The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
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.
Overview
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
Verification
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“We 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
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measured
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“We 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
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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 cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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 cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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.
Citations
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
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
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 12,935
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
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 5,135
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
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
Wavelet Methods for Time SeriesAnalysis
Percival, D. B., & Walden, A. T. (2000) · Cambridge University Press eBooks · doi:10.1017/cbo9780511841040 · Cited by 3,210
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
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
Cited by
Sorted by citations
Items 301–400 of 997
Evolutionary and medical consequences of archaic introgression into modern human genomes
Dolgova, O., & Lao, O. (2018) · Genes · doi:10.3390/genes9070358 · Cited by 34
Ingelman‐Sundberg, M., Persson, A., & Jukić, M. M. (2014) · Pharmacogenomics · doi:10.2217/pgs.14.151 · Cited by 34
Ghost admixture in eastern gorillas
Pawar, H., Rymbekova, A., Cuadros-Espinoza, S., Huang, X., de Manuel, M., van der Valk, T., Lobón, I., Álvarez-Estapé, M., Haber, M., Dolgova, O., et al. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-023-02145-2 · Cited by 37
The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal
Vallini, L., Zampieri, C., Shoaee, M. J., Bortolini, E., Marciani, G., Aneli, S., Pievani, T., Benazzi, S., Barausse, A., Mezzavilla, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46161-7 · Cited by 41
Tephra studies and the reconstruction of Middle-to-Upper Paleolithic cultural trajectories
d’Errico, F., & Banks, W. E. (2014) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2014.05.014 · Cited by 33
Ancient humans and the origin of modern humans
Kelso, J. F., & Prüfer, K. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.09.004 · Cited by 35
Self-citationAnderson, C. J., Cunha, L., Sechi, P., Kille, P., & Spurgeon, D. J. (2017) · BMC Genetics · doi:10.1186/s12863-017-0557-8 · Cited by 35
What’s new in IBD therapy: An “omics network” approach
Fiocchi, C., & Iliopoulos, D. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104886 · Cited by 34
The Population-Specific Impact of Neandertal Introgression on Human Disease
Dannemann, M. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evaa250 · Cited by 33
Self-citationHuang, Y., Huang, W., Meng, Z., Braz, G. T., Li, Y., Wang, K., Wang, H., Lai, J., Jiang, J., Dong, Z., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02448-2 · Cited by 34
Introduction to Special Issue on Primate Hybridization and Hybrid Zones
Cortés‐Ortiz, L., Roos, C., & Zinner, D. P. (2019) · International Journal of Primatology · doi:10.1007/s10764-019-00076-z · Cited by 33
Tournebize, R., & Chikhi, L. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02591-6 · Cited by 41
Rohde, K., Hau, Y., Weyer, J., & Hochkirch, A. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0460-8 · Cited by 32
Admixture in Mammals and How to Understand Its Functional Implications
Fontsere, C., de Manuel, M., Marquès‐Bonet, T., & Kuhlwilm, M. (2019) · BioEssays · doi:10.1002/bies.201900123 · Cited by 29
Wheat speciation and adaptation: perspectives from reticulate evolution
Zhao, X., Fu, X., Yin, C., & Lü, F. (2021) · aBIOTECH · doi:10.1007/s42994-021-00047-0 · Cited by 30
Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
Ahlquist, K. D., Bañuelos, M. M., Funk, A., Lai, J., Rong, S., Villanea, F. A., & Witt, K. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab115 · Cited by 36
The Spatial Signature of Introgression After a Biological Invasion With Hybridization
Quilodrán, C. S., Tsoupas, A., & Currat, M. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.569620 · Cited by 31
