Evidence for archaic adaptive introgression in humans
Open accessAbstract
As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments - a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.
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Papuans and Indigenous Australians carry the largest amount of Denisovan introgression (~1% to 5%), followed by East and South Asians (~0.06% to 0.5%), and Indigenous Americans (~0.05% to 0.4%).
“It has been shown that Papuans and Indigenous Australians carry the largest amount of Denisovan introgression (∼1% to 5%), followed by East and South Asians (∼0.06% to 0.5%), and Indigenous Americans (∼0.05% to 0.4%) (Reich et al. 2010; Racimo et al. 2015; Mallick et al. 2016; Sankararaman et al. 2016; Browning et al. 2018).”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Racimo et al. 2015
The Introduction’s “Archaic gene flow” section reports 3–6% Denisovan ancestry in Melanesians, Papuans and Australians, versus about 0.2% in East Asians, supporting the broad ordering but not the quoted 1–5% range. It does not provide the claimed ranges for South Asians or Indigenous Americans. (LLM, conf=0.88)
Experimental — accuracy not yet measuredMost archaic ancestry in AMH was subject to strong negative selection, but some introgressed alleles remaining in AMH populations show evidence of adaptation.
“Most of the archaic ancestry in AMH was subject to strong negative selection, but some of these introgressed alleles remaining in AMH populations show evidence of adaptation (Racimo et al. 2015; Gower et al. 2021).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Racimo et al. 2015
The Genome-wide admixture maps section reports signatures of negative selection pushing introgressed variants to low frequencies, alongside considerable evidence of adaptive introgression. It does not establish that most archaic ancestry was subject to strong negative selection; that extent and strength overstate what this passage says. (LLM, conf=0.86)
Experimental — accuracy not yet measuredArchaic alleles have been associated with differences in hemoglobin levels at higher altitude in Tibetans, immune resistance to new pathogens, levels of skin pigmentation, and fat composition.
“For example, archaic alleles have been associated with differences in hemoglobin levels at higher altitude in Tibetans, immune resistance to new pathogens, levels of skin pigmentation, and fat composition (Huerta-Sánchez et al. 2014; Racimo et al. 2015; Racimo, Gokhman, et al. 2017; Dannemann and Kelso 2017; Racimo, Marnetto, and Huerta-Sánchez 2017; McArthur et al. 2021).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Racimo et al. 2015
The Altitude and Genotype-phenotype associations sections report that introgressed EPAS1 variants in Tibetans are associated with hemoglobin levels; the Pigmentation section reports an association between a BNC2 SNP and skin pigmentation. The Defense against pathogens section discusses introgressed immune-gene haplotypes but does not establish resistance to new pathogens. The Metabolism section reports differences in brain lipid concentrations alongside evidence concerning Neanderthal-like lipid-catabolism genes, rather than a direct association between archaic alleles and fat composition (page numbers unavailable in our copy). (LLM, conf=0.84)
Experimental — accuracy not yet measuredMost genetic variation introduced by introgression experienced strong negative selection in AMH, while a smaller portion is thought to have provided adaptive benefits in new environments.
“While most of this genetic variation experienced strong negative selection in AMH, a smaller portion is thought to have provided adaptive benefits in the new environments (Racimo et al. 2015).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Racimo et al. 2015
The Genome-wide admixture maps section reports negative selection pushing introgressed variants to low frequencies alongside evidence of adaptive introgression. The Conclusions say adaptive introgression helped humans adapt to new environmental conditions. Neither passage establishes that most introduced variation experienced strong negative selection or quantifies the adaptive portion as smaller. (LLM, conf=0.86)
Experimental — accuracy not yet measuredEvidence in favor of hybridization between Neanderthals and modern humans has accumulated during the past decade.
“Evidence in favor of hybridization has accumulated during the past decade (4–6).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [6]
Gene flow from Eurasian archaic hominins into AMH contributed to adaptations to some new environmental conditions encountered outside Africa.
