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Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea

Nature Ecology & Evolution volume 7, pages 2160–2172 (2023)Cite this article

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An Author Correction to this article was published on 22 January 2024

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Abstract

Populations genetically related to present-day Europeans first appeared in Europe at some point after 38,000–40,000 years ago, following a cold period of severe climatic disruption. These new migrants would eventually replace the pre-existing modern human ancestries in Europe, but initial interactions between these groups are unclear due to the lack of genomic evidence from the earliest periods of the migration. Here we describe the genomes of two 36,000–37,000-year-old individuals from Buran-Kaya III in Crimea as belonging to this newer migration. Both genomes share the highest similarity to Gravettian-associated individuals found several thousand years later in southwestern Europe. These genomes also revealed that the population turnover in Europe after 40,000 years ago was accompanied by admixture with pre-existing modern human populations. European ancestry before 40,000 years ago persisted not only at Buran-Kaya III but is also found in later Gravettian-associated populations of western Europe and Mesolithic Caucasus populations.

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Fig. 1: Genomic affinities between Buran-Kaya III and other ancient individuals.
Fig. 2: Relationships among individuals and genetic clusters of MUP Europe.
Fig. 3: Detection of Zlatý Kůň gene flow and Buran-Kaya III population modelling.
Fig. 4: Genomic affinity to CHG ancestry relative to the two Buran-Kaya III individuals and shared CHG/Zlatý Kůň-like ancestry.

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Data availability

Sequence data generated in this study are available through the EBI Sequence Read Archive PRJEB64496. The mitochondrial sequences are available through GenBank (accession number MK934322 and OR327029).

Code availability

No new code and sequence analysis methods were developed. Details on the analysis settings are provided in Methods section.

Change history

References

  1. Hajdinjak, M. et al. Initial upper palaeolithic humans in europe had recent neanderthal ancestry. Nature 592, 253–257 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Slimak, L. et al. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. Sci. Adv. 8, eabj9496 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Prüfer, K. et al. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nat. Ecol. Evol. 5, 820–825 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Vallini, L. et al. Genetics and material culture support repeated expansions into Paleolithic Eurasia from a population hub out of Africa. Genome Biol. Evol. 14, evac045 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Giaccio, B., Hajdas, I., Isaia, R., Deino, A. & Nomade, S. High-precision 14C and 40Ar/39Ar dating of the Campanian Ignimbrite (Y-5) reconciles the time-scales of climatic-cultural processes at 40 ka. Sci. Rep. 7, 45940 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Fedele, F. et al. in Living Under the Shadow: Cultural Impacts of Volcanic Eruptions (eds Grattan, J. & Torrence, R.) Ch. 2 (Left Coast Press, 2007).

  9. Fitzsimmons, K. E., Hambach, U., Veres, D. & Iovita, R. The Campanian Ignimbrite eruption: new data on volcanic ash dispersal and its potential impact on human evolution. PLoS ONE 8, e65839 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Black, B. A., Neely, R. R. & Manga, M. Campanian Ignimbrite volcanism, climate, and the final decline of the Neanderthals. Geology 43, 411–414 (2015).

    Article  CAS  Google Scholar 

  11. Heinrich, H. Origin and consequences of cyclic ice rafting in the northeast Atlantic Ocean during the past 130,000 years. Quat. Res. 29, 142–152 (1988).

    Article  Google Scholar 

  12. Zilhão, J. Neandertals and moderns mixed, and it matters. Evol. Anthropol. 15, 183–195 (2006).

    Article  Google Scholar 

  13. Seguin-Orlando, A. et al. Genomic structure in Europeans dating back at least 36,200 years. Science 346, 1113–1118 (2014).

    Article  CAS  PubMed  Google Scholar 

  14. Sikora, M. et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 659–662 (2017).

    Article  CAS  PubMed  Google Scholar 

  15. Posth, C. et al. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature 615, 117–126 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Prat, S. et al. The oldest anatomically modern humans from far southeast Europe: direct dating, culture and behavior. PLoS ONE 6, e20834 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Péan, S. et al. The Middle to Upper Paleolithic Sequence of Buran-Kaya III (Crimea, Ukraine): new stratigraphic, paleoenvironmental, and chronological results. Radiocarbon 55, 1454–1469 (2013).

    Article  Google Scholar 

  18. Yanevich, A. Les occupations gravettiennes de Buran-Kaya III (Crimée): contexte archéologique. L’Anthropologie 118, 554–566 (2014).