Statistical methods for analyzing ancient DNA from hominins
Slatkin, M. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.08.004 · Cited by 32
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information
Pang, X., & Zhang, D. (2023) · Systematic Biology · doi:10.1093/sysbio/syad077 · Cited by 31
A history of multiple Denisovan introgression events in modern humans
Ongaro, L., & Huerta‐Sánchez, E. (2024) · Nature Genetics · doi:10.1038/s41588-024-01960-y · Cited by 34
Explosive genetic evidence for explosive human population growth
Gao, F., & Keinan, A. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.09.002 · Cited by 32
Human adaptation over the past 40,000 years
Mathieson, I. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.06.003 · Cited by 32
Mavengere, H., Mattox, K., Teixeira, M. D. M., Sepúlveda, V. E., Gómez, O. M., Hernández, O., McEwen, J. G., & Matute, D. R. (2020) · mBio · doi:10.1128/mbio.01999-20 · Cited by 32
Garcia‐Erill, G., Jørgensen, C. H. F., Muwanika, V. B., Wang, X., Rasmussen, M. S., de Jong, Y. A., Gaubert, P., Olayemi, A., Salmona, J., Butynski, T. M., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac134 · Cited by 33
The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach
Saeb, A. T. M., & Alnaqeb, D. (2016) · Scientifica · doi:10.1155/2016/2079704 · Cited by 31
The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium
Zaitlen, N., Huntsman, S., Hu, D., Spear, M. L., Eng, C. S., Oh, S. S., White, M. J., Mak, A. C. Y., Davis, A. J., Meade, K., et al. (2016) · Genetics · doi:10.1534/genetics.116.192138 · Cited by 33
Genomics of a complete butterfly continentPreprint
Zhang, J., Cong, Q., Shen, J., Opler, P. A., & Grishin, N. V. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/829887 · Cited by 34
A test for ancient selective sweeps and an application to candidate sites in modern humans
Racimo, F., Kuhlwilm, M., & Slatkin, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu255 · Cited by 30
Tan, X., Qi, J., Liu, Z., Fan, P., Liu, G., Zhang, L., Shen, Y., Li, J., Roos, C., Zhou, X., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad229 · Cited by 35
The “Skinny” on brown fat, obesity, and bone
Devlin, M. J. (2014) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22661 · Cited by 33
Esteller-Cucala, P., Maceda, I., Børglum, A. D., Demontis, D., Faraone, S. V., Cormand, B., & Lao, Ó. (2020) · Scientific Reports · doi:10.1038/s41598-020-65322-4 · Cited by 35
The genomes of ancient date palms germinated from 2,000 y old seeds
Gros‐Balthazard, M., Flowers, J. M., Hazzouri, K. M., Ferrand, S., Aberlenc‐Bertossi, F., Sallon, S., & Purugganan, M. D. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2025337118 · Cited by 33
Iberian Neanderthals in forests and savannahs
Ochando, J., Amorós, G., Carrión, J. S., Fernández, S., Munuera, M., Camuera, J., Jiménez‐Moreno, G., González‐Sampériz, P., Burjachs, F., Marín-Arroyo, A. B., et al. (2021) · Journal of Quaternary Science · doi:10.1002/jqs.3339 · Cited by 30
DLX5/6 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 23
The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations
Witt, K. E., Funk, A., Añorve-Garibay, V., Fang, L. L., & Huerta-Sánchez, E. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad066 · Cited by 25
Zhang, X., Kim, B., Singh, A., Sankararaman, S., Durvasula, A., & Lohmueller, K. E. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad001 · Cited by 29
Self-citationFunctional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Buckley, M. A., Woods, N. T., Tyrer, J. P., Mendoza-Fandiño, G., Lawrenson, K., Hazelett, D. J., Najafabadi, H. S., Gjyshi, A., Carvalho, R. S., Junior, P. C. M. L., et al. (2018) · Cancer Research · doi:10.1158/0008-5472.can-17-3864 · Cited by 28
The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes
Sharbrough, J., Havird, J. C., Noe, G. R., Warren, J. M., & Sloan, D. B. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx114 · Cited by 27
Manual laterality and cognition through evolution: An archeological perspective.
Uomini, N., & Ruck, L. (2018) · Progress in Brain Research · doi:10.1016/bs.pbr.2018.06.015 · Cited by 26
Archaic admixture in human history
Wall, J. D., & Brandt, D. Y. C. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.07.002 · Cited by 29
Evolutionary Genomics and the Domestication of Grapes
Zhou, Y., Muyle, A., & Gaut, B. S. (2019) · Compendium of plant genomes · doi:10.1007/978-3-030-18601-2_3 · Cited by 27
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
“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].”
