The phenotypic legacy of admixture between modern humans and Neandertals
Open accessAbstract
The legacy of human-Neandertal interbreeding: Non-African humans are estimated to have inherited on average 1.5 to 4% of their genomes from Neandertals. However, how this genetic legacy affects human traits is unknown. Simonti et al. combined genotyping data with electronic health records. Individual Neandertal alleles were correlated with clinically relevant phenotypes in individuals of European descent. These archaic genetic variants were associated with medical conditions affecting the skin, the blood, and the risk of depression. Science , this issue p. 737
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The majority of archaic alleles that are strongly associated with disease in single-locus tests are risk-increasing in the context of modern human populations.
“the majority of archaic alleles that are strongly associated with disease in single-locus tests are risk-increasing in the context of modern human populations3.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]
The paper’s single-locus PheWAS reports four strongly associated, replicated Neanderthal SNP–phenotype associations (passage labeled Abstract; page unavailable). It explicitly says the coagulation-associated allele increases risk and describes the malnutrition-associated allele as potentially harmful, but the available passages do not establish that a majority of the four alleles increase disease risk. Its separate combined-SNP analysis reports similar numbers of risk-increasing and risk-decreasing alleles; that analysis does not settle the single-locus claim. (LLM, conf=0.78)
Experimental — accuracy not yet measuredFor psychiatric traits, tobacco use disorders trend towards enrichment (1.2-fold enriched, q = 0.23), while introgressed variants are depleted for contribution to personality-related functions (1.4-fold depleted, q = 0.07).
“For psychiatric traits, tobacco use disorders trend towards enrichment (1.2-fold enriched, CI: 1.0-1.5, q = 0.23), consistent with previous observations, while introgressed variants are depleted for contribution to personality-related functions (1.4-fold depleted, CI: 1.1–1.8, q = 0.07, Fig. 2E)3,4.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]
The paper reports a replicated association between a Neanderthal SNP and tobacco use disorder, and says Neanderthal SNPs were associated with more psychiatric phenotypes (main text, indexed as Abstract; page unavailable). It does not report the claimed 1.2-fold tobacco enrichment or 1.4-fold depletion for personality-related functions, or their q-values. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThis is consistent with previous hypotheses that genomic regions associated with skin traits tolerated introgression and with previous tests for genome-wide effects of Neanderthal ancestry on complex traits that found enrichment for traits related to skin and hair.
“This is consistent with previous hypotheses that genomic regions associated with skin traits tolerated introgression and with previous tests for genome-wide effects of Neanderthal ancestry on complex traits that found enrichment for traits related to skin and hair3,19.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredIn populations of European descent, a phenome-wide association study of Neanderthal-introgressed alleles showed a wide range of associations with physiological conditions related to the immune system, skin pigmentation, and metabolic pathways, and with pathological outcomes such as depression, actinic keratosis, hypercoagulation, and tobacco use.
“In populations of European descent (EUR), a phenome-wide association study of Neanderthal-introgressed alleles showed a wide range of associations with physiological conditions related to the immune system, skin pigmentation, and metabolic pathways, and with pathological outcomes such as depression, actinic keratosis, hypercoagulation, and tobacco use [15].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]
The paper’s Abstract (page unavailable in our copy) describes an analysis of about 28,000 adults of European ancestry and reports associations involving immune and skin phenotypes, metabolism, depression, actinic keratosis, hypercoagulation, and tobacco use. It discusses skin phenotypes and keratinocytes, but the passages do not establish an association with skin pigmentation specifically. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIntrogression from extinct Neanderthal and Denisovan human species contributes to the genetic pool of modern human populations and their phenotypic spectrum.
“Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum.”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]
The opening passage (section labeled Abstract; page unavailable) reports interbreeding involving Neanderthals and Denisovans and identifies Neanderthal DNA in modern Eurasian genomes. The Abstract also reports associations between Neanderthal alleles and human phenotypes. It does not directly establish a Denisovan contribution to modern humans’ phenotypic variation, although it cites a study of Denisovan-like DNA and altitude adaptation. (LLM, conf=0.79)
Experimental — accuracy not yet measured
Myocardial infarction and coronary atherosclerosis were previously associated with Neanderthal-introgressed loci in EUR.
