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Higher Levels of Neanderthal Ancestry in East Asians than in Europeans
Open accessAbstract
Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from ∼30,000 to 300,000 years ago (KYA). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1–4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50–80 KYA. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal–modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.
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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 [4]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Studies estimate that non-African populations have 1–4% Neanderthal admixture, with East Asian populations exhibiting more Neanderthal introgression than West Eurasian populations (Wall et al. 2013; Sankararaman et al. 2014), perhaps due to more archaic admixture events with ancestral East Asians, but other plausible scenarios have been proposed (Coll Macià et al. 2021; Witt et al. 2022).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Wall et al. 2013
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“While NE ancestry is relatively uniform among modern Eurasian populations (1, 2), it is approximately 8 to 24% higher in East Asia than in Europe (5, 10, 12, 13).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [10]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neanderthal inheritance22.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [21]
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“Neanderthal ancestry is also found in some African populations via admixture with Eurasian populations that harbored archaic ancestry migrating back into Africa (Wall et al. 2013).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Wall et al. 2013
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“This second range expansion is essential for explaining the pattern currently observed of lower NE ancestry in western Europe than in East Asia (5, 10, 12, 13).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [10]
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Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
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
Self-citationGenetic Structure of Human Populations
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Genetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991
Self-citationA high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Self-citationGutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · cited 5×
“Consequently, estimates of East Asian–European population divergence of ,30 KYA (Gutenkunst et al. 2009; Gravel et al. 2011) are unlikely to be correct.”
BackgroundInfluentialThe Genetic Structure and History of Africans and African Americans
Tishkoff, S. A., Reed, F. A., Friedlaender, F. R., Ehret, C., Ranciaro, A., Froment, A., Hirbo, J. B., Awomoyi, A. A., Bodo, J.-M., Doumbo, O., et al. (2009) · Science · doi:10.1126/science.1172257 · Cited by 1,573 · cited 1×
“…with recent findings of African admixture into Middle Eastern and Southern European populations during the same timescale (Moorjani et al. 2011) and a greater genetic similarity between East African and non-African samples than between West African and non-African samples (Tishkoff et al. 2009).”
BackgroundTesting for ancient admixture between closely related populations
Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr048 · Cited by 1,375
Self-citationNeandertal DNA Sequences and the Origin of Modern Humans
Krings, M., Stone, A. C., Schmitz, R. W., Krainitzki, H., Stoneking, M., & Pääbo, S. (1997) · Cell · doi:10.1016/s0092-8674(00)80310-4 · Cited by 1,339
Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010) · Science · doi:10.1126/science.1181498 · Cited by 1,212
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The complete genome sequence of a Neanderthal from the Altai Mountains
Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254
Self-citationThe Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584
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
The timing and spatiotemporal patterning of Neanderthal disappearance
Higham, T., Douka, K., Wood, R. E., Ramsey, C. B., Brock, F., Basell, L., Camps, M., Valbuena, Á. A., Preysler, J. B., Ruíz, C. B., et al. (2014) · Nature · doi:10.1038/nature13621 · Cited by 907
Metadata
- Authors
- Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S., Gignoux, C., Woerner, A., Hammer, M. F., & Slatkin, M.
- Affiliations
- University of California, San Francisco (US)
- University of California, Berkeley (US)
- University of Arizona (US)
- Corresponding author
- Wall, Jeffrey D
- ORCID
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-05-01
- Volume
- 194
- Issue
- 1
- Pages
- 199-209
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC3632468
- OpenAlex
- W2127362327
- Cited by
- 249
- References
- 41
- Citations by year
- 2026: 8 · 2025: 4 · 2024: 8 · 2023: 15 · 2022: 15 · 2021: 17 · 2020: 19 · 2019: 23 · 2018: 29 · 2017: 15 · 2016: 39 · 2015: 17 · 2014: 29 · 2013: 11
- FWCI
- 149.48
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG005226, T32HG00047, T32HG000047)
- National Institute of General Medical Sciences (R01GM040282, R01‑GM40282)
- 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, East Asian populations, European populations, Maasai, Neanderthal genome, population divergence
- MeSH terms
- Animals, Asia, Eastern, Gene Pool, Genetics, Population, Haplotypes, Humans, Models, Genetic, Phylogeny, Genome, Human, White People, Asian People, Neanderthals
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