    Article  Google Scholar 

  19. Prat, S. et al. The first anatomically modern humans from south-eastern Europe. Contributions from the Buran-Kaya III Site (Crimea). Bull. Mém. Soc. Anthropol. Paris https://doi.org/10.3166/bmsap-2018-0032 (2018).

    Article  Google Scholar 

  20. Hublin, J.-J. The modern human colonization of western Eurasia: when and where? Quat. Sci. Rev. 118, 194–210 (2015).

    Article  Google Scholar 

  21. Reynolds, N. & Green, C. Spatiotemporal modelling of radiocarbon dates using linear regression does not indicate a vector of demic dispersal associated with the earliest Gravettian assemblages in Europe. J. Archaeol. Sci. Rep. 27, 101958 (2019).

    Google Scholar 

  22. Reynolds, N. in Culture History and Convergent Evolution (ed. Groucutt, H. S.) 187–212 (Springer, 2020).

  23. Reynolds, N. in Les Sociétés Gravettiennes du Nord-Ouest Européen: Nouveaux Sites, Nouvelles Données, Nouvelles Lectures (eds Touzé, O. et al.) 309–321 (Presses Universitaires de Liège, 2021).

  24. Demidenko, Y. E. in Encyclopedia of Global Archaeology (ed. Smith, C.) 1782–1791 (Springer, 2014).

  25. Cullen, V. L. et al. A revised AMS and tephra chronology for the Late Middle to Early Upper Paleolithic occupations of Ortvale Klde, Republic of Georgia. J. Hum. Evol. 151, 102908 (2021).

    Article  PubMed  Google Scholar 

  26. Golovanova, L. V. et al. The Early Upper Paleolithic in the northern Caucasus (new data from Mezmaiskaya Cave, 1997 excavation). Eurasian Prehistory 4, 43–78 (2012).

    Google Scholar 

  27. Bar-Yosef, O. et al. Dzudzuana: an Upper Palaeolithic cave site in the Caucasus foothills (Georgia). Antiquity 85, 331–349 (2011).

    Article  Google Scholar 

  28. Hoffecker, J. F. A New Framework for the Upper Paleolithic of Eastern Europe (INSTAAR, 2022); https://instaar.colorado.edu/uploads/research/projects/kostenki/hoffecker-ESHE-2012-a-new-framework.pdf

  29. Hoffecker, J. F. & Holliday, V. T. in The Upper Paleolithic of Northern Eurasia and America: Sites, Cultures, Traditions (eds Vasil’ev, S. A. & Tkach, E. S.) 140–158 (Russian Academy of Sciences, 2014).

  30. Svoboda, J. A. The Gravettian on the Middle Danube. PALEO Rev. Archéol. Préhistorique 19, 203–220 (2007).

    Google Scholar 

  31. Hoffecker, J. F. The Early Upper Paleolithic of Eastern Europe reconsidered. Evol. Anthropol. Issues N. Rev. 20, 24–39 (2011).

    Article  Google Scholar 

  32. Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques 59, 87–93 (2015).

    Article  PubMed  Google Scholar 

  33. Glocke, I. & Meyer, M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth. Genome Res. 27, 1230–1237 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Weissensteiner, H. et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 31, 309–316 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013).

    Article  CAS  Google Scholar 

  37. Brunel, S. et al. Ancient genomes from present-day France unveil 7,000 years of its demographic history. Proc. Natl Acad. Sci. USA 117, 12791–12798 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Svensson, E. et al. Genome of peştera muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr. Biol. 31, 2973–2983.e9 (2021).

    Article  CAS  PubMed  Google Scholar 

  39. Hublin, J.-J. et al. Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature 581, 299–302 (2020).

    Article  CAS  PubMed  Google Scholar 

  40. Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Higham, T. et al. The timing and spatiotemporal patterning of Neanderthal disappearance. Nature 512, 306–309 (2014).

    Article  CAS  PubMed  Google Scholar 

  42. Petr, M., Pääbo, S., Kelso, J. & Vernot, B. Limits of long-term selection against Neandertal introgression. Proc. Natl Acad. Sci. USA 116, 1639–1644 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Teschler-Nicola, M. et al. Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic. Commun. Biol. 3, 650 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015).

    Article  CAS  PubMed  Google Scholar 

  47. Jeong, C. et al. The genetic history of admixture across inner Eurasia. Nat. Ecol. Evol. 3, 966–976 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Lazaridis, I. et al. Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. Preprint at bioRxiv https://doi.org/10.1101/423079 (2018).