“Two related cardiovascular phenotypes, myocardial infarction, and coronary atherosclerosis were previously associated with Neanderthal-introgressed loci in EUR [15].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]
The passage on genome-wide complex trait analysis (indexed under Abstract; page unavailable) reports that Neanderthal SNPs collectively explained a significant fraction of myocardial infarction risk in the European-ancestry discovery cohort, while the result for coronary atherosclerosis was only nominally significant. It does not identify individual introgressed loci associated with either phenotype, as the citing sentence implies. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe first PheWAS of Neanderthal-introgressed alleles in EUR found that Neanderthal alleles explained a significant proportion of variance in risk in coronary atherosclerosis.
“The first PheWAS of Neanderthal-introgressed alleles in EUR found that Neanderthal alleles explained a significant proportion of variance in risk in coronary atherosclerosis [15].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]
The passage describing the GCTA results (page unavailable) lists coronary atherosclerosis among traits with a nominally significant result (P < 0.1), not among the three meeting the paper’s corrected significance threshold (FDR < 0.05). It also distinguishes that variance-explained analysis from the subsequent PheWAS, so the claim overstates the significance and conflates the two analyses. (LLM, conf=0.90)
Experimental — accuracy not yet measuredDenisovan DNA is absent from modern European genomes, making it impossible to link Denisovan variants to phenotype, unlike segregating Neanderthal variants.
“Because Denisovan DNA is not present in the genomes of modern Europeans, which make up the vast diversity of biomedical genetics cohorts, it has been impossible to link them to phenotype, unlike segregating Neanderthal variants [16, 25].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [25]
The Abstract (page not provided) reports associations between Neanderthal variants and phenotypes in adults of European ancestry, supporting the contrast in the claim. Our copy does not state that Denisovan DNA is absent from modern European genomes or that linking Denisovan variants to phenotypes is impossible. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe full set of Neandertal-introgressed variants included 132,296 variants that differ from the Homo sapiens-Neandertal common ancestor and match the Neandertal sequence.
“The full set included 132,296 variants that differ from the Homo sapiens–Neandertal common ancestor and match the Neandertal sequence.”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [20]
The passage on identifying Neanderthal alleles (indexed under Abstract; page unavailable) reports approximately 135,000 high-confidence SNPs among introgressed haplotypes. It does not give the exact count of 132,296 or say that these variants differ from the human–Neanderthal common ancestor and match the Neanderthal sequence. (LLM, conf=0.82)
Experimental — accuracy not yet measuredIn one study analyzing health record data in about 28,000 individuals, neurological and psychiatric disorders showed the highest proportional Neandertal DNA contribution.
“In one study that analyzed health record data in ~28,000 individuals, the authors demonstrated that neurological and psychiatric disorders showed the highest proportional Neandertal DNA contribution [21].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [21]
The paper reports an analysis of EHR-derived phenotypes in about 28,000 adults of European ancestry. Its discussion of Fig. 2 says Neanderthal SNPs were associated with more neurological and psychiatric phenotypes than matched non-Neanderthal SNPs, but it does not establish that those disorders had the highest proportional Neanderthal DNA contribution among all disorder classes. (LLM, conf=0.83)
Experimental — accuracy not yet measuredSome archaic alleles and haplotypes are adaptive and persist at high frequencies in human populations.
“For instance, substantial evidence suggests that some archaic alleles and haplotypes are adaptive and persist at high frequencies in human populations [10, 13–19].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [19]
Analyses of available genome-wide association studies and large-scale biobank data revealed that alleles of Neanderthal ancestry are associated with diverse traits in modern Eurasians.
“Analyses of available genome-wide association studies and large-scale biobank data revealed that alleles of Neanderthal ancestry are associated with diverse traits in modern Eurasians1,3–5.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]
S-LDSC requires only GWAS summary statistics, rather than individual-level data as in the GCTA analysis of 46 specific traits in Simonti et al., which enabled us to test effects on over 400 traits across many domains in a larger cohort.
“S-LDSC requires only GWAS summary statistics, rather than individual-level data as in the GCTA analysis of 46 specific traits in Simonti et al.3. This enabled us to test effects on over 400 traits across many domains in a larger cohort.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [3]
Single loci inherited from Neanderthals and Denisovans can contribute to the phenotypic variation of human populations.
