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Genome-wide patterns of selection in 230 ancient Eurasians
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Abstract
Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
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“PCA on present-day West Eurasian populations (Methods) (Extended Data Fig. 1) on which we projected the ancient individuals (Fig. 1b) replicates previous findings of a Europe-Near East contrast along the horizontal Principal Component 1 (PC1) and parallel clines (PC2) in both Europe and the Near East (Extended Data Fig. 1)7,8,13.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [8]
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
“We combined our data with previously published ancient data7,8,9,10,8,10-15 to form a dataset of 281 ancient individuals.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [8]
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 the latter is both time and cost effective 160 and remains the only methodology showing sufficient sensitivity to gather data from extremely degraded specimens 119 , it considerably restricts the amount of information retrieved from samples showing better molecular preservation.”
From Ancient DNA analysis (2021) · cites this paper as [160]
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
“In ancient human genome studies, this approach typically queries 1.2 million positions known to be polymorphic amongst a worldwide panel of contemporary human populations 160 , leaving other positions and other DNA material present in the extracts, like those from pathogens or microbiota, unexplored.”
From Ancient DNA analysis (2021) · cites this paper as [160]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“To the west, the early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians8.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [8]
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“The spread of Near Eastern ancestry into the Eurasian steppe was previously inferred7 without access to ancient samples, by hypothesizing a population related to present-day Armenians as a source7,8.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [8]
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In the citing paper
“This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41, consistent with the ancestral affinity shown above.”
From Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods (2017) · cites this paper as [41]
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In the citing paper
“This suggests that the allele was rising in frequency in Chalcolithic and Bronze Age Near Eastern populations at the same time as it was rising in frequency in Europe.”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [31]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“that has been argued to have been under positive selection by Mathieson et al.31”
From Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation (2018) · cites this paper as [31]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“a result that finds some support from Y chromosome analysis which shows that the Natufians and successor Levantine Neolithic populations carried haplogroup E, of likely ultimate African origin, which has not been detected in other ancient males from West Eurasia (Supplementary Information, section 6) 7,8.”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [8]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Scandinavian hunter-gatherers7,8,13 (SHG) are a mix of EHG and WHG;”
From Genomic insights into the origin of farming in the ancient Near East (2016) · cites this paper as [8]
Experimental — accuracy not yet measuredIn the citing paper
“However, western hunter-gatherers of central and southern European populations survived in Palaeolithic Europe with dark skin pigmentation [44, 45]”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [44]
In the citing paper
“Consistent with this hypothesis, aDNA analyses show that Scandinavian hunter-gatherers and Early European farmers indeed carried derived alleles contributing to light skin [44].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [44]
In the citing paper
“increasing dramatically in just the past 3000 years”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [44]
In the citing paper
“In fact, only a limited number of strong selective sweeps associated with diet and pigmentation can be associated with agriculture in Europe [44].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [44]
In the citing paper
“being found in only 10 % of Bronze Age Europeans”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [44]
In the citing paper
“Even lactose tolerance, assumed to be associated with pastoralism, appears to have been absent in early European farmers”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [44]
In the citing paper
“Additional pigmentation-associated loci, including HERC2/OCA2 , TYR and GRM5 , also show evidence of allele-frequency change or selection during this period, reflecting the complex evolution of skin, hair, and eye pigmentation in European populations ( Mathieson et al., 2015 ; Irving-Pease et al., 2024 ).”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Mathieson et al., 2015
In the citing paper
“This allele rose rapidly in frequency in Early Neolithic Europe, largely through migration, and continued to be subject to selection after admixture with local hunter-gatherer populations ( Mathieson et al., 2015 ).”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Mathieson et al., 2015
In the citing paper
“A significant contribution came from Neolithic farmer populations of Anatolian ancestry, who introduced the derived light pigmentation-associated SLC24A5 rs1426654-A allele (p.Ala111Thr) into Europe during their northward and westward expansion.”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Mathieson et al., 2015
In the citing paper
“In contrast, light pigmentation-associated variation at SLC45A2 , particularly rs16891982 (p.Leu374Phe), was initially present at lower frequency in ancient European populations but underwent strong positive selection during the Holocene, eventually approaching very high frequency in many present-day Europeans ( Mathieson et al., 2015 ; Irving-Pease et al., 2024 ).”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Mathieson et al., 2015
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“A second set of methods for reduced representation uses restriction enzymes to isolate small pieces of DNA (such as restriction-associated digest sequencing [RAD-seq] or genotyping by sequencing [GBS; reviewed in Puritz et al. 2014 b ; Andrews et al. 2016]; table A2).”