BackgroundEvolution, systematics, and the unnatural history of mitochondrial DNA
Schwartz, J. H. (2021) · Mitochondrial DNA Part A · doi:10.1080/24701394.2021.1899165 · Cited by 29
Genomic Correlates of Atherosclerosis in Ancient Humans
Zink, A., Wann, L. S., Thompson, R. C., Keller, A., Maixner, F., Allam, A. H., Finch, C. E., Frøhlich, B., Kaplan, H. S., Lombardi, G. P., et al. (2014) · Global Heart · doi:10.1016/j.gheart.2014.03.2453 · Cited by 29
Inference of multiple-wave admixtures by length distribution of ancestral tracks
Ni, X., Yuan, K., Yang, X. W., Feng, Q., Guo, W., Ma, Z.-M., & Xu, S. (2018) · Heredity · doi:10.1038/s41437-017-0041-2 · Cited by 27
Cabrera, V. M., Marrero, P., Abu‐Amero, K. K., & Larruga, J. M. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1211-4 · Cited by 28
Characterizing the effect of background selection on the polygenicity of brain-related traits
Wendt, F. R., Pathak, G. A., Overstreet, C., Tylee, D. S., Gelernter, J., Atkinson, E. G., & Polimanti, R. (2021) · Genomics · doi:10.1016/j.ygeno.2020.11.032 · Cited by 27
Inferring Adaptive Introgression Using Hidden Markov Models
Svedberg, J., Shchur, V., Reinman, S., Nielsen, R., & Corbett-Detig, R. B. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab014 · Cited by 32
Were Neanderthals and Homo sapiens ‘good species’?
Meneganzin, A., & Bernardi, M. (2023) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2023.107975 · Cited by 29
Longevity and aging. Mechanisms and perspectives
Labat‐Robert, J., & Robert, L. (2015) · Pathologie Biologie · doi:10.1016/j.patbio.2015.08.001 · Cited by 27
Recently evolved human-specific methylated regions are enriched in schizophrenia signals
Banerjee, N., Polushina, T. V., Bettella, F., Giddaluru, S., Steen, V. M., Andreassen, O. A., & Hellard, S. L. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1177-2 · Cited by 27
Cortés‐Ortiz, L., Baiz, M. D., Hermida‐Lagunes, J., García‐Orduña, F., Negrín, A. R., Kitchen, D. M., Bergman, T. J., Dias, P. A. D., & Canales‐Espinosa, D. (2018) · International Journal of Primatology · doi:10.1007/s10764-018-0056-4 · Cited by 27
Enabling interpretable machine learning for biological data with reliability scores
Ahlquist, K. D., Sugden, L. A., & Ramachandran, S. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011175 · Cited by 28
Sato, D. X., & Kawata, M. (2018) · Evolution Letters · doi:10.1002/evl3.81 · Cited by 27
On the Distribution of Tract Lengths During Adaptive Introgression
Shchur, V., Svedberg, J., Medina, P., Corbett-Detig, R. B., & Nielsen, R. (2020) · G3 Genes Genomes Genetics · doi:10.1534/g3.120.401616 · Cited by 27
Quiver, M. H., & Lachance, J. (2021) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2021.100083 · Cited by 28
Rong, S., Neil, C. R., Welch, A., Duan, C., Maguire, S., Meremikwu, I. C., Meyerson, M., Evans, B. J., & Fairbrother, W. G. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218308120 · Cited by 25
The evolution of the human genome
Simonti, C., & Capra, J. A. (2015) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.08.005 · Cited by 24
A selection pressure landscape for 870 human polygenic traits
Song, W., Shi, Y., Wang, W., Pan, W., Qian, W., Yu, S., Zhao, M., & Lin, G. N. (2021) · Nature Human Behaviour · doi:10.1038/s41562-021-01231-4 · Cited by 25
Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species
