The genomic landscape of Neanderthal ancestry in present-day humans
Open accessAbstract
Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
East Asians have the greatest number of sites containing archaic alleles, followed by South Asians, while Europeans have the fewest.
“We found that East Asians have the greatest number of sites containing archaic alleles, followed by South Asians, while Europeans have the fewest (fig. 2A), as has been previously established (Sankararaman et al. 2014, 2016).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Sankararaman et al. 2014
The paper reports a higher mean proportion of Neandertal ancestry in East Asians (1.38%) than in Europeans (1.15%) in the passage labeled Abstract (no page supplied). It does not establish the claimed ranking by number of sites containing archaic alleles, and the population comparison in that passage does not include South Asians. (LLM, conf=0.84)
Experimental — accuracy not yet measuredIntrogressed archaic alleles are mostly observed outside protein-coding sequences, distributed over non-functional and regulatory regions.
“At the genomic level these introgressed archaic alleles are mostly observed outside protein-coding sequences, distributed over non-functional and regulatory regions [8, 9].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [8]
The paper reports reduced Neandertal ancestry near genes and in regions dense with functionally important elements (Abstract; page unavailable). That supports a relative depletion in such regions, but our copy does not establish that most introgressed alleles lie outside protein-coding sequences or specify their distribution across non-functional and regulatory regions. (LLM, conf=0.85)
Experimental — accuracy not yet measuredPrevious attempts to identify archaic fragments in contemporary humans have generally relied on existing archaic genomes, which partially represent the haplotypic diversity of archaic populations.
“Previous attempts to identify archaic fragments in contemporary humans have generally relied on existing archaic genomes [14][15][16] , which partially represent the haplotypic diversity of the archaic populations.”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [15]
The paper’s Abstract and Online Methods (Preparation of 1000 Genomes Data; page unavailable) say its method used the Altai Neandertal genome as a reference to identify Neandertal haplotypes in present-day humans. This supports an example of reliance on an existing archaic genome, but the cited passages do not establish that previous attempts generally did so or discuss how fully existing genomes represent archaic haplotypic diversity. (LLM, conf=0.82)
Experimental — accuracy not yet measuredHumans in Central and East Asia are known to have elevated Neanderthal ancestry compared to other populations.
“Humans in Central and East Asia are known to have elevated Neanderthal ancestry compared to other populations (22).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [22]
The paper’s ancestry comparison (Table 1, in the supplied passage) reports higher mean Neanderthal ancestry in East Asians than Europeans: 1.38% versus 1.15%. It does not report a corresponding finding for Central Asians, so the claim’s inclusion of Central Asia is unsupported. (LLM, conf=0.89)
Experimental — accuracy not yet measuredThe increased Neanderthal ancestry in Central and East Asian populations relative to others is due to weaker selection against alleles that may be mildly deleterious, made possible because of smaller historical population sizes in this part of Eurasia, rather than to additional admixture events.
“This observation favors the hypothesis that the increased Neanderthal ancestry in these populations relative to others is due to weaker selection against alleles that may be mildly deleterious (32), made possible because of smaller historical population sizes in this part of Eurasia, rather than to additional admixture events (22).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [22]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
Previous studies of regions with Neanderthal ancestry found depletion for evidence of background selection and functional annotations, such as genes and gene regulatory elements active in specific tissues.
“First, previous studies of regions with Neanderthal ancestry found depletion for evidence of background selection and functional annotations, such as genes and gene regulatory elements active in specific tissues18,19,27,29.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [19]
The paper’s main text (indexed under “Abstract”; no page supplied) reports that low Neanderthal ancestry correlates with a low B-statistic, a measure associated with functionally important regions. It also finds reduced ancestry near genes and in genes specifically expressed in testis. It does not establish depletion in tissue-active gene regulatory elements, and its tissue-specific finding is limited to testis-expressed genes. (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 [19]
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 measuredSignatures of archaic introgression have been reported in genes associated with hair and skin pigmentation, immunity, neoplasms and metabolic traits, and male sterility.
“Additionally, signatures of archaic introgression have been reported in genes associated with hair and skin pigmentation, immunity [16, 17, 19, 20, 22], neoplasms and metabolic traits [19, 23, 24], and male sterility [17, 18].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [17]
The paper’s main text (page unavailable) reports Neandertal ancestry in genes involved in keratin filaments, alleles associated with immune-related conditions and type 2 diabetes, and evidence consistent with male hybrid sterility. It does not establish an association with hair or skin pigmentation specifically, and the passages examined do not report neoplasms. (LLM, conf=0.84)
Experimental — accuracy not yet measuredPrevious 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 [17]
In the paper’s section labeled Abstract (page unavailable), the authors identify Neanderthal-derived alleles associated with lupus, Crohn’s disease, IL-18 levels, smoking behavior, and type 2 diabetes, and suggest effects on skin and hair. The passage does not establish associations with cardiovascular or psychiatric outcomes, or a dermatological outcome specifically; it also does not place every listed association in European populations. (LLM, conf=0.87)
Experimental — accuracy not yet measuredThe regions of the novel T2T-CHM13 haplotypes included previously recognized targets of adaptive introgression, such as SGCB and SPATA18.
