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Multiple episodes of interbreeding between Neanderthal and modern humans
Open accessAbstract
Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the 'dilution' hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.
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“In Europeans, archaic ancestry is consistent with contributions by a single population of Neanderthals 3 through one or more pulses [4][5][6][7] .”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [7]
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“These observations suggest that the population-specific haplotype blocks may be the result of more recent population-specific Neanderthal admixture, as has recently been suggested (26–28, 30).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [30]
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“When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans.”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Villanea and Schraiber 2019
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“When AMH migrated into Eurasia, they interbred with the archaic hominins that were native to the continent, initially with Neanderthals (Green et al. 2010; Villanea and Schraiber 2019) around 60 ka (Sankararaman et al. 2012; Skoglund and Mathieson 2018) and later with Denisovans (Jacobs et al. 2019).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Villanea and Schraiber 2019
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Cites
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318
The complete genome sequence of a Neanderthal from the Altai Mountains
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A high-coverage genome sequence from an archaic denisovan individual
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Self-citationAncient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357
Self-citationThe genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107
Genomic insights into the origin of farming in the ancient Near East
Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al. (2016) · Nature · doi:10.1038/nature19310 · Cited by 955
An early modern human from Romania with a recent Neanderthal ancestor
Fu, Q., Hajdinjak, M., Moldovan, O. T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., et al. (2015) · Nature · doi:10.1038/nature14558 · Cited by 802
A high-coverage Neandertal genome from Vindija Cave in Croatia
Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., et al. (2017) · Science · doi:10.1126/science.aao1887 · Cited by 719
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
Kelleher, J., Etheridge, A. M., & McVean, G. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004842 · Cited by 666
Scaling Learning Algorithms toward AI
Bengio, Y., & LeCun, Y. (2007) · The MIT Press eBooks · doi:10.7551/mitpress/7496.003.0016 · Cited by 483
Cited by
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Origins of modern human ancestry
Bergström, A., Stringer, C. B., Hajdinjak, M., Scerri, E. M. L., & Skoglund, P. (2021) · Nature · doi:10.1038/s41586-021-03244-5 · Cited by 445
A high-coverage Neandertal genome from Chagyrskaya Cave
Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Chen, L., Wolf, A. B., Fu, W., Li, L., & Akey, J. M. (2020) · Cell · doi:10.1016/j.cell.2020.01.012 · Cited by 254
Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France
Slimak, L., Zanolli, C., Higham, T., Frouin, M., Schwenninger, J., Arnold, L. J., Demuro, M., Douka, K., Mercier, N., Guèrin, G., et al. (2022) · Science Advances · doi:10.1126/sciadv.abj9496 · Cited by 234
The evolution and changing ecology of the African hominid oral microbiome
Yates, J. A. F., Velsko, I. M., Aron, F., Posth, C., Hofman, C. A., Austin, R. M., Parker, C., Mann, A. E., Nägele, K., Arthur, K. W., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021655118 · Cited by 180
Metadata
- Authors
- Villanea, F. A., & Schraiber, J. G.
- Affiliations
- Temple University (US)
- Corresponding author
- Schraiber, Joshua G.
- Venue
- Nature Ecology & Evolution
- Published
- 2018-11-26
- Volume
- 3
- Issue
- 1
- Pages
- 39-44
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC6309227
- OpenAlex
- W2900471700
- Cited by
- 192
- References
- 36
- Citations by year
- 2026: 18 · 2025: 12 · 2024: 21 · 2023: 32 · 2022: 28 · 2021: 39 · 2020: 28 · 2019: 12 · 2018: 2
- FWCI
- 85.66
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R35GM124745)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- 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
- Keywords
- Neanderthal admixture, Neanderthal ancestry, gene flow, demographic models, human migration out of Africa
- MeSH terms
- Animals, Humans, Hybridization, Genetic, Models, Theoretical, Genome, Human, Gene Flow, Neanderthals
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