Earliest modern human genomes constrain timing of Neanderthal admixture

Arev P. Sümer*, Hélène Rougier, Vanessa Villalba-Mouco, Yilei Huang, Leonardo N. M. Iasi, Elena Essel, Alba Bossoms Mesa, Anja Furtwaengler, Stéphane Peyrégne, Cesare de Filippo, Adam B. Rohrlach, Federica Pierini, Fabrizio Mafessoni, Helen Fewlass, Elena I. Zavala, Dorothea Mylopotamitaki, Raffaela A. Bianco, Anna Schmidt, Julia Zorn, Birgit NickelAnna Patova, Cosimo Posth, Geoff M Smith, Karen Ruebens, Virginie Sinet-Mathiot, Alexander Stoessel, Holger Dietl, Jörg Orschiedt, Janet Kelso, Hugo Zeberg, Kirsten I. Bos, Frido Welker, Marcel Weiss, Shannon McPherron, Tim Schüler, Jean-Jacques Hublin, Petr Velemínský, Jaroslav Brůžek, Benjamin M. Peter, Matthias Meyer, Harald Meller, Harald Ringbauer, Mateja Hajdinjak, Kay Prüfer*, Johannes Krause*

*Corresponding author for this work

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Abstract

Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals1, 2, 3–4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia3 and Bacho Kiro, Bulgaria2. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany4, and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000–49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.

Original languageEnglish
Article number246
JournalNature
Volume638
Issue number8051
Pages (from-to)711-717
ISSN0028-0836
DOIs
Publication statusPublished - 20 Feb 2025

Bibliographical note

Funding Information:
We thank A. Aximu-Petri, S. Nagel, A. Busch, L. Gerullat, A. Weihmann, B. Schellbach, J. Visagie and T. Lamnidis for assistance in the laboratory, sequencing and data processing; R. Radzeviciute for handling and transferring samples; S. T\u00FCpke for professional photographs and assistance with some of the figures; H. Temming for micro-CT scans of the specimens; S. Zhang for providing the reuse permit for the Tianyuan specimen photograph; and L. Wacker for running the AMS for radiocarbon dating. We thank S. Schiffels, L. Pagani and L. Vallini for helpful discussions and L. Huang for help with processing of HGDP/SGDP data. We acknowledge support from the National Genomics Infrastructure in Stockholm funded by the Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and NAISS for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. This study was funded by the Max Planck Society. H. Rougier received funding from CSUN\u2019s RSCA Awards and College of Social and Behavioral Sciences. V.V.-M. is supported by the grant \u2018Ayudas para contratos Ram\u00F3n y Cajal\u2019 (no. RYC2022-035700-I) funded by Ministerio de Ciencia, Innovaci\u00F3n y Universidades. L.N.M.I. and B.M.P. are funded by the European Research Council (ERC) under the European Union\u2019s Horizon Europe research and innovation programme (grant agreement no. 101042421 NEADMIX, awarded to B.M.P.). E.I.Z. is supported by the Miller Institute for Basic Research in Science, University of California Berkeley. V.S.-M. is supported by a Fyssen Foundation postdoctoral fellowship (2023\u20132025). P.V. and J.B. are supported by The Czech Science Foundation grant no. GA23-06822S. P.V. is also supported by The Ministry of Culture of the Czech Republic (DKRVO grant no. 2024-2028/7.I.a, 00023272). This project has received funding from the ERC under the European Union\u2019s Horizon 2020 research and innovation programme (grant agreement no. 948365, awarded to F.W.), and ERC Starting grant credited to K.I.B. under grant agreement no. 805268 (CoDisEASe).

Publisher Copyright:
© The Author(s) 2024.

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