“These regions included previously recognized targets of adaptive introgression, such as SGCB and SPATA18 [13, 14, 17].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [13]
The Abstract (page unavailable) discusses Neandertal-introgressed regions that may show positive selection. Our copy does not identify SGCB or SPATA18 as targets of adaptive introgression, and it does not address the novel T2T-CHM13 haplotypes. Searches for both gene names found no matching passage. (LLM, conf=0.78)
Experimental — accuracy not yet measuredWe began with a list of 95,462 SNPs that are likely to be Neanderthal-derived from Sankararaman et al., 2014.
“We began with a list of 95,462 SNPs that are likely to be Neanderthal-derived from Sankararaman et al., 2014.”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Sankararaman et al., 2014
The Online Methods section, “Identifying alleles born in Neandertals” (page unavailable), describes a list of inferred Neandertal-derived SNPs, supporting the attribution of such a list to this paper. It reports 97,365 SNPs, however, not the claimed 95,462; our copy does not establish whether the citing authors used a subset. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIntrogressed archaic DNA has mainly been deleterious and actively removed from coding sequences and conserved non-coding elements.
“beyond general agreement that introgressed archaic DNA has mainly been deleterious and actively removed from coding sequences and conserved non-coding elements [8, 12–14]”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [8]
The paper reports widespread negative selection against Neandertal ancestry and reduced ancestry near genes and functionally important elements (Abstract; page unavailable). It does not establish that introgressed archaic DNA was mainly deleterious or specifically show its removal from conserved non-coding elements; it also identifies potentially adaptive introgressed alleles. (LLM, conf=0.86)
Experimental — accuracy not yet measuredSeveral 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 [17]
The paper’s section labeled Abstract (page unavailable) identifies Neandertal-derived alleles associated with immune-related conditions, type 2 diabetes, and smoking behavior, and suggests that alleles affecting skin and hair may have aided adaptation to non-African environments. It does not link those alleles specifically to temperature, sunlight, depression, or addiction; smoking behavior alone does not establish an addiction association. (LLM, conf=0.87)
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 [13]
Many Neanderthal variants appear to have been deleterious in the modern human genetic background, leading to a reduction in Neanderthal ancestry in conserved genomic regions.
“On the other hand, many Neanderthal variants appear to have been deleterious in the modern human genetic background leading to a reduction in Neanderthal ancestry in conserved genomic regions (Sankararaman et al., 2014; Vernot and Akey, 2014; Harris and Nielsen, 2016; Juric et al., 2016; Petr et al., 2019).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Sankararaman et al., 2014
Neanderthal ancestry is depleted in regions of the genome with strong background selection and evolutionary conservation.
“First, Neanderthal ancestry is depleted in regions of the genome with strong background selection and evolutionary conservation18,19,27.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [19]
Archaic introgression tends to be rarer in gene-rich regions.
“archaic introgression tends to be rarer in gene-rich regions (15)”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [15]
The X chromosome is particularly devoid of archaic introgression.
“The X chromosome is particularly devoid of archaic introgression as previously reported 15 (Fig. 1d).”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [15]
Maps produced by SARGE are about as concordant with published maps as the published maps are with each other.
“We found that maps produced by SARGE are about as concordant with the published maps as the published maps are with each other (fig. S25).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [22]
Non-African populations have 1-4% Neanderthal admixture, with East Asian populations exhibiting more Neanderthal introgression than West Eurasian populations.
“Studies estimate that non-African populations have 1–4% Neanderthal admixture, with East Asian populations exhibiting more Neanderthal introgression than West Eurasian populations (Wall et al. 2013; Sankararaman et al. 2014), perhaps due to more archaic admixture events with ancestral East Asians, but other plausible scenarios have been proposed (Coll Macià et al. 2021; Witt et al. 2022).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Sankararaman et al. 2014
On average, an East Asian individual carries a higher percentage of Neanderthal genome DNA than a European individual (1.4% and 1.1%, respectively).
“earlier studies found that on average, an EAS individual carries a higher percentage of Neanderthal genome DNA than a EUR individual (1.4% and 1.1%, respectively) [17].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [17]
Most studies of archaic introgression have relied on the GRCh37 human reference genome.
“However, most studies of archaic introgression have relied on the GRCh37 human reference genome [8, 10, 11, 13, 14, 20].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [13]
Neanderthal alleles tend to be distributed further away from regions of the genome under selective constraint.