  49. Allentoft, M. E. et al. Population genomics of Stone Age Eurasia. Preprint at bioRxiv https://doi.org/10.1101/2022.05.04.490594 (2022).

  50. Marín-Arroyo, A. B., Terlato, G., Vidal-Cordasco, M. & Peresani, M. Subsistence of early anatomically modern humans in Europe as evidenced in the Protoaurignacian occupations of Fumane Cave, Italy. Sci. Rep. 13, 3788 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Fedele, F. G., Giaccio, B., Isaia, R. & Orsi, G. in Volcanism and the Earth’s Atmosphere (eds Robock, A. & Oppenheimer, C.) 301–325 (American Geophysical Union, 2003).

  52. Hoffecker, J. F. Desolate Landscapes: Ice-Age Settlement in Eastern Europe (Rutgers Univ. Press, 2002).

  53. Marti, A., Folch, A., Costa, A. & Engwell, S. Reconstructing the Plinian and co-Ignimbrite sources of large volcanic eruptions: a novel approach for the Campanian Ignimbrite. Sci. Rep. 6, 21220 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Reimer, P. J. et al. The IntCal20 northern hemisphere radiocarbon age calibration curve (0–55 cal kbp). Radiocarbon 62, 725–757 (2020).

    Article  CAS  Google Scholar 

  55. Bennett, E. A. et al. Library construction for ancient genomics: single strand or double strand? BioTechniques 56, 289–298 (2014).

    Article  CAS  PubMed  Google Scholar 

  56. Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).

    Article  PubMed  Google Scholar 

  58. Massilani, D. et al. Past climate changes, population dynamics and the origin of bison in Europe. BMC Biol. 14, 93 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  59. Renaud, G., Stenzel, U. & Kelso, J. LeeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. 42, e141 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. van der Valk, T. et al. Million-year-old DNA sheds light on the genomic history of mammoths. Nature 591, 265–269 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  62. Li, H. et al. The sequence alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  63. de Filippo, C., Meyer, M. & Prüfer, K. Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences. BMC Biol. 16, 121 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  65. Okonechnikov, K., Conesa, A. & García-Alcalde, F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics https://doi.org/10.1093/bioinformatics/btv566 (2015).

  66. Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755 (2001).

    Article  CAS  PubMed  Google Scholar 

  68. Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9, 772 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Martiniano, R., De Sanctis, B., Hallast, P. & Durbin, R. Placing ancient DNA sequences into reference phylogenies. Mol. Biol. Evol. 39, msac017 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Rohland, N. et al. Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs. Genome Res. 32, 2068–2078 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  73. Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  75. Maier, R., Flegontov, P., Flegontova, O., Changmai, P. & Reich, D. On the limits of fitting complex models of population history to genetic data. eLife 12, e85492 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  76. Kahle, D. & Wickham, H. ggmap: spatial visualization with ggplot2. R J. 5, 144–161 (2013).

    Article  Google Scholar 

  77. Stamen. Stamen map tiles. maps.stamen.com http://maps.stamen.com/#terrain/12/37.7706/-122.3782 (accessed 20 July 2022).

  78. Petr, M., Pääbo, S., Kelso, J. & Vernot, B. The limits of long-term selection against Neandertal introgression. Proc. Natl Acad. Sci. USA 116, 1639–1644 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The palaeogenomic facility of the Institut Jacques Monod obtained support from the University Paris Diderot within the programme ‘Actions de recherches structurantes’. The sequencing facility of the Institut Jacques Monod, Paris, is supported by grants from the University Paris Diderot, the Fondation pour la Recherche Médicale (DGE20111123014) and the Région Ile-de-France (11015901). Moreover, we acknowledge support from the French national research centre CNRS and EUR G.E.N.E. (ANR-17-EURE-0013; IdEx #ANR-18-IDEX-0001 l’Université de Paris; Programme d’Investissements d’Avenir) for supporting the PhD fellowship extension of O.P. We thank the National Academy of Sciences of Ukraine for permission to excavate at Buran-Kaya III and all the team members of the excavations. We also thank the French National Research Agency (ANR-05-JCJC-0240-01), the Fyssen Foundation, the Muséum national d’Histoire naturelle and the Centre National de la Recherche Scientifique (CNRS) for their financial support (excavations and anthropological analyses). We thank O. Gorgé for assistance with some of the sequencing.