Zhang, W., Ding, Y., Cao, Y., Li, P., Yang, Y., Pang, X., Bai, W., & Zhang, D. (2024) · The Plant Journal · doi:10.1111/tpj.16859 · Cited by 24
Zhou, Q., Karunarathne, P., Li, L., Chen, C., Opgenoorth, L., Heer, K., Vendramin, G. G., Piotti, A., Николаевна, Н. Е., Lascoux, M., et al. (2024) · Molecular Ecology · doi:10.1111/mec.17495 · Cited by 26
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
Deng, Y. K., Nielsen, R., & Song, Y. S. (2025) · Nature Genetics · doi:10.1038/s41588-025-02317-9 · Cited by 71
Reduced purine biosynthesis in humans after their divergence from Neandertals
Stepanova, V. V., Moczulska, K. E., Vacano, G. N., Kurochkin, I., Ju, X.-C., Riesenberg, S., Macak, D., Maričić, T., Dombrowski, L., Schörnig, M., et al. (2021) · eLife · doi:10.7554/elife.58741 · Cited by 27
Self-citationChromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans
Rogers, R. L. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv204 · Cited by 27
Ni, X., Yang, X. W., Guo, W., Yuan, K., Zhou, Y., Ma, Z.-M., & Xu, S. (2016) · Scientific Reports · doi:10.1038/srep20048 · Cited by 26
Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?
Irving-Pease, E. K., Muktupavela, R., Dannemann, M., & Racimo, F. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.703541 · Cited by 27
Self-citationGregory, 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
Langdon, Q. K., Groh, J. S., Aguillon, S. M., Powell, D. L., Gunn, T. R., Payne, C. Y., Baczenas, J. J., Donny, A. E., Dodge, T. O., Du, K., et al. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002742 · Cited by 30
Holliday, T. W., Gautney, J. R., & Friedl, L. (2014) · Current Anthropology · doi:10.1086/679068 · Cited by 24
Maroja, L. S., Larson, E. L., Bogdanowicz, S. M., & Harrison, R. G. (2015) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.021246 · Cited by 24
Learning the properties of adaptive regions with functional data analysis
Mughal, M. R., Koch, H., Huang, J., Chiaromonte, F., & DeGiorgio, M. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008896 · Cited by 24
Predicting Archaic Hominin Phenotypes from Genomic Data
Brand, C. M., Colbran, L. L., & Capra, J. A. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111521-121903 · Cited by 24
A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms
Jordan, V. E., Walker, J. A., Beckstrom, T. O., Steely, C. J., McDaniel, C. L., Romain, C. P. S., Worley, K. C., Phillips‐Conroy, J. E., Jolly, C. J., Rogers, J., et al. (2018) · Mobile DNA · doi:10.1186/s13100-018-0118-3 · Cited by 24
Rabbit exploitation in the Middle Paleolithic at Gruta Nova da Columbeira, Portugal
Carvalho, M. M., Pereira, T., & Manso, C. (2018) · Journal of Archaeological Science Reports · doi:10.1016/j.jasrep.2018.09.003 · Cited by 26
Ferrer, J., James, H. F., Chesser, R. T., Bretagnolle, V., González‐Solís, J., Rozas, J., Riutort, M., & Welch, A. J. (2021) · Systematic Biology · doi:10.1093/sysbio/syaa101 · Cited by 26
Bednarik, R. G. (2020) · Encyclopedia · doi:10.3390/encyclopedia3030067 · Cited by 25
Recombination and selection against introgressed DNAPreprint
Veller, C., Edelman, N. B., Muralidhar, P., & Nowak, M. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/846147 · Cited by 22
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
“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].”