“since prior work has shown that Neanderthal alleles tend to be distributed further away from regions of the genome under selective constraint (Sankararaman et al., 2014; Juric et al., 2016).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Sankararaman et al., 2014
The model does not exclude the possibility that differences in population sizes or generation time between eastern and western Asia may also have played a role in shaping Neanderthal ancestry patterns.
“This model does not exclude the possibility that differences in population sizes (15) or in generation time (53) between eastern and western Asia may also have played a role in shaping NE ancestry patterns, but a modeling study focusing on these aspects would be”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [15]
Introgressed fragments of Neandertal DNA can be reliably identified in modern humans and are estimated to account for 1%-2% of the genomes of non-African individuals, such that collectively about 40% of the Neandertal genome is represented in people living today.
“Introgressed fragments of Neandertal DNA can be reliably identified in modern humans and are estimated to account for 1%–2% of the genomes of non-African individuals, such that collectively ~40% of the Neandertal genome is represented in people living today [17–19].”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [17]
After modern humans left Africa more than 60,000 years ago, multiple admixture events around 55,000 years ago occurred between modern humans and now extinct archaic humans including Neandertals and Denisovans.
“After modern humans left Africa more than 60,000 years ago, genetic evidence suggests multiple admixture events ~55,000 years [9] between modern humans and now extinct archaic humans including Neandertals [10–12] and Denisovans [13, 14].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
Previous studies have pointed out that Neandertal DNA shows a lower prevalence in regions associated with higher functional capacity in the human genome.
“previous studies have pointed out that Neandertal DNA shows a lower prevalence in regions that are associated with higher functional capacity in the human genome [12, 34].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
Some remaining Neandertal variants have reached high frequencies in some present-day populations, suggesting they might have conferred advantages at some point since admixture.
“Some of the remaining Neandertal variants have reached high frequencies in some present-day populations, suggesting that they might have conferred advantages at some point since admixture [12, 18, 19].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
Previous analyses have demonstrated that Neandertal DNA shows signals of depletion around functional gene groups, making the current setup rather conservative as it should not result in an artificial enrichment result due to functional genome context.
“However, given that previous analyses have demonstrated that Neandertal DNA is showing signals of depletion around functional gene groups [12, 34], makes our current setup rather conservative as it shouldn’t result in an artificial enrichment result due to functional genome context.”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [12]
Genomic regions experiencing strong levels of background selection are depleted in Neanderthal ancestry.
“Recent data indicated that genomic regions experiencing strong levels of background selection are depleted in Neanderthal ancestry54.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [54]
Neanderthal alleles are enriched in genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans adapt to non-African cold environments.
“Other examples include Neanderthal alleles that are enriched in genes affecting keratin filaments, which make up most of the outer layer of human skin and produce hair, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African cold environments [42].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
Archaic admixture appears to have introduced a few beneficial alleles, such as EPAS1.
“On the other hand, archaic admixture appears to have also introduced a few beneficial alleles, such as EPAS1.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
Strong purifying selection appears to have acted on the genome of modern humans to purge harmful archaic alleles.
“Indeed, strong purifying selection appears to have acted on the genome of modern humans to purge harmful archaic alleles.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
Genes that are highly expressed in testes have reduced Neanderthal ancestry.
“For example, genes that are highly expressed in testes have reduced Neanderthal ancestry [42].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [42]
Some archaic alleles have been shown to confer an adaptive advantage for modern humans.
“Some archaic alleles have been shown to confer an adaptive advantage for modern humans”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
The depletion of archaic ancestry around functional elements in the genomes of present-day people reflects widespread purifying selection against archaic variants.
“the depletion of archaic ancestry around functional elements in the genomes of present-day people reflects widespread purifying selection against archaic variants [5–7]”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
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 [5]
Neandertal alleles are depleted in more constrained, functional regions of the genome and, on average, selection has acted to remove introgressed Neandertal alleles from the modern human population.
“Recent studies have shown that Neandertal alleles are depleted in more constrained, functional regions of the genome and that, on average, selection has acted to remove introgressed Neandertal alleles from the modern human population [5, 7, 39].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
The decrease in frequency of Neandertal alleles contributing to protein sequence and expression variation is particularly the case near protein coding genes, and is consistent with negative selection on Neandertal DNA in modern humans.