“single loci inherited from Neanderthals and Denisovans can still contribute to the phenotypic variation of human populations [15].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]
Previous studies showed that Neanderthal-introgressed loci are associated with immunological, neurological, psychiatric, metabolic, cardiovascular, and dermatological outcomes in EUR populations.
“Previous studies showed that Neanderthal-introgressed loci are associated with immunological, neurological, psychiatric, metabolic, cardiovascular, and dermatological outcomes in EUR populations [10, 15–17].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [15]
Several studies have associated Neandertal-introgressed genetic variants with variability in phenotypes in modern humans, such as immunity, metabolism, adaptation to environmental conditions, and neurological and behavioral phenotypes related to depression and addiction.
“Several studies have associated Neandertal-introgressed genetic variants with variability in phenotypes in modern humans, such as immunity, metabolism, and adaptation to environmental conditions, like temperature and sunlight, as well as neurological and behavioral phenotypes related to depression and addiction [17–20, 51].”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [20]
Neanderthal alleles contribute to addiction and, possibly, pain sensitivity in modern humans.
“It has been found that Neanderthal alleles contribute to addiction and, possibly, pain sensitivity in modern humans176,177.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [176]
A number of instances of adaptive introgression have been described, generally affecting systems that influence immune and metabolic phenotypes.
“a number of instances of adaptive introgression have been described, generally affecting systems that influence immune and metabolic phenotypes [1, 5, 10, 22, 40, 41].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [41]
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Cites
Kessler, R. C., Chiu, W. T., Demler, O., & Walters, E. E. (2005) · Archives of General Psychiatry · doi:10.1001/archpsyc.62.6.617 · Cited by 12,052 · see citing works
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248 · see citing works
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692 · see citing works
GCTA: a tool for genome-wide complex trait analysis
Yang, J., Lee, S. H., Goddard, M. E., & Visscher, P. M. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.11.011 · Cited by 8,279 · see citing works
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
The GTEx Consortium, Ardlie, K. G., Deluca, D. S., Segrè, A. V., Sullivan, T. J., Young, T. R., Gelfand, E. T., Trowbridge, C. A., Maller, J. B., Tukiainen, T., et al. (2015) · Science · doi:10.1126/science.1262110 · Cited by 5,062 · see citing works
GREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502 · see citing works
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 · see citing works
Howie, B. N., Donnelly, P., & Marchini, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000529 · Cited by 3,928 · see citing works
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 · see citing works
Purcell, S., Cherny, S. S., & Sham, P. C. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.1.149 · Cited by 2,057 · see citing works
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations
Denny, J. C., Ritchie, M. D., Basford, M. A., Pulley, J. M., Bastarache, L., Brown-Gentry, K., Wang, D., Masys, D. R., Roden, D. M., & Crawford, D. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq126 · Cited by 1,219 · see citing works
Self-citationAltitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sánchez, E., Jin, X., Asan, Bianba, Z., Peter, B. M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., et al. (2014) · Nature · doi:10.1038/nature13408 · Cited by 1,208 · see citing works
The 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 · see citing works
Denny, J. C., Bastarache, L. A., Ritchie, M. D., Carroll, R. J., Zink, R., Mosley, J. D., Field, J. R., Pulley, J. M., Ramirez, A. H., Bowton, E., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2749 · Cited by 978 · see citing works
Self-citationThe 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 898 · see citing works
Golden, R. N., Gaynes, B. N., Ekstrom, R. D., Hamer, R. M., Jacobsen, F. M., Suppes, T., Wisner, K. L., & Nemeroff, C. B. (2005) · American Journal of Psychiatry · doi:10.1176/appi.ajp.162.4.656 · Cited by 896 · see citing works
