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 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.
“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]
The Methods (‘Population history analysis’; page not provided) confirm that the paper performed PCA on 777 West Eurasian individuals and projected ancient individuals onto it. The passages in our copy do not describe a Europe–Near East contrast on PC1 or parallel European and Near Eastern clines on PC2, so they do not support those specific findings. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe dataset combines the newly reported ancient individuals with previously published ancient data to form a dataset of 281 ancient individuals.
“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]
The ‘Genome-wide ancient DNA from West Eurasia’ section says the authors combined 67 previously published samples with newly reported data. But it gives the resulting dataset as 230 ancient individuals, not 281; the cited paper therefore supports the combination but not the claimed total. No page number is available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians.
“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]
The spread of Near Eastern ancestry into the Eurasian steppe was previously inferred without access to ancient samples, by hypothesizing a population related to present-day Armenians as a source.
“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]
Sample JK2911 had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia, consistent with the ancestral affinity shown above.
“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]
The allele (G) at rs6903823 was rising in frequency in Chalcolithic and Bronze Age Near Eastern populations at the same time as it was rising in frequency in Europe.
“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]
The “Twelve signals of selection” section discusses changes in allele frequencies in Europe, but the passages retrieved for rs6903823 do not identify that SNP. The passages on Near Eastern ancestry in “Insight into population transformations” do not report its frequency in Chalcolithic or Bronze Age Near Eastern populations. Our copy therefore does not establish the claimed simultaneous rise. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThe allele (G) at rs6903823 has been argued to have been under positive selection by Mathieson et al.
“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]
The ‘Twelve signals of selection’ section discusses selection at several named SNPs and loci, but the passages in our copy do not identify rs6903823 or its G allele as a target. Searches for rs6903823 and for ‘rs6903823 G positive selection’ found no passage addressing that specific allele. (LLM, conf=0.72)
Experimental — accuracy not yet measuredY chromosome analysis 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.
“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]
The ‘Insight into population transformations’ section reports Y-chromosome haplogroup G2a in Anatolian Neolithic individuals, not haplogroup E in Natufians or Levantine Neolithic populations (page unavailable). Searches for Natufians, Levantine Neolithic haplogroup E, and the claimed African origin found no passage in our copy addressing those points or the asserted absence in other ancient West Eurasian males. (LLM, conf=0.73)
Experimental — accuracy not yet measuredScandinavian hunter-gatherers (SHG) are a mix of EHG and WHG.
“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]
The ‘Twelve signals of selection’ section describes Scandinavian hunter-gatherers from Motala as closely related to western hunter-gatherers, but does not say they were a mix of WHG and EHG. The passages on EHG admixture concern steppe populations, not SHG; searches for SHG admixture and Motala ancestry found no passage establishing the claimed mixture. (LLM, conf=0.72)
Experimental — accuracy not yet measuredWestern hunter-gatherers of central and southern European populations survived in Palaeolithic Europe with dark skin pigmentation.
“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]
aDNA analyses show that Scandinavian hunter-gatherers and Early European farmers carried derived alleles contributing to light skin.
“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]
Lactose tolerance increased dramatically in just the past 3000 years.
“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]
Only a limited number of strong selective sweeps associated with diet and pigmentation can be associated with agriculture in Europe.
“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]
Lactose tolerance was found in only 10% of Bronze Age Europeans.
“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]
Lactose tolerance appears to have been absent in early European farmers.
“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]
Additional pigmentation-associated loci, including HERC2/OCA2, TYR, and GRM5, show evidence of allele-frequency change or selection during the Holocene in European populations.
“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
The SLC24A5 rs1426654-A 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.
“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
Neolithic farmer populations of Anatolian ancestry introduced the derived light pigmentation-associated SLC24A5 rs1426654-A allele into Europe during their northward and westward expansion.
“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
Light pigmentation-associated variation at SLC45A2, particularly rs16891982, 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.