“This is particularly the case near protein coding genes, and is consistent with negative selection on Neandertal DNA in modern humans [5, 6, 7, 39].”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [5]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data
Lafferty, J., McCallum, A., & Pereira, F. C. N. (2001) · ScholarlyCommons (University of Pennsylvania) · Cited by 12,953 · 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
Self-citationDerrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,017 · 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
Self-citationHindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013 · see citing works
Wavelet Methods for Time SeriesAnalysis
Percival, D. B., & Walden, A. T. (2000) · Cambridge University Press eBooks · doi:10.1017/cbo9780511841040 · Cited by 3,120 · see citing works
Wavelet methods for time series analysis
Percival, D. B., & Walden, A. T. (2001) · Choice Reviews Online · doi:10.5860/choice.38-4508 · Cited by 2,570 · see citing works
The Jackknife and the Bootstrap for General Stationary Observations
Künsch, H. R. (1989) · The Annals of Statistics · doi:10.1214/aos/1176347265 · Cited by 2,454 · see citing works
Generating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397 · 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
Self-citationGenetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991 · see citing works
Self-citationA high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
Self-citationSpeciation and Its Consequences
Shaffer, H. B., Otte, D., & Endler, J. A. (1990) · Evolution · doi:10.2307/2409350 · Cited by 1,245 · see citing works
A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome
Myers, S., Bottolo, L., Freeman, C., McVean, G., & Donnelly, P. (2005) · Science · doi:10.1126/science.1117196 · Cited by 1,134 · see citing works
An Introduction to Conditional Random Fields for Relational Learning
Sutton, C. A., & McCallum, A. (2007) · The MIT Press eBooks · doi:10.7551/mitpress/7432.003.0006 · Cited by 849 · see citing works
Representations of quasi-Newton matrices and their use in limited memory methods
Byrd, R. H., Nocedal, J., & Schnabel, R. B. (1994) · Mathematical Programming · doi:10.1007/bf01582063 · Cited by 758 · see citing works
Pruitt, K. D., Harrow, J., Harte, R., Wallin, C., Diekhans, M., Maglott, D. R., Searle, S. M. J., Farrell, C. M., Loveland, J. E., Ruef, B. J., et al. (2009) · Genome Research · doi:10.1101/gr.080531.108 · Cited by 558 · see citing works
THE EVOLUTION OF POSTZYGOTIC ISOLATION: ACCUMULATING DOBZHANSKY-MULLER INCOMPATIBILITIES
Orr, H. A., & Turelli, M. (2001) · Evolution · doi:10.1111/j.0014-3820.2001.tb00628.x · Cited by 553 · see citing works
The 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
Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico
Williams, A. L., Jacobs, S. B. R., Churchhouse, C. L., Burtt, N. P., Florez, J. C., Altshuler, D., Ripke, S., Manning, A. K., Neale, B. M., Reich, D., et al. (2013) · Nature · doi:10.1038/nature12828 · Cited by 498 · see citing works
Self-citationThe Date of Interbreeding between Neandertals and Modern Humans
Sankararaman, S., Patterson, N., Li, H., Pääbo, S., & Reich, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002947 · Cited by 460 · see citing works
Self-citationWidespread Genomic Signatures of Natural Selection in Hominid Evolution
McVicker, G., Gordon, D., Davis, C., & Green, P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000471 · Cited by 456 · see citing works
Davis, A. W. (1993) · The American Naturalist · doi:10.1086/285534 · Cited by 405 · see citing works
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.Preprint
Paten, B., Herrero, J., Beal, K., Fitzgerald, S., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.076554.108 · Cited by 348 · see citing works
Sex chromosomes and speciation in Drosophila
Presgraves, D. C. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.04.007 · Cited by 336 · see citing works
Lachance, J., Vernot, B., Elbers, C. C., Ferwerda, B., Froment, A., Bodo, J.-M., Lema, G., Fu, W., Nyambo, T., Rebbeck, T. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.009 · Cited by 334 · see citing works
Population Genetics Models of Local Ancestry
Gravel, S. (2012) · Genetics · doi:10.1534/genetics.112.139808 · Cited by 311 · see citing works
Keinan, A., Mullikin, J. C., Patterson, N., & Reich, D. (2007) · Nature Genetics · doi:10.1038/ng2116 · Cited by 272 · see citing works
Self-citationHigher 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
FUNC: a package for detecting significant associations between gene sets and ontological annotations
Prüfer, K., Muetzel, B., Do, H.-H., Weiss, G., Khaitovich, P., Rahm, E., Pääbo, S., Lachmann, M., & Enard, W. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-41 · Cited by 173 · see citing works
Self-citationABRUPT CLINE FOR SEX CHROMOSOMES IN A HYBRID ZONE BETWEEN TWO SPECIES OF MICE
Tucker, P. K., Sage, R. D., Warner, J., Wilson, A. C., & Eicher, E. M. (1992) · Evolution · doi:10.1111/j.1558-5646.1992.tb00625.x · Cited by 168 · see citing works