“The gene flow from Eurasian archaic hominins into AMH contributed to adaptations to some of the new environmental conditions encountered outside of Africa (Racimo et al. 2015).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Racimo et al. 2015
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Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans
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Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
Lohse, K., & Frantz, L. (2014) · Genetics · doi:10.1534/genetics.114.162396 · Cited by 86 · see citing works
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Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens
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Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations
Mendez, F. L., Watkins, J. C., & Hammer, M. F. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr301 · Cited by 79 · see citing works
Neanderthal Introgression at Chromosome 3p21.31 Was Under Positive Natural Selection in East Asians
Ding, Q., Hu, Y., Xu, S., Wang, J., & Li, J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst260 · Cited by 75 · see citing works
Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity.
Ziętkiewicz, E., Yotova, V., Gehl, D., Wambach, T., Arrieta, I., Batzer, M., Cole, D., Hechtman, P., Kaplan, F., Modiano, D., et al. (2003) · American Journal of Human Genetics · doi:10.1086/378777 · Cited by 66 · see citing works
An X-Linked Haplotype of Neandertal Origin Is Present Among All Non-African Populations
Yotova, V., Lefebvre, J.-F., Moreau, C., Gbeha, E., Hovhannesyan, K., Bourgeois, S., Bédarida, S., Azevedo, L., Amorim, A., Sarkisian, T., et al. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr024 · Cited by 65 · see citing works
Evolution: Replacing Genes and Traits through Hybridization
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Lalioti, V. S., Muruáis, G., Dinarina, A., Damme, J. V., Vandekerckhove, J. S., & Sandoval, I. V. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900218106 · Cited by 59 · see citing works
Ding, Q., Hu, Y., Xu, S., Wang, C., Li, H., Zhang, R., Yan, S. L., Wang, J., & Li, J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu180 · Cited by 40 · see citing works
Temme, S., Zacharias, M., Neumann, J., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.515767 · Cited by 38 · see citing works
A genetic legacy from archaic Homo
Hawks, J. D., Cochran, G. M., Harpending, H. C., & Lahn, B. T. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.10.003 · Cited by 38 · see citing works
Ancient human genomes suggest three ancestral populations for present-day Europeans
Krause, J., Reich, D., Lazaridis, I., Patterson, N. J., & Mittnik, A. (2015) · The 80th Annual Meeting of the Society for American Archaeology · Cited by 36 · see citing works
Non-Neanderthal Origin of the HLA-DPB1*0401
Ding, Q., Hu, Y., & Li, J. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.l114.547505 · Cited by 10 · see citing works
Waddell, P. J. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1312.7749 · Cited by 8 · see citing works
Setó‐Salvia, N., Sánchez‐Quinto, F., Carbonell, E., Lorenzo, C., Comas, D., & Clarimón, J. (2012) · Human Biology · doi:10.3378/027.084.0605 · Cited by 5 · see citing works
Waddell, P. J., & Tan, X. L. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1212.6820 · Cited by 3 · see citing works
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- [21]Hawks J Cochran G Dynamics of adaptive introgression from archaic to modern humans PaleoAnthropology 101–115 2006 A visionary review that proposed adaptive introgression as a mode of adaptation in humans, before the availability of archaic genome sequences
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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 · see citing works
Tracing the peopling of the world through genomics
Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728 · see citing works
Self-citationNatural selection interacts with recombination to shape the evolution of hybrid genomes
Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G., et al. (2018) · Science · doi:10.1126/science.aar3684 · Cited by 412 · see citing works
Self-citationThe inflated significance of neutral genetic diversity in conservation genetics