Author information

Author notes

  1. E. Andrew Bennett

    Present address: Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China

  2. Oğuzhan Parasayan

    Present address: Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France

  3. These authors contributed equally: E. Andrew Bennett, Oğuzhan Parasayan.

Authors and Affiliations

  1. Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France

    E. Andrew Bennett, Oğuzhan Parasayan, Thierry Grange & Eva-Maria Geigl

  2. UMR 7194 (HNHP), MNHN/CNRS/UPVD, Alliance Sorbonne Université, Musée de l’Homme, Palais de Chaillot, Paris, France

    Sandrine Prat

  3. UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d’Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France

    Stéphane Péan & Laurent Crépin

  4. Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine

    Alexandr Yanevich

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Contributions

E.-M.G., S. Prat and S. Péan initiated the project. E.-M.G. and T.G. supervised the study. E.A.B., E.-M.G. and T.G. produced data. O.P. and E.A.B. performed formal analyses. O.P., E.A.B., T.G. and E.-M.G. interpreted the data. S. Prat, S. Péan, L.C. and A.Y. provided samples and information to the archaeological context. E.A.B. wrote the paper with input from all authors.

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Correspondence to Thierry Grange or Eva-Maria Geigl.

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Extended data

Extended Data Fig. 1 Recalibration of comparative AMS 14C dates of Buran-Kaya III.

Buran-Kaya III (BuKa3) layers 6-1 and 6-2 with Upper Palaeolithic samples. All dates were calibrated using the software OxCal v4.4.4 based on the IntCal20 calibration data set. Climatic events are represented by the orange band, the Campanian Ignimbrite (CI) volcanic super-eruption event by the darker orange band, the Heinrich Event 4 by the lighter orange band.

Extended Data Fig. 2 Bayesian phylogenetic tree of mitochondrial sequences.

Excluding Hyper-Variable Regions, from Early and Mid-Upper Palaeolithic individuals including those from Buran-Kaya III (red). Posterior probability indicated at the nodes. Scale bar denotes substitutions per site. Sources for mitochondrial sequences are listed in Supplementary Table 3. Additional ancient and canonical N sequences are included to give branching details. Inset gives detailed mutation information from mtphyl v.5.003 (https://sites.google.com/site/mtphyl/home) for both BuKa3 individuals. References for mitochondrial sequences are given in Supplementary Table 11.

Extended Data Fig. 3 Neanderthal ancestry calculated for ancient individuals.

Neanderthal ancestry calculated using direct f4-ratio test78. α values calculated in the form of (Vindija33.19, Chimp; test, Mbuti)/(Vindija33.19, Chimp; Chagyrskaya, Mbuti). The error bars represent ±1 standard error, which were calculated using weighted block jackknife and a block size of 5 Mb.

Extended Data Fig. 4 Genetic affinities between Buran-Kaya III and present-day populations.

Heatmap showing the shared genetic drift calculated by f3-statistics in the form of f3(Mbuti; BuKa3, modern). Higher f3 values indicate greater allele sharing between Buran-Kaya III (BuKa3) and populations from the HGDP dataset. The left half of the circles shows f3 values tested with BuKa3C while the right side show those tested with BuKa3A. The map was created with ggmap76 using Stamen Design map tiles.

Extended Data Fig. 5 2D Multidimensional scaling (MDS).

MDS calculated using the pairwise genetic distance matrix coming from inverted f3 values (1-f3) in the form of f3(Mbuti; ancient1, ancient2), for the first three dimensions representing 8, 6 and 5% of the total variance. See also Supplementary Video 1 and Supplementary Fig. 2.

Extended Data Fig. 6 Summary of f4 statistics involving BuKa3 and pre-CI genomes.

A. Results of f4(Mbuti, pre-CI; BuKa3, pre-CI) B. Results of f4(Mbuti, BuKa3; pre-CI, pre-CI). Full results in Supplementary Table 5.

Extended Data Fig. 7 Modeling BuKa3 ancestry by qpGraph without admixture.

Best-fitting qpGraph models of BuKa3A (A) and BuKa3C (B) without admixture (compare with Fig. 3b). Buran-Kaya III individuals modeled with pre-LGM shotgun genomes using allsnps: NO parameters. The Z-score for the worst f4-statistic residuals is indicated.

Supplementary information

Supplementary Information

Supplementary Figs. 1–7 and Notes 1 and 2.

Reporting Summary

Peer Review File

Supplementary Tables

Supplementary Tables 1–11 in Excel file.

Supplementary Video 1

Animation of the 3D MDS scatterplot featured in Fig. 1c.

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Bennett, E.A., Parasayan, O., Prat, S. et al. Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea. Nat Ecol Evol 7, 2160–2172 (2023). https://doi.org/10.1038/s41559-023-02211-9

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