Mendez, F. L., Watkins, J. C., & Hammer, M. F. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.06.015 · Cited by 156 · see citing works
A Complex Genetic Basis to X-Linked Hybrid Male Sterility Between Two Species of House Mice
Good, J. M., Dean, M. D., & Nachman, M. W. (2008) · Genetics · doi:10.1534/genetics.107.085340 · Cited by 150 · see citing works
Neandertal Origin of Genetic Variation at the Cluster of OAS Immunity Genes
Mendez, F. L., Watkins, J. C., & Hammer, M. F. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst004 · Cited by 113 · see citing works
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
Hellenthal, G., & Stephens, M. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl622 · Cited by 105 · see citing works
Bhatia, G., Tandon, A., Patterson, N. J., Aldrich, M. C., Ambrosone, C. B., Amos, C. I., Bandera, E. V., Berndt, S. I., Bernstein, L., Blot, W. J., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.08.011 · Cited by 81 · see citing works
Self-citationIntroduction to Statistical Relational Learning
Sutton, C. A., & McCallum, A. (2007) · Cited by 81 · 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
Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixturePreprint
Bhatia, G., Tandon, A., Aldrich, M. C., Ambrosone, C. B., Amos, C. I., Bandera, E. V., Berndt, S. I., Bernstein, L., Blot, W. J., Bock, C. H., et al. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1312.2675 · Cited by 2 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
Haber, M., Mezzavilla, M., Xue, Y., & Tyler-Smith, C. (2016) · Genome Biology · doi:10.1186/s13059-015-0866-z · Cited by 1,924 · see citing works
GERAD1 Consortium, Pardiñas, A. F., CRESTAR Consortium, Holmans, P., Pocklington, A. J., Escott-Price, V., Ripke, S., Carrera, N., Legge, S. E., Bishop, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0059-2 · Cited by 1,552 · see citing works
Altitude 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
Insights into human genetic variation and population history from 929 diverse genomes
Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020 · see citing works
Self-citationThe genetic history of Ice Age Europe
Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., et al. (2016) · Nature · doi:10.1038/nature17993 · Cited by 959 · see citing works
Self-citationRobust and scalable inference of population history from hundreds of unphased whole genomes
Terhorst, J., Kamm, J., & Song, Y. S. (2016) · Nature Genetics · doi:10.1038/ng.3748 · Cited by 950 · see citing works
Hybridization, Introgression, and the Nature of Species Boundaries
Harrison, R. G., & Larson, E. L. (2014) · Journal of Heredity · doi:10.1093/jhered/esu033 · Cited by 738 · see citing works
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
Martin, S. H., Davey, J. W., & Jiggins, C. D. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu269 · Cited by 721 · 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
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
Self-citationHaplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works
Extensive introgression in a malaria vector species complex revealed by phylogenomics
Fontaine, M. C., Pease, J. B., Steele, A., Waterhouse, R. M., Neafsey, D. E., Sharakhov, I. V., Jiang, X., Hall, A. B., Catteruccia, F., Kakani, E. G., et al. (2014) · Science · doi:10.1126/science.1258524 · Cited by 630 · see citing works
The major genetic risk factor for severe COVID-19 is inherited from Neanderthals
Zeberg, H., & Pääbo, S. (2020) · Nature · doi:10.1038/s41586-020-2818-3 · Cited by 636 · see citing works
Self-citationInsights from genomes into the evolutionary importance and prevalence of hybridization in nature
Taylor, S. A., & Larson, E. L. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0777-y · Cited by 585 · see citing works
Ancient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature · doi:10.1038/nature16544 · Cited by 577 · see citing works
Self-citationA genomic perspective on hybridization and speciation
Payseur, B. A., & Rieseberg, L. H. (2016) · Molecular Ecology · doi:10.1111/mec.13557 · Cited by 544 · see citing works
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller, I., Baglione, V., Unneberg, P., Wikelski, M. C., Grabherr, M. G., et al. (2014) · Science · doi:10.1126/science.1253226 · Cited by 542 · see citing works
Evidence for archaic adaptive introgression in humans
Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3936 · Cited by 521 · see citing works
Self-citationGenetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z. A., Pacis, A., Dumaine, A., Grenier, J.-C., Freiman, A., Sams, A. J., Hebert, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.025 · Cited by 512 · see citing works
Genetic adaptation and Neandertal admixture shaped the immune system of human populations
Quach, H., Rotival, M., Pothlichet, J., Loh, Y.-H. E., Dannemann, M., Zidane, N., Laval, G., Patin, E., Harmant, C., Lopez, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.024 · Cited by 475 · see citing works
Self-citationThe Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans
