Complex History of Admixture between Modern Humans and Neandertals
Open accessAbstract
Recent analyses have found that a substantial amount of the Neandertal genome persists in the genomes of contemporary non-African individuals. East Asians have, on average, higher levels of Neandertal ancestry than do Europeans, which might be due to differences in the efficiency of purifying selection, an additional pulse of introgression into East Asians, or other unexplored scenarios. To better define the scope of plausible models of archaic admixture between Neandertals and anatomically modern humans, we analyzed patterns of introgressed sequence in whole-genome data of 379 Europeans and 286 East Asians. We found that inferences of demographic history restricted to neutrally evolving genomic regions allowed a simple one-pulse model to be robustly rejected, suggesting that differences in selection cannot explain the differences in Neandertal ancestry. We show that two additional demographic models, involving either a second pulse of Neandertal gene flow into the ancestors of East Asians or a dilution of Neandertal lineages in Europeans by admixture with an unknown ancestral population, are consistent with the data. Thus, the history of admixture between modern humans and Neandertals is most likely more complex than previously thought.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Farmers could have acted as a population that diluted Neanderthal ancestry in western Eurasia.
“Thus, FAs could have acted as a population that diluted NE ancestry in western Eurasia (text S4), as previously suggested (16, 17).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [17]
In Europeans, archaic ancestry is consistent with contributions by a single population of Neanderthals through one or more pulses.
“In Europeans, archaic ancestry is consistent with contributions by a single population of Neanderthals 3 through one or more pulses [4][5][6][7] .”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [6]
Early farmers are partly genetically derived from the previously identified basal Eurasian lineage.
“It has been proposed that the early FAs are partly genetically derived from the previously identified “basal Eurasian” lineage (16, 17, 51).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [17]
The basal Eurasian lineage diverged from other Eurasian hunter-gatherer populations before the latter mixed with Neanderthals, and therefore had a lower Neanderthal ancestry.
“This lineage is thought to have diverged from other Eurasian HG populations before the latter mixed with the NE, and therefore had a lower NE ancestry (16, 17, 51).”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [17]
Cites
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
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
A 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
Evolution and functional impact of rare coding variation from deep sequencing of human exomes
Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. (2012) · Science · doi:10.1126/science.1219240 · Cited by 1,613 · see citing works
Self-citationAncient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
Approximate Bayesian Computation (ABC) in practice
Csilléry, K., Blum, M. G. B., Gaggiotti, O. E., & François, O. (2010) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2010.04.001 · Cited by 1,302 · see citing works
The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107 · see citing works
abc: an R package for approximate Bayesian computation (ABC)
Csilléry, K., François, O., & Blum, M. G. B. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00179.x · Cited by 709 · see citing works
Siva, N. (2008) · Nature Biotechnology · doi:10.1038/nbt0308-256b · Cited by 629 · see citing works
Demographic history and rare allele sharing among human populations
Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G., Clark, A. G., Yu, F., Gibbs, R. A., The 1000 Genomes Project, Bustamante, C. D., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019276108 · Cited by 625 · see citing works
Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Vernot, B., & Akey, J. M. (2014) · Science · doi:10.1126/science.1245938 · Cited by 562 · see citing works
Self-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
Non-linear regression models for Approximate Bayesian Computation
Blum, M. G. B., & François, O. (2009) · Statistics and Computing · doi:10.1007/s11222-009-9116-0 · Cited by 449 · 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
Higher Levels of Neanderthal Ancestry in East Asians than in Europeans
Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S., Gignoux, C., Woerner, A., Hammer, M. F., & Slatkin, M. (2013) · Genetics · doi:10.1534/genetics.112.148213 · Cited by 249 · see citing works
The History of African Gene Flow into Southern Europeans, Levantines, and Jews
Moorjani, P., Patterson, N. J., Hirschhorn, J. N., Keinan, A., Hao, L., Atzmon, G., Burns, E. R., D, H. O. M., Price, A. L., & Reich, D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001373 · Cited by 240 · see citing works
Kim, B. Y., & Lohmueller, K. E. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.029 · Cited by 82 · see citing works
Wang, S., Lachance, J., Tishkoff, S. A., Hey, J., & Xing, J. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt160 · Cited by 34 · see citing works
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
An early modern human from Romania with a recent Neanderthal ancestor
Fu, Q., Hajdinjak, M., Moldovan, O. T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., et al. (2015) · Nature · doi:10.1038/nature14558 · Cited by 802 · 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
Self-citationA 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-citationGenetic 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
The 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
Excavating 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
Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture
Browning, S. R., Browning, B. L., Zhou, Y., Tucci, S., & Akey, J. M. (2018) · Cell · doi:10.1016/j.cell.2018.02.031 · Cited by 381 · see citing works
Self-citationA 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
The 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
Slatkin, M., & Racimo, F. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1524306113 · Cited by 252 · 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
Self-citationDannemann, 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
Population Stratification in Genetic Association Studies
Hellwege, J. N., Keaton, J. M., Giri, A., Gao, X., Edwards, D. R. V., & Edwards, T. L. (2017) · Current Protocols in Human Genetics · doi:10.1002/cphg.48 · Cited by 211 · see citing works
Limits of long-term selection against Neandertal introgression
Petr, M., Pääbo, S., Kelso, J., & Vernot, B. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814338116 · Cited by 211 · see citing works
Self-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
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
Multiple 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
Detecting Long-Term Balancing Selection Using Allele Frequency Correlation
Siewert, K. M., & Voight, B. F. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx209 · Cited by 179 · 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
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
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
Mondal, M., Bertranpetit, J., & Lao, O. (2019) · Nature Communications · doi:10.1038/s41467-018-08089-7 · Cited by 124 · see citing works
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
Schaefer, N. K., Shapiro, B., & Green, R. E. (2021) · Science Advances · doi:10.1126/sciadv.abc0776 · Cited by 106 · see citing works
“However, there is debate over whether this elevated Neanderthal ancestry is due to smaller past population size relative to other groups and the resulting stronger effect of genetic drift (22) or to additional pulses of Neanderthal admixture specific to these populations (9, 29).”
