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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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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
About these checks
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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