Sankararaman, S., Mallick, S., Patterson, N., & Reich, D. (2016) · Current Biology · doi:10.1016/j.cub.2016.03.037 · Cited by 465 · see citing works
Self-citationExcavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., et al. (2016) · Science · doi:10.1126/science.aad9416 · Cited by 459 · see citing works
Self-citationOrigins of modern human ancestry
Bergström, A., Stringer, C. B., Hajdinjak, M., Scerri, E. M. L., & Skoglund, P. (2021) · Nature · doi:10.1038/s41586-021-03244-5 · Cited by 426 · 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
Natural 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-citationHarnessing genomic information for livestock improvement
Georges, M., Charlier, C., & Hayes, B. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0082-2 · Cited by 384 · 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
Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery
Greater Middle East Variome Consortium, Scott, E. M., Halees, A., Itan, Y., Spencer, E. G., He, Y., Azab, M. A., Gabriel, S. B., Belkadi, A., Boisson, B., et al. (2016) · Nature Genetics · doi:10.1038/ng.3592 · Cited by 376 · see citing works
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biologyPreprint
Gardner, E. J., Lam, V. K. L., Harris, D., Chuang, N. T., Scott, E., Pittard, W. S., Mills, R. E., & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 371 · see citing works
The phenotypic legacy of admixture between modern humans and Neandertals
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., et al. (2016) · Science · doi:10.1126/science.aad2149 · Cited by 330 · see citing works
Recombination rate variation shapes barriers to introgression across butterfly genomes
Martin, S. H., Davey, J. W., Salazar, C. A., & Jiggins, C. D. (2019) · PLoS Biology · doi:10.1371/journal.pbio.2006288 · Cited by 326 · see citing works
The genomic consequences of hybridization
Moran, B. M., Payne, C. Y., Langdon, Q. K., Powell, D. L., Brandvain, Y. J., & Schumer, M. E. (2021) · eLife · doi:10.7554/elife.69016 · Cited by 326 · see citing works
Genomic structure in Europeans dating back at least 36,200 years
Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., et al. (2014) · Science · doi:10.1126/science.aaa0114 · Cited by 315 · see citing works
Chimpanzee genomic diversity reveals ancient admixture with bonobos
de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V. C., Desai, T., Prado-Martinez, J., Hernández-Rodríguez, J., Dupanloup, I., Lao, Ó., Hallast, P., et al. (2016) · Science · doi:10.1126/science.aag2602 · Cited by 297 · see citing works
A high-coverage Neandertal genome from Chagyrskaya Cave
Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309 · see citing works
Self-citationThe 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
Comparative primate genomics: emerging patterns of genome content and dynamics
Rogers, J., & Gibbs, R. A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3707 · Cited by 295 · see citing works
Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa
Gallego-Llorente, M., Jones, E. R., Eriksson, A., Siska, V., Arthur, K. W., Arthur, J. W., Curtis, M. C., Stock, J. T., Coltorti, M., Pieruccini, P., et al. (2015) · Science · doi:10.1126/science.aad2879 · Cited by 291 · see citing works
The 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
Neandertal Demise: An Archaeological Analysis of the Modern Human Superiority Complex
Villa, P., & Roebroeks, W. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096424 · Cited by 274 · see citing works
Ancestral Origins and Genetic History of Tibetan Highlanders
Lu, D., Lou, H., Yuan, K., Wang, X., Wang, Y., Zhang, C., Lü, Y., Yang, X. W., Deng, L., Zhou, Y., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.07.002 · Cited by 272 · see citing works
Kaufman, D. A., & Himmelmann, N. P. (2024) · Oxford University Press eBooks · doi:10.1093/oso/9780198807353.003.0042 · Cited by 263 · see citing works
Late Quaternary megafaunal extinctions on the continents: a short review
Stuart, A. J. (2014) · Geological Journal · doi:10.1002/gj.2633 · Cited by 255 · see citing works
Speciation and introgression between Mimulus nasutus and Mimulus guttatus
Brandvain, Y., Kenney, A. M., Flagel, L., Coop, G., & Sweigart, A. L. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004410 · Cited by 259 · see citing works
Slatkin, M., & Racimo, F. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1524306113 · Cited by 252 · see citing works
Deschamps, M., Laval, G., Fagny, M., Itan, Y., Abel, L., Casanova, J.-L., Patin, E., & Quintana-Murci, L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.014 · Cited by 257 · 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
Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa
Gurdasani, D., Carstensen, T., Fatumo, S., Chen, G., Franklin, C. S., Prado-Martinez, J., Bouman, H. J., Abascal, F., Haber, M., Tachmazidou, I., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.004 · Cited by 254 · 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
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
When did <i>Homo sapiens</i> first reach Southeast Asia and Sahul?
