, Uyghur; UZB, Uzbek; VPS, Veps; XIB, Xibo; YKT, Yakut; YKG_F, Yukagir_Forest; YKG_T, Yukagir_Tundra; KNY.SG, Russia_Yenisei_Krasnoyarsk_LBA.SG; KNY_o1.SG, Russia_Yenisei_Krasnoyarsk_LBA_o1.SG.
Extended Data Fig. 12 f4 statistics of the form f4(Ethiopia_4500BP.SG, X, Yana.SG, China_Paleolithic) plotted against f4(AG3, X, Yakutia_LNBA, East Eurasian Population).
China_Paleolithic includes the Tianyuan and Amur_River_33K genomes, “East Eurasian Population” is some population grouping in Siberia or Northeast Asia other than Yakutia_LNBA, and X are Admixed Inner Eurasian populations (AIEA populations) including ancient Central Asian nomads from the Late Bronze to Iron Age down to the Scytho-Sarmatian period, as well as modern or ancient populations that speak languages from the Yukaghiric, Yeniseian (Kets), Uralic, Turkic, Mongolic, Tungusic, and Nivkh language families. Modern Uralic-speaking populations, and ancient putatively Uralic-speaking populations uniformly prefer Yakutia_LNBA to other East Asian ancestries no matter the other population used in the comparison. Furthermore, at any level of admixture between East and West Eurasian ancestries, the population with the greatest affinity to Yakutia_LNBA is always a Uralic-speaking population. f4-statistics therefore highlight the connection between Uralic populations and Yakutia_LNBA ancestry over other sources of East Asian ancestry.
Extended Data Fig. 13 Characteristic Seima-Turbino artifacts.
1. Double-bladed dagger with a ring-shaped pommel, robbery find, unknown provenance (probable Omsk region or Rostovka). 2. Double-bladed dagger with a horse figurine on the pommel, an accidental find near Shemonaikha, East Kazakhstan. 3., 5., 7. Crook-backed knives with figurines on pommels: 3. from Seyma; 5. from Elunino-1, burial 1, 7. from Rostovka, burial 2. 4. Scapula-shaped celt with goat image, Rostovka, cluster of finds near burial 21. 6. double-bladed plate dagger with a double elk-head figurine pommel, an accidental find near Perm’ (probably associated with the Turbino site). 8. Top of staff with a horse figurine, an accidental find near Omsk. 9a. & 9b. Single-ear long spearhead with a relief figurine of a Felidae predator (tiger or mountain leopard) on the socket (9a. the spear tip,10b. the detail of the socket), an accidental find near Omsk.
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This file includes sections 1–11, Supplementary Figs. 1–101 and Supplementary Tables 1–35. It includes discussion of archaeological context, details of sample preparation, details of population genetic analysis using PCA, ADMIXTURE, qpAdm and other formal methods such as f4-statistics, relatedness analysis, uniparental markers, and also linguistic discussion and archaeological interpretation.
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Supplementary Data 1–7
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Zeng, T.C., Vyazov, L.A., Kim, A. et al. Ancient DNA reveals the prehistory of the Uralic and Yeniseian peoples. Nature 644, 122–132 (2025). https://doi.org/10.1038/s41586-025-09189-3
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DOI: https://doi.org/10.1038/s41586-025-09189-3