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Metadata
- Authors
- Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S. A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., Sirak, K., Gamba, C., Jones, E. R., Llamas, B., Dryomov, S., Pickrell, J., Arsuaga, J. L., de Castro, J. M. B., Carbonell, E., Gerritsen, F., Khokhlov, A., Kuznetsov, P., Lozano, M., Meller, H., Mochalov, O., Moiseyev, V., Guerra, M. A. R., Roodenberg, J., Vergès, J. M., Krause, J., Cooper, A., Alt, K. W., Brown, D., Anthony, D., Lalueza-Fox, C., Haak, W., Pinhasi, R., & Reich, D.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Howard Hughes Medical Institute (US)
- University College Dublin (IE)
- Trinity College Dublin (IE)
- The University of Adelaide (AU)
- Institute of Molecular and Cell Biology (RU)
- Universidad Complutense de Madrid (ES)
- Institut Català de Paleoecologia Humana i Evolució Social (ES)
- Netherlands Institute in Turkey (TR)
- Peter the Great's Museum of Anthropology and Ethnography (RU)
- Max Planck Institute of Geoanthropology (DE)
- Danube Private University (AT)
- Hartwick College (US)
- Corresponding author
- Mathieson, Iain
- Haak, Wolfgang
- Pinhasi, Ron
- Reich, David
- ORCID
- Mathieson, Iain
- Lazaridis, Iosif
- Rohland, Nadin
- Mallick, Swapan
- Patterson, Nick
- Fernandes, Daniel
- Novak, Mario
- Sirak, Kendra
- Gamba, Cristina
- Jones, Eppie R.
- Llamas, Bastien
- Arsuaga, Juan Luís
- Carbonell, Eudald
- Gerritsen, Fokke
- Khokhlov, Aleksandr
- Kuznetsov, Pavel
- Lozano, Marina
- Meller, Harald
- Moiseyev, Vyacheslav
- Krause, Johannes
- Cooper, Alan
- Alt, Kurt W.
- Brown, Dorcas
- Anthony, David
- Haak, Wolfgang
- Pinhasi, Ron
- Reich, David
- Venue
- Nature
- Published
- 2015-11-23
- Volume
- 528
- Issue
- 7583
- Pages
- 499-503
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4918750
- OpenAlex
- W2177180777
- Semantic Scholar
- fb48d03b320fc6c6aa0188fc169630258225a80b
- Cited by
- 1,515
- References
- 92
- Citations by year
- 2026: 92 · 2025: 169 · 2024: 139 · 2023: 155 · 2022: 153 · 2021: 164 · 2020: 130 · 2019: 131 · 2018: 137 · 2017: 146 · 2016: 87 · 2015: 10
- FWCI
- 87.07
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- VU Research Portal (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- National Science Foundation (1032255)
- Howard Hughes Medical Institute
- Irish Research Council for the Humanities and Social Sciences
- Deutsche Forschungsgemeinschaft (KR 4015/1-1)
- Irish Research Council
- Russian Foundation for Basic Research
- National Institutes of Health (GM100233)
- Australian Research Council (DP130102158)
- National Institute of General Medical Sciences (GM100233, R01GM100233)
- Topics
- 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
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- natural selection, ancient DNA, Neolithic farmers, Neolithic Europe, lactase persistence, diet, pigmentation, immunity, height, human evolution
- MeSH terms
- Agriculture, Asia, Body Height, Bone and Bones, Diet, DNA, Europe, Genetics, Population, Haplotypes, Humans, Immunity, Male, Pigmentation, Selection, Genetic, Genome, Human, Sequence Analysis, DNA, Multifactorial Inheritance, History, Ancient
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