Genome partitioning of genetic variation for complex traits using common SNPs
Yang, J., Manolio, T. A., Pasquale, L. R., Boerwinkle, E., Caporaso, N., Cunningham, J. M., de Andrade, M., Feenstra, B., Feingold, E., Hayes, M. G., et al. (2011) · Nature Genetics · doi:10.1038/ng.823 · Cited by 890 · see citing works
The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future
Gottesman, O., Kuivaniemi, H., Tromp, G. C., Faucett, W. A., Li, R., Manolio, T. A., Sanderson, S. C., Kannry, J. L., Zinberg, R. E., Basford, M., et al. (2013) · Genetics in Medicine · doi:10.1038/gim.2013.72 · Cited by 698 · see citing works
Self-citationA General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
O'Connell, J., Gurdasani, D., Delaneau, O., Pirastu, N., Ulivi, S., Cocca, M., Traglia, M., Huang, J., Huffman, J. E., Rudan, I., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004234 · Cited by 593 · see citing works
Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Vernot, B., & Akey, J. M. (2014) · Science · doi:10.1126/science.1245938 · Cited by 562 · see citing works
Self-citationThe shaping of modern human immune systems by multiregional admixture with archaic humans
Abi-Rached, L., Jobin, M. J., Kulkarni, S., McWhinnie, A., Dalva, K., Gragert, L., Babrzadeh, F., Gharizadeh, B., Luo, M., Plummer, F. A., et al. (2011) · Science · doi:10.1126/science.1209202 · Cited by 537 · see citing works
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment
Carroll, R. J., Bastarache, L. A., & Denny, J. C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu197 · Cited by 452 · see citing works
Self-citationKujovich, J. L. (2010) · Genetics in Medicine · doi:10.1097/gim.0b013e3181faa0f2 · Cited by 422 · see citing works
Obesity and socioeconomic status in adults: United States, 2005-2008.
Ogden, C. L., Lamb, M. M., Carroll, M. D., & Flegal, K. M. (2010) · PubMed · Cited by 397 · see citing works
Antidepressant use in persons aged 12 and over: United States, 2005-2008.
Pratt, L. A., Brody, D. J., & Gu, Q. (2011) · PubMed · Cited by 389 · see citing works
The role of thiamine deficiency in alcoholic brain disease.
Martin, P., Singleton, C. K., & Hiller-Sturmhöfel, S. (2003) · PubMed · Cited by 383 · see citing works
Electronic Medical Records for Genetic Research: Results of the eMERGE Consortium
Kho, A. N., Pacheco, J. A., Peissig, P. L., Rasmussen, L., Newton, K. M., Weston, N., Crane, P. K., Pathak, J., Chute, C. G., Bielinski, S. J., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3001807 · Cited by 336 · see citing works
Self-citationREGULATION OF PLATELET FUNCTIONS BY P2 RECEPTORS
Gachet, C. G. (2005) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.46.120604.141207 · Cited by 295 · see citing works
Possible Ancestral Structure in Human Populations
Plagnol, V., & Wall, J. D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020105 · Cited by 275 · see citing works
Higher Levels of Neanderthal Ancestry in East Asians than in Europeans
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. (2013) · Genetics · doi:10.1534/genetics.112.148213 · Cited by 249 · see citing works
Prevalence of Actinic Keratosis and Its Risk Factors in the General Population: The Rotterdam Study
Flohil, S. C., van der Leest, R. J. T., Dowlatshahi, E. A., et al. (2013) · Journal of Investigative Dermatology · doi:10.1038/jid.2013.134 · Cited by 235 · see citing works
SCAN: SNP and copy number annotation
Gamazon, E. R., Zhang, W., Konkashbaev, A. I., Duan, S., Kistner, E. O., Nicolae, D. L., Dolan, M. E., & Cox, N. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp644 · Cited by 230 · see citing works
Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J. F., Pääbo, S., Meshorer, E., & Carmel, L. (2014) · Science · doi:10.1126/science.1250368 · Cited by 219 · see citing works
Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants
Zou, F., Chai, H. S., Younkin, C. S., Allen, M., Crook, J. E., Pankratz, V. S., Carrasquillo, M. M., Rowley, C. N., Nair, A., Middha, S., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002707 · Cited by 216 · see citing works
Fryar, C. D., Hirsch, R., Eberhardt, M. S., Yoon, S. S., & Wright, J. D. (2010) · PsycEXTRA Dataset · doi:10.1037/e665422010-001 · Cited by 175 · see citing works
Genome- and Phenome-Wide Analyses of Cardiac Conduction Identifies Markers of Arrhythmia Risk