Teixeira, J. C., & Huber, C. D. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2015096118 · Cited by 474 · see citing works
The Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419 · see citing works
Self-citationChen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04737-0 · Cited by 403 · see citing works
Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture
Browning, S. R., Browning, B. L., Zhou, Y., Tucci, S., & Akey, J. M. (2018) · Cell · doi:10.1016/j.cell.2018.02.031 · Cited by 381 · see citing works
The Strength of Selection against Neanderthal Introgression
Juric, I., Aeschbacher, S., & Coop, G. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006340 · Cited by 309 · see citing works
Dannemann, M., Andrés, A. M., & Kelso, J. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.015 · Cited by 249 · see citing works
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 · see citing works
Limits of long-term selection against Neandertal introgression
Petr, M., Pääbo, S., Kelso, J., & Vernot, B. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814338116 · Cited by 211 · see citing works
Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
Gittelman, R. M., Schraiber, J. G., Vernot, B., Mikacenic, C., Wurfel, M. M., & Akey, J. M. (2016) · Current Biology · doi:10.1016/j.cub.2016.10.041 · Cited by 181 · see citing works
Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans
Enard, D., & Petrov, D. A. (2018) · Cell · doi:10.1016/j.cell.2018.08.034 · Cited by 208 · see citing works
The Contribution of Neanderthals to Phenotypic Variation in Modern Humans
Dannemann, M., & Kelso, J. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.09.010 · Cited by 193 · see citing works
“Strikingly, more than half of the significantly associated alleles that we identified are related to skin and hair traits, consistent with previous evidence that genes associated with skin and hair biology are over-represented in introgressed archaic regions.(4,9,11) It was previously only possible to speculate about…”
The origin of domestication genes in goats
Zheng, Z., Wang, X., Li, M., Li, Y., Yang, Z., Wang, X., Pan, X., Gong, M., Zhang, Y., Guo, Y., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz5216 · Cited by 184 · see citing works
Sams, A. J., Dumaine, A., Nédélec, Y., Yotova, V., Alfieri, C., Tanner, J. E., Messer, P. W., & Barreiro, L. B. (2016) · Genome Biology · doi:10.1186/s13059-016-1098-6 · Cited by 140 · see citing works
Ancient Biomolecules and Evolutionary Inference
Cappellini, E., Prohaska, A., Racimo, F., Welker, F., Pedersen, M. W., Allentoft, M. E., de Barros Damgaard, P., Gutenbrunner, P., Dunne, J., Hammann, S., et al. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012002 · Cited by 118 · see citing works
Self-citationHsieh, P., Woerner, A. E., Wall, J. D., Lachance, J., Tishkoff, S. A., Gutenkunst, R. N., & Hammer, M. F. (2016) · Genome Research · doi:10.1101/gr.196634.115 · Cited by 105 · see citing works
Detecting adaptive introgression in human evolution using convolutional neural networks
Gower, G., Picazo, P. I., Fumagalli, M., & Racimo, F. (2021) · eLife · doi:10.7554/elife.64669 · Cited by 95 · see citing works
Self-citationHuman evolution: a tale from ancient genomes
Llamas, B., Willerslev, E., & Orlando, L. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0484 · Cited by 100 · see citing works
Something old, something borrowed: admixture and adaptation in human evolution
Dannemann, M., & Racimo, F. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.05.009 · Cited by 87 · see citing works
Self-citationQuantifying the contribution of Neanderthal introgression to the heritability of complex traits
McArthur, E., Rinker, D. C., & Capra, J. A. (2021) · Nature Communications · doi:10.1038/s41467-021-24582-y · Cited by 71 · see citing works
Model‐based detection and analysis of introgressed Neanderthal ancestry in modern humans
Steinrücken, M., Spence, J. P., Kamm, J. A., Wieczorek, E., & Song, Y. S. (2018) · Molecular Ecology · doi:10.1111/mec.14565 · Cited by 73 · see citing works
Signatures of archaic adaptive introgression in present-day human populations
Racimo, F., Marnetto, D., & Huerta-Sánchez, E. (2016) · doi:10.1101/045237 · Cited by 200 · see citing works
Self-citationGouy, A., & Excoffier, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz306 · Cited by 63 · see citing works