BackgroundSelf-citationGerchen, J., Reichert, S. J., Roehr, J. T., Dieterich, C., Kloas, W., & Stöck, M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0156419 · Cited by 23
Neanderthal and Denisova tooth protein variants in present-day humans
Zanolli, C., Hourset, M., Esclassan, R., & Mollereau, C. (2017) · PLoS ONE · doi:10.1371/journal.pone.0183802 · Cited by 24
Tonzo, V., Papadopoulou, A., & Ortego, J. (2020) · Molecular Ecology · doi:10.1111/mec.15475 · Cited by 21
Glauberman, P., Gasparyan, B., Wilkinson, K., Frahm, E., Nahapetyan, S., Arakelyan, D., Raczynski-Henk, Y., Haydosyan, H., & Adler, D. S. (2020) · Journal of Paleolithic Archaeology · doi:10.1007/s41982-020-00071-4 · Cited by 23
Gregory, M. D., Kippenhan, J. S., Kohn, P. D., Eisenberg, D. P., Callicott, J. H., Kolachana, B. S., & Berman, K. F. (2020) · Brain Connectivity · doi:10.1089/brain.2020.0809 · Cited by 24
McGee, M. D., Reustle, J. W., Oufiero, C. E., & Wainwright, P. C. (2015) · The American Naturalist · doi:10.1086/683464 · Cited by 23
Genome Data Exploration Using Correspondence Analysis
Tekaia, F. (2016) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s39614 · Cited by 23
Ancient oncogenesis, infection and human evolution
Rifkin, R. F., Potgieter, M., Ramond, J., & Cowan, D. A. (2017) · Evolutionary Applications · doi:10.1111/eva.12497 · Cited by 26
FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations
Szpak, M., Mezzavilla, M., Ayub, Q., Chen, Y., Xue, Y., & Tyler‐Smith, C. (2018) · Genome biology · doi:10.1186/s13059-017-1380-2 · Cited by 23
Moran, P. A., Pascoal, S., Cezard, T., Risse, J. E., Ritchie, M. G., & Bailey, N. W. (2018) · Molecular Ecology · doi:10.1111/mec.14725 · Cited by 21
How well do we understand the basis of classic selective sweeps in humans?
Szpak, M., Xue, Y., Ayub, Q., & Tyler‐Smith, C. (2019) · FEBS Letters · doi:10.1002/1873-3468.13447 · Cited by 22
Complex Phenotypes: Mechanisms Underlying Variation in Human Stature
Muthuirulan, P., & Capellini, T. D. (2019) · Current Osteoporosis Reports · doi:10.1007/s11914-019-00527-9 · Cited by 24
McArthur, E., Rinker, D. C., Cheng, Y., Wang, Q., Wang, J., Gilbertson, E. N., Fudenberg, G., Pittman, M., Keough, K. C., Yue, F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.07.479462 · Cited by 22
Bidirectional Introgression between Mus musculus domesticus and Mus spretus
Banker, S. E., Bonhomme, F., & Nachman, M. W. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evab288 · Cited by 23
Apportioning archaic variants among modern populations
Witt, K. E., Villanea, F. A., Loughran, E., Zhang, X., & Huerta‐Sánchez, E. (2022) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0411 · Cited by 27
Gautam, P., Chaurasia, A., Bhattacharya, A., Grover, R., Mukerji, M., & Natarajan, V. T. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu342 · Cited by 22
SELAM: simulation of epistasis and local adaptation during admixture with mate choice
Corbett-Detig, R. B., & Jones, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw365 · Cited by 22
Холмогорова, А. Б. (2016) · Cultural-Historical Psychology · doi:10.17759/chp.2016120305 · Cited by 24
Warren, K. A., Ritzman, T. B., Humphreys, R. A., Percival, C. J., Hallgrímsson, B., & Ackermann, R. (2018) · Journal of Human Evolution · doi:10.1016/j.jhevol.2017.12.002 · Cited by 24
Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions
Dannemann, M., He, Z., Heide, C., Vernot, B., Sidow, L., Kanton, S., Weigert, A., Treutlein, B., Pääbo, S., Kelso, J. F., et al. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2020.05.018 · Cited by 22
Self-citationEcosystem Health Disorders - changing perspectives in clinical medicine and nutrition.
Wahlqvist, M. L. (2014) · PubMed · doi:10.6133/apjcn.2014.23.1.20 · Cited by 21
Wang, X., Yang, X., Zhou, L., Wyckhuys, K. A. G., Jiang, S., Liem, N. V., Vi, L. X., Ali, A., & Wu, K. (2021) · Pest Management Science · doi:10.1002/ps.6670 · Cited by 21
Metadata
- 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
- 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