O’Connell, J. F., Allen, J., Williams, M. A. J., Williams, A. N., Turney, C. S. M., Spooner, N. A., Kamminga, J., Brown, G., & Cooper, A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1808385115 · Cited by 236 · see citing works
A framework for incorporating evolutionary genomics into biodiversity conservation and management
Hoffmann, A. A., Griffin, P. C., Dillon, S. K., Catullo, R. A., Rane, R., Byrne, M. M., Jordan, R., Oakeshott, J. G., Weeks, A. R., Joseph, L., et al. (2015) · Climate Change Responses · doi:10.1186/s40665-014-0009-x · Cited by 228 · see citing works
Harrison, R. G., & Larson, E. L. (2016) · Molecular Ecology · doi:10.1111/mec.13582 · Cited by 223 · 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
Physical activity, aging, and physiological function
Harridge, S. D. R., & Lazarus, N. R. (2017) · Physiology · doi:10.1152/physiol.00029.2016 · Cited by 214 · see citing works
Moorjani, P., Sankararaman, S., Fu, Q., Przeworski, M., Patterson, N. J., & Reich, D. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514696113 · Cited by 201 · see citing works
Self-citationLimits 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-citationEvidence 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
Genomic 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
Interpreting the genomic landscape of introgression
Martin, S. H., & Jiggins, C. D. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.08.007 · Cited by 206 · see citing works
Analysis of Population Genomic Data from Hybrid Zones
Gompert, Z., Mandeville, E. G., & Buerkle, C. A. (2017) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110316-022652 · Cited by 193 · 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
Signatures of Archaic Adaptive Introgression in Present-Day Human Populations
Racimo, F., Marnetto, D., & Huerta-Sánchez, E. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw216 · Cited by 200 · see citing works
The Human Condition—A Molecular Approach
Pääbo, S. (2014) · Cell · doi:10.1016/j.cell.2013.12.036 · Cited by 197 · see citing works
Self-citationHaplotype-resolved genome sequencing: experimental methods and applications
Snyder, M. W., Adey, A., Kitzman, J. O., & Shendure, J. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3903 · Cited by 189 · see citing works
The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference
Flagel, L., Brandvain, Y. J., & Schrider, D. R. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy224 · Cited by 183 · 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
Self-citationMultiple episodes of interbreeding between Neanderthal and modern humans
Villanea, F. A., & Schraiber, J. G. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0735-8 · Cited by 192 · see citing works
ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs
Yang, H., Wu, J., Huang, X., Zhou, Y., Zhang, Y., Liu, M., Liu, Q., Ke, S., He, M., Fu, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04769-z · Cited by 195 · see citing works
Harnessing ancient genomes to study the history of human adaptation
Marciniak, S., & Perry, G. H. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.65 · Cited by 182 · see citing works
Okada, Y., Momozawa, Y., Sakaue, S., Kanai, M., Ishigaki, K., Akiyama, M., Kishikawa, T., Arai, Y., Sasaki, T., Kosaki, K., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03274-0 · Cited by 180 · 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
A unified genealogy of modern and ancient genomes
Wohns, A. W., Wong, Y., Jeffery, B., Akbari, A., Mallick, S., Pinhasi, R., Patterson, N. J., Reich, D., Kelleher, J., & McVean, G. (2022) · Science · doi:10.1126/science.abi8264 · Cited by 182 · see citing works
Self-citationHuman Immunology through the Lens of Evolutionary Genetics
Quintana‐Murci, L. (2019) · Cell · doi:10.1016/j.cell.2019.02.033 · Cited by 174 · see citing works
Taming the Past: Ancient DNA and the Study of Animal Domestication
MacHugh, D. E., Larson, G., & Orlando, L. (2016) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-022516-022747 · Cited by 169 · see citing works
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears
Cahill, J. A., Stirling, I., Kistler, L., Salamzade, R., Ersmark, E., Fulton, T. L., Stiller, M., Green, R. E., & Shapiro, B. (2014) · Molecular Ecology · doi:10.1111/mec.13038 · Cited by 167 · see citing works
Human Dispersal Out of Africa: A Lasting Debate
López, S., van Dorp, L., & Hellenthal, G. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s33489 · Cited by 158 · see citing works
Denisovan Ancestry in East Eurasian and Native American Populations
Qin, P., & Stoneking, M. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv141 · Cited by 152 · see citing works
Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution
Pollen, A. A., Kilik, U., Lowe, C. B., & Camp, J. G. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-022-00568-4 · Cited by 157 · see citing works
Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation
Burgarella, C., Barnaud, A., Kane, N. A., Jankowski, F., Scarcelli, N., Billot, C., Vigouroux, Y., & Berthouly‐Salazar, C. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00004 · Cited by 145 · see citing works