Silvert, M., Quintana-Murci, L., & Rotival, M. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.04.016 · Cited by 58 · see citing works
The evolution of FOXP2 in the light of admixture
Kuhlwilm, M. (2018) · Current Opinion in Behavioral Sciences · doi:10.1016/j.cobeha.2018.04.006 · Cited by 56 · see citing works
The lingering effects of Neanderthal introgression on human complex traits
Wei, X., Robles, C. R., Pazokitoroudi, A., Ganna, A., Gusev, A., Durvasula, A., Gazal, S., Loh, P.-R., Reich, D., & Sankararaman, S. (2023) · eLife · doi:10.7554/elife.80757 · Cited by 43 · see citing works
Self-citationNeanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
Rinker, D. C., Simonti, C. N., McArthur, E., Shaw, D., Hodges, E., & Capra, J. A. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1261-z · Cited by 44 · see citing works
Zhang, X., Kim, B., Singh, A., Sankararaman, S., Durvasula, A., & Lohmueller, K. E. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad001 · Cited by 29 · see citing works
Self-citationEvolutionary and medical consequences of archaic introgression into modern human genomes
Dolgova, O., & Lao, O. (2018) · Genes · doi:10.3390/genes9070358 · Cited by 34 · see citing works
The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations
Witt, K. E., Funk, A., Añorve-Garibay, V., Fang, L. L., & Huerta-Sánchez, E. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad066 · Cited by 29 · see citing works
“In some cases, these past introgression events likely resulted in adaptive introgression (Bustamante and Henn 2010; Green et al. 2010; Reich et al. 2010)—selection favoring archaic variants to facilitate adaptation to novel environments in modern humans (Racimo et al. 2015).”
BackgroundSelf-citationArchaic Introgression Shaped Human Circadian Traits
Velazquez-Arcelay, K., Colbran, L. L., McArthur, E., Brand, C. M., Rinker, D. C., Siemann, J. K., McMahon, D. G., & Capra, J. A. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad203 · Cited by 18 · see citing works
“The Eurasian environments where Neanderthals and Denisovans lived for several hundred thousand years are located at higher latitudes with more variable photoperiods than the landscape where AMH evolved before leaving Africa.”
BackgroundMethodInfluentialPast human expansions shaped the spatial pattern of Neanderthal ancestry
Quilodrán, C. S., Rio, J., Tsoupas, A., & Currat, M. (2023) · Science Advances · doi:10.1126/sciadv.adg9817 · Cited by 12 · see citing works
Caporale, A. L., Cinalli, A. R., Rubinstein, M., & Franchini, L. F. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae186 · Cited by 7 · see citing works
“(Reich et al. 2010; Racimo et al. 2015; Mallick et al. 2016; Sankararaman et al. 2016; Browning et al. 2018).”
Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings
Pauly, R., Johnson, L., Feltus, F. A., & Casanova, E. L. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02593-7 · Cited by 7 · see citing works
Effects of introgressed Neanderthal alleles on present-day brain morphology
Zeloni, R., Amaolo, A., Morez Jacobs, A., Zapparoli, E., Akl, Y., Shafie, M., Huerta-Sanchez, E., Pizzagalli, F., Provero, P., Pagani, L., et al. (2026) · bioRxiv · doi:10.64898/2026.04.14.718380
Self-citation
- Authors
- Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E.
- Affiliations
- University of California, Berkeley (US)
- Harvard University (US)
- Venue
- Nature Reviews Genetics
- Published
- 2015-05-12
- Volume
- 16
- Issue
- 6
- Pages
- 359-371
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC4478293
- OpenAlex
- W1558762228
- Cited by
- 521
- References
- 99
- Citations by year
- 2026: 37 · 2025: 30 · 2024: 40 · 2023: 50 · 2022: 41 · 2021: 50 · 2020: 47 · 2019: 54 · 2018: 62 · 2017: 52 · 2016: 48 · 2015: 10
- FWCI
- 73.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- Funders
- National Human Genome Research Institute (R01HG003229)
- National Institute of General Medical Sciences (R01GM040282, K99GM111744, 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 introgression, Denisovan introgression, positive selection, ancient DNA, selection inference, human evolution
- MeSH terms
- Adaptation, Biological, Animals, Haplotypes, Humans, Markov Chains, Models, Genetic, Phylogeny, Selection, Genetic, Linkage Disequilibrium, Genome, Human, Evolution, Molecular, Gene Flow, Neanderthals
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