Ritchie, M. D., Denny, J. C., Zuvich, R. L., Crawford, D. C., Schildcrout, J. S., Bastarache, L. A., Ramirez, A. H., Mosley, J. D., Pulley, J. M., Basford, M., et al. (2013) · Circulation · doi:10.1161/circulationaha.112.000604 · Cited by 175 · see citing works
Self-citationFunction and Regulation of AUTS2, a Gene Implicated in Autism and Human Evolution
Oksenberg, N., Stevison, L., Wall, J. D., & Ahituv, N. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003221 · Cited by 167 · see citing works
Imiquimod for Actinic Keratosis: Systematic Review and Meta-Analysis
Hadley, G., Derry, S., & Moore, R. A. (2006) · Journal of Investigative Dermatology · doi:10.1038/sj.jid.5700264 · Cited by 161 · see citing works
Two gene co-expression modules differentiate psychotics and controls
Chen, C., Cheng, L., Grennan, K., Pibiri, F., Zhang, C., Badner, J. A., Members of the Bipolar Disorder Genome Study (BiGS) Consortium, Gershon, E. S., & Liu, C. (2013) · Molecular Psychiatry · doi:10.1038/mp.2012.146 · Cited by 157 · see citing works
Heit, J. A., Armasu, S. M., Asmann, Y. W., Cunningham, J. M., Matsumoto, M., Petterson, T. M., & de Andrade, M. (2012) · Journal of Thrombosis and Haemostasis · doi:10.1111/j.1538-7836.2012.04810.x · Cited by 156 · see citing works
Imputation and quality control steps for combining multiple genome-wide datasets
Verma, S. S., de Andrade, M., Tromp, G., Kuivaniemi, H., Pugh, E., Namjou‐Khales, B., Mukherjee, S., Jarvik, G. P., Kottyan, L. C., Burt, A., et al. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00370 · Cited by 127 · see citing works
Self-citationNeanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans
Khrameeva, E. E., Bożek, K., He, L., Zheng, Y., Jiang, X., Wei, Y., Tang, K., Gelfand, M. S., Prüfer, K., Kelso, J. F., et al. (2014) · Nature Communications · doi:10.1038/ncomms4584 · Cited by 89 · see citing works
A PheWAS approach in studying HLA-DRB1*1501
Hebbring, S. J., Schrodi, S. J., Ye, Z., Zhou, Z., Page, D., & Brilliant, M. H. (2013) · Genes and Immunity · doi:10.1038/gene.2013.2 · Cited by 84 · see citing works
Self-citationHeit, J. A., CUNNINGHAM, J. M., Petterson, T. M., Armasu, S. M., Rider, D. N., & de Andrade, M. (2011) · Journal of Thrombosis and Haemostasis · doi:10.1111/j.1538-7836.2011.04272.x · Cited by 72 · see citing works
Basal Ganglia and Functions of the Autonomic Nervous System
Pazo, J. H., & Belforte, J. E. (2002) · Cellular and Molecular Neurobiology · doi:10.1023/a:1021844605250 · Cited by 53 · see citing works
Deciding whether follow-up studies have replicated findings in a preliminary large-scale omics study
Heller, R., Bogomolov, M., & Benjamini, Y. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314814111 · Cited by 51 · see citing works
Schroeder, L. F., Robilotti, E. V., Peterson, L. R., et al. (2013) · Journal of Clinical Microbiology · doi:10.1128/jcm.02777-13 · Cited by 42 · see citing works
Rallapalli, P. M., Orengo, C. A., Studer, R. A., & Perkins, S. J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu248 · Cited by 27 · see citing works
Crosslin, D. R., Tromp, G. C., Burt, A., Kim, D. S., Verma, S. S., Lucas, A., Bradford, Y., Crawford, D. C., Armasu, S. M., Heit, J. A., et al. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00352 · Cited by 17 · see citing works
Self-citationPickering, C., Bergenheim, V., Schiöth, H. B., & Ericson, M. (2008) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2008.05.011 · Cited by 6 · see citing works
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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-citationThe Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419 · 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
Self-citationThe influence of evolutionary history on human health and disease
Benton, M. L., Abraham, A., LaBella, A. L., Abbot, P., Rokas, A., & Capra, J. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00305-9 · Cited by 291 · see citing works
Self-citationIdentifying 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
Self-citationAncient Genomics of Modern Humans: The First Decade
Skoglund, P., & Mathieson, I. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021749 · Cited by 246 · see citing works
Neanderthal language revisited: not only us
Dediu, D., & Levinson, S. C. (2018) · Current Opinion in Behavioral Sciences · doi:10.1016/j.cobeha.2018.01.001 · Cited by 218 · 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