Complex History of Admixture between Modern Humans and Neandertals
Vernot, B., & Akey, J. M. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.01.006 · Cited by 149 · see citing works
A working model of the deep relationships of diverse modern human genetic lineages outside of Africa
Lipson, M., & Reich, D. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw293 · Cited by 145 · see citing works
Self-citationCorbett-Detig, R. B., & Nielsen, R. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006529 · Cited by 134 · see citing works
The 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
The Hybrid Origin of “Modern” Humans
Ackermann, R., Mackay, A., & Arnold, M. L. (2015) · Evolutionary Biology · doi:10.1007/s11692-015-9348-1 · Cited by 142 · see citing works
Genome-wide introgression among distantly related Heliconius butterfly species
Zhang, W., Dasmahapatra, K. K., Mallet, J., Moreira, G. R. P., & Kronforst, M. R. (2016) · Genome biology · doi:10.1186/s13059-016-0889-0 · Cited by 144 · see citing works
Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment
Trujillo, C. A., Rice, E. S., Schaefer, N. K., Chaim, I. A., Wheeler, E. C., Madrigal, A. A., Buchanan, J., Preißl, S., Wang, A., Negraes, P. D., et al. (2021) · Science · doi:10.1126/science.aax2537 · Cited by 146 · see citing works
Signatures of Long-Term Balancing Selection in Human Genomes
Bitarello, B. D., de Filippo, C., Teixeira, J. C., Schmidt, J. M., Kleinert, P., Meyer, D., & Andrés, A. M. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy054 · Cited by 132 · 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
Campbell, C. R., Poelstra, J. W., & Yoder, A. D. (2018) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/bly063 · Cited by 131 · see citing works
An evolutionary anthropological perspective on modern human origins.
Marean, C. W. (2015) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-102313-025954 · Cited by 135 · see citing works
Runemark, A., Vallejo‐Marín, M., & Meier, J. I. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008404 · Cited by 129 · see citing works
Hubisz, M. J., Williams, A. L., & Siepel, A. (2020) · PLOS Genetics · doi:10.1371/journal.pgen.1008895 · Cited by 130 · see citing works
Međugorac, I., Graf, A., Grohs, C., Rothammer, S., Zagdsuren, Y., Александровна, Г. Е., Zinovieva, N. A., Barbieri, J., Seichter, D., Ruß, I., et al. (2017) · Nature Genetics · doi:10.1038/ng.3775 · Cited by 128 · see citing works
Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation
Arnold, M. L., & Kunte, K. K. (2017) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2017.05.007 · Cited by 129 · see citing works
The Genomics of Human Local Adaptation
Rees, J., Castellano, S., & Andrés, A. M. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.03.006 · Cited by 126 · see citing works
Incomplete Lineage Sorting in Mammalian Phylogenomics
Scornavacca, C., & Galtier, N. (2016) · Systematic Biology · doi:10.1093/sysbio/syw082 · Cited by 124 · see citing works
Competitive Science: Is Competition Ruining Science?
Fang, F. C., & Casadevall, A. (2015) · Infection and Immunity · doi:10.1128/iai.02939-14 · Cited by 129 · see citing works
Roebroeks, W., & Soressi, M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521269113 · Cited by 123 · see citing works
Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes
Buckley, M. T., Racimo, F., Allentoft, M. E., Jensen, M. K., Jonsson, A. E., Huang, H., Hormozdiari, F., Sikora, M., Marnetto, D., Eskin, E., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx103 · Cited by 121 · see citing works
- Authors
- Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D.
- Affiliations
- Broad Institute (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Sankararaman, Sriram
- Reich, David
- ORCID
- Venue
- Nature
- Published
- 2014-01-29
- Volume
- 507
- Issue
- 7492
- Pages
- 354-357
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4072735
- OpenAlex
- W2009494639
- Cited by
- 1,107
- References
- 41
- Citations by year
- 2026: 49 · 2025: 93 · 2024: 131 · 2023: 69 · 2022: 58 · 2021: 110 · 2020: 81 · 2019: 80 · 2018: 98 · 2017: 96 · 2016: 108 · 2015: 66 · 2014: 65 · 2013: 3
- FWCI
- 535.37
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Human Genome Research Institute (R01HG006399)
- National Institute of General Medical Sciences (GM100233, R01GM100233)
- 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 Associations and Epidemiology
- Keywords
- Neanderthal ancestry, Neanderthal admixture, keratin genes, disease risk alleles, X chromosome, testis-expressed genes, male fertility, human evolution, modern human genomes, Neanderthal introgression
- MeSH terms
- Alleles, Animals, Female, Haplotypes, Humans, Hybridization, Genetic, Infertility, Male, Keratins, Male, Organ Specificity, Phylogeny, Selection, Genetic, Testis, X Chromosome, Genome, Human, Genetic Predisposition to Disease, Genomics, Gene Flow, Neanderthals
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 ›
Are you an author, or do you see a problem with this page? Request a review