“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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Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers
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Identifying Recent Adaptations in Large-Scale Genomic Data
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Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
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Evidence of widespread selection on standing variation in Europe at height-associated SNPs
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Self-citationAncient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity
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Self-citationGenomic structure in Europeans dating back at least 36,200 years
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Self-citationAncient genomes link early farmers from Atapuerca in Spain to modern-day Basques
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Self-citationZKSCAN3 Is a Master Transcriptional Repressor of Autophagy
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Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
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A Common Variation in EDAR Is a Genetic Determinant of Shovel-Shaped Incisors
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The Horse, the Wheel, and Language
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Self-citationThe phylogenetic and geographic structure of Y-chromosome haplogroup R1a
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2000 Years of Parallel Societies in Stone Age Central Europe
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Tracing the genetic origin of Europe's first farmers reveals insights into their social organization
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Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers
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Self-citationGenetic Architecture of Skin and Eye Color in an African-European Admixed Population
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Leprosy and the Adaptation of Human Toll-Like Receptor 1
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A global view of the OCA2-HERC2 region and pigmentation
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Evidence for bronze age cannibalism in El Mirador Cave (Sierra de Atapuerca, Burgos, Spain)
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Self-citationEfficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow
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Self-citationAdaptive Evolution of the FADS Gene Cluster within Africa
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The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland
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Crohn's Disease and Genetic Hitchhiking at IBD5
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Breaking the Bond: Investigating The Neolithic Expansion in Asia Minor in the Seventh Millennium BC
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Self-citationThe Earliest Neolithic Levels at Barcın Höyük, Northwestern Turkey
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Self-citationEarly Settlement in the Plain of Yenişehir (NW Anatolia)
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Self-citationNewly Found Human Remains from Menteşe in the Yenişehir Plain
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Self-citationSierra de Atapuerca archaeological sites
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Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
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Genetic determinants of the gut microbiome in UK twins
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Genomic insights into the origin of farming in the ancient Near East
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Self-citationFinding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions
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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).”
InfluentialThe formation of human populations in South and Central Asia
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Self-citationThe Beaker phenomenon and the genomic transformation of northwest Europe
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Self-citationTracing the peopling of the world through genomics
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The genomic history of southeastern Europe
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Self-citationThe genomic history of the Iberian Peninsula over the past 8000 years
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Self-citationGreenlandic Inuit show genetic signatures of diet and climate adaptation
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A method for genome-wide genealogy estimation for thousands of samples
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137 ancient human genomes from across the Eurasian steppes
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Early farmers from across Europe directly descended from Neolithic Aegeans
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Self-citationGenetic adaptation and Neandertal admixture shaped the immune system of human populations
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The population history of northeastern Siberia since the Pleistocene
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Self-citationAncient genomes document multiple waves of migration in Southeast Asian prehistory
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Self-citationReconstructing Prehistoric African Population Structure
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Self-citationThe first horse herders and the impact of early Bronze Age steppe expansions into Asia
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Self-citationUpper Palaeolithic genomes reveal deep roots of modern Eurasians
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Self-citationSignatures of negative selection in the genetic architecture of human complex traits
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The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes
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Self-citationUpdate on lactose malabsorption and intolerance: pathogenesis, diagnosis and clinical management
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Parallel palaeogenomic transects reveal complex genetic history of early European farmers
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Self-citationpong: fast analysis and visualization of latent clusters in population genetic data
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Going global by adapting local: A review of recent human adaptation
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Detection of human adaptation during the past 2000 years
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Self-citationOn the Evolution of Lactase Persistence in Humans
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Self-citationAncient genomes from northern China suggest links between subsistence changes and human migration
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Self-citationAncient genomes show social and reproductive behavior of early Upper Paleolithic foragers
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Population genomics of the Viking world
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Self-citationReduced signal for polygenic adaptation of height in UK Biobank
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Self-citation
- 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 · 2012: 1
- 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
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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