Self-citationArchaic 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
Self-citationGenomic insights into population history and biological adaptation in Oceania
Choin, J., Mendoza-Revilla, J., Arauna, L. R., Cuadros-Espinoza, S., Cassar, O., Larena, M., Ko, A. M.-S., Harmant, C., Laurent, R., Verdu, P., et al. (2021) · Nature · doi:10.1038/s41586-021-03236-5 · Cited by 208 · see citing works
Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression
McCoy, R. C., Wakefield, J., & Akey, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.01.038 · Cited by 200 · see citing works
Self-citationThe 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
“It showed that a large number of Neanderthal variants at different loci influence risk of a number of disease traits, including depression, skin lesions, and blood-clotting disorders, and that Neanderthals contributed both risk and protective alleles for these traits.(12) However, evaluating the broader contribution o…”
InfluentialThe nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2225-9 · Cited by 145 · see citing works
Karnes, J. H., Bastarache, L., Shaffer, C. M., Gaudieri, S., Xu, Y., Glazer, A. M., Mosley, J. D., Zhao, S., Raychaudhuri, S., Mallal, S., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aai8708 · Cited by 126 · see citing works
Self-citationNeandertal Introgression Sheds Light on Modern Human Endocranial Globularity
Gunz, P., Tilot, A. K., Wittfeld, K., Teumer, A., Shapland, C. Y., van Erp, T. G. M., Dannemann, M., Vernot, B., Neubauer, S., Guadalupe, T., et al. (2019) · Current Biology · doi:10.1016/j.cub.2018.10.065 · Cited by 117 · see citing works
“These SNPs cover 42% of the known, high-confidence Neandertal haplotypes [20] (Figures 3A and 3B).”
Self-citationMondal, M., Bertranpetit, J., & Lao, O. (2019) · Nature Communications · doi:10.1038/s41467-018-08089-7 · Cited by 124 · see citing works
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108 · see citing works
Functional implications of Neandertal introgression in modern humans
Dannemann, M., Prüfer, K., & Kelso, J. (2017) · Genome biology · doi:10.1186/s13059-017-1181-7 · Cited by 92 · see citing works
“Despite these general patterns, a number of instances of adaptive introgression have been described, generally affecting systems that influence immune and metabolic phenotypes [1, 5, 10, 22, 40, 41].”
BackgroundHuman 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
Quantifying 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
Self-citationModel‐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
Gouy, A., & Excoffier, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz306 · Cited by 63 · see citing works
Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences
Colbran, L. L., Gamazon, E. R., Zhou, D., Evans, P., Cox, N. J., & Capra, J. A. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0996-x · Cited by 50 · see citing works
Self-citationSilvert, 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 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
“In contrast to these attempts to associate individual introgressed variants with a trait, studies have attempted to measure the aggregate contribution of introgressed Neanderthal SNPs to trait variation (Simonti et al., 2016; McArthur et al., 2021).”
Denisovan introgression has shaped the immune system of present-day Papuans
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46 · see citing works
“Because Denisovan DNA is not present in the genomes of modern Europeans, which make up the vast diversity of biomedical genetics cohorts, it has been impossible to link them to phenotype, unlike segregating Neanderthal variants [16,23].”
Neanderthal 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
Self-citationZhang, 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
Evolutionary 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
Koller, D., Wendt, F. R., Pathak, G. A., De Lillo, A., De Angelis, F., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2022) · BMC Biology · doi:10.1186/s12915-022-01449-2 · Cited by 27 · see citing works
“loci Although we observed only SNP-h2 enrichment with respect to Denisovan-introgressed loci for coronary artery disease in EAS, single loci inherited from Neanderthals and Denisovans can still contribute to the phenotypic variation of human populations [15].”
BackgroundInfluential<i>DLX5/6</i> GABAergic Expression Affects Social Vocalization: Implications for Human Evolution
Levi, G., de Lombares, C., Giuliani, C., Iannuzzi, V., Aouci, R., Garagnani, P., Franceschi, C., Grimaud-Hervé, D., & Narboux-Nême, N. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab181 · Cited by 29 · see citing works
Dannemann, M., Milaneschi, Y., Yermakovich, D., Stiglbauer, V., Kariis, H. M., Krebs, K., Friese, M. A., Otte, C., Estonian Biobank Research Team, Esko, T., et al. (2022) · Translational Psychiatry · doi:10.1038/s41398-022-02196-2 · Cited by 23 · see citing works
“Testing for the proportional association strength to phenotypes In order to quantify the association strength of archaic variants, we compared their number of significantly associated tag aSNPs to the number of frequency-matched non-archaic tag SNPs following similar approaches that have previously been used for such…”
BackgroundResultGregory, M. D., Eisenberg, D. P., Hamborg, M., Kippenhan, J. S., Kohn, P., Kolachana, B., Dickinson, D., & Berman, K. F. (2021) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32872 · Cited by 24 · see citing works
Mozzi, A., Forni, D., Cagliani, R., Pozzoli, U., Clerici, M., & Sironi, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-06440-4 · Cited by 19 · see citing works
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
Liang, S.-A., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., He, Y., McCoy, R. C., Fu, Q., Akey, J. M., et al. (2025) · Genome Biology · doi:10.1186/s13059-025-03502-z · Cited by 8 · see citing works
Self-citationEffects 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
“Among others, behavioural and neuropsychiatric traits emerged as especially impacted: depression 21 , schizophrenia and anorexia 17 were found significantly affected; sleeping patterns, pain, mental health, smoking and alcohol consumption even showed signs of enrichment in Neanderthal-derived…”
Influential
- Authors
- Simonti, C. N., Vernot, B., Bastarache, L., Bottinger, E., Carrell, D. S., Chisholm, R. L., Crosslin, D. R., Hebbring, S. J., Jarvik, G. P., Kullo, I. J., Li, R., Pathak, J., Ritchie, M. D., Roden, D. M., Verma, S. S., Tromp, G., Prato, J. D., Bush, W. S., Akey, J. M., Denny, J. C., & Capra, J. A.
- Affiliations
- Vanderbilt University (US)
- University of Washington (US)
- Mount Sinai School of Medicine, New York, NY, USA.
- University of Washington Medical Center (US)
- Northwestern University (US)
- Marshfield Clinic (US)
- Mayo Clinic (US)
- National Institutes of Health (US)
- Pennsylvania State University (US)
- Stellenbosch University (ZA)
- Case Western Reserve University (US)
- Corresponding author
- Pathak, Jyotishman
- Akey, Joshua M.
- Denny, Joshua C.
- Capra, John A.
- ORCID
- Venue
- Science
- Published
- 2016-02-12
- Volume
- 351
- Issue
- 6274
- Pages
- 737-741
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4849557
- OpenAlex
- W2279984879
- Cited by
- 330
- References
- 51
- Citations by year
- 2026: 17 · 2025: 13 · 2024: 24 · 2023: 27 · 2022: 26 · 2021: 49 · 2020: 28 · 2019: 57 · 2018: 29 · 2017: 36 · 2016: 24
- FWCI
- 190.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Johns Hopkins University (U01HG004438)
- Group Health Cooperative and University of Washington, Seattle (U01HG004610, U01HG008657)
- Marshfield Clinic (U01HG004608, 1K22LM011938)
- Essentia Institute of Rural Health (U01HG006389)
- Mayo Clinic (U01HG04599, U01HG006379)
- Northwestern University (U01HG004609, U01HG006388)
- Vanderbilt University (U01HG04603, U01HG006378)
- Coordinating Center of the eMERGE Network (U01HG006385)
- Geisinger Clinic (U01HG006382)
- Mount Sinai School of Medicine (U01HG006380)
- PheWAS (R01LM010685)
- NIH (5T32EY021453, R01GM110068, 1R01GM114128)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- electronic health records, depression, actinic keratosis, sun exposure, skin lesions, hypercoagulability, tobacco use, psychiatric phenotypes, neurological phenotype, immunological phenotype, European ancestry, disease risk
- MeSH terms
- Alleles, Animals, Depression, Disease, Haplotypes, Humans, Phenotype, Genetic Variation, Genome, Human, Evolution, Molecular, White People, Keratosis, Actinic, Neanderthals
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