BackgroundEarly history of Neanderthals and Denisovans
Rogers, A. R., Bohlender, R. J., & Huff, C. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706426114 · Cited by 106 · see citing works
Hsieh, P., Woerner, A. E., Wall, J. D., Lachance, J., Tishkoff, S. A., Gutenkunst, R. N., & Hammer, M. F. (2016) · Genome Research · doi:10.1101/gr.196634.115 · Cited by 105 · see citing works
Human evolution: a tale from ancient genomes
Llamas, B., Willerslev, E., & Orlando, L. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0484 · Cited by 100 · see citing works
Understanding rare and common diseases in the context of human evolution
Quintana‐Murci, L. (2016) · Genome biology · doi:10.1186/s13059-016-1093-y · Cited by 97 · see citing works
Pimenoff, V. N., de Oliveira, C. M., & Bravo, I. G. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw214 · Cited by 98 · see citing works
A Comprehensive Map of Genetic Variation in the World’s Largest Ethnic Group—Han Chinese
Chiang, C. W. K., Mangul, S., Robles, C. R., Kretzschmar, W. W., Cai, N., Kendler, K. S., Sankararam, S., & Flint, J. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy170 · Cited by 89 · see citing works
Something old, something borrowed: admixture and adaptation in human evolution
Dannemann, M., & Racimo, F. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.05.009 · Cited by 87 · see citing works
Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years
Li, L., Comi, T. J., Bierman, R., & Akey, J. M. (2024) · Science · doi:10.1126/science.adi1768 · Cited by 84 · see citing works
Self-citationKim, B. Y., & Lohmueller, K. E. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.029 · Cited by 82 · see citing works
The contribution of Neanderthal introgression to modern human traits
Reilly, P. F., Tjahjadi, A., Miller, S. L., Akey, J. M., & Tucci, S. (2022) · Current Biology · doi:10.1016/j.cub.2022.08.027 · Cited by 80 · see citing works
Self-citationSmall Amounts of Archaic Admixture Provide Big Insights into Human History
Vattathil, S., & Akey, J. M. (2015) · Cell · doi:10.1016/j.cell.2015.09.042 · Cited by 74 · see citing works
Self-citationSignatures of archaic adaptive introgression in present-day human populations
Racimo, F., Marnetto, D., & Huerta-Sánchez, E. (2016) · doi:10.1101/045237 · Cited by 200 · see citing works
Model‐based detection and analysis of introgressed Neanderthal ancestry in modern humans
Steinrücken, M., Spence, J. P., Kamm, J. A., Wieczorek, E., & Song, Y. S. (2018) · Molecular Ecology · doi:10.1111/mec.14565 · Cited by 73 · see citing works
Outstanding questions in the study of archaic hominin admixture
Wolf, A. B., & Akey, J. M. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007349 · Cited by 66 · see citing works
Self-citationInsights into Modern Human Prehistory Using Ancient Genomes
Yang, M. A., & Fu, Q. (2018) · Trends in Genetics · doi:10.1016/j.tig.2017.11.008 · Cited by 65 · see citing works
More than a decade of genetic research on the Denisovans
Peyrégne, S., Slon, V., & Kelso, J. F. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00643-4 · Cited by 66 · see citing works
Detecting hybridization using ancient DNA
Schaefer, N. K., Shapiro, B., & Green, R. E. (2016) · Molecular Ecology · doi:10.1111/mec.13556 · Cited by 63 · see citing works
Toward high-resolution population genomics using archaeological samples
Морозова, И., Flegontov, P., Mikheyev, A. S., Bruskin, S. A., Asgharian, H., Пономаренко, П. М., Klyuchnikov, V., GaneshPrasad, A., Prokhortchouk, E., Gankin, Y. V., et al. (2016) · DNA Research · doi:10.1093/dnares/dsw029 · Cited by 58 · see citing works
Advancements and Challenges in Ancient DNA Research: Bridging the Global North–South Divide
Dalal, V., Pasupuleti, N., Chaubey, G., Rai, N., & Shinde, V. S. (2023) · Genes · doi:10.3390/genes14020479 · Cited by 55 · see citing works
The success of failed Homo sapiens dispersals out of Africa and into Asia
Rabett, R. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0436-8 · Cited by 54 · see citing works
Meltzer, D. J. (2021) · Cambridge University Press eBooks · doi:10.1017/9781108632867 · Cited by 63 · see citing works
Kim, B. Y., Wei, X., Fitz‐Gibbon, S. T., Lohmueller, K. E., Ortego, J., Gugger, P. F., & Sork, V. L. (2018) · Molecular Ecology · doi:10.1111/mec.14869 · Cited by 48 · see citing works
Genomic signatures of sex-biased demography: progress and prospects
Webster, T. H., & Sayres, M. A. W. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.08.002 · Cited by 46 · see citing works
Yew, C.-W., Lu, D., Deng, L., Wong, L.-P., Ong, R. T., Lü, Y., Wang, X., Yunus, Y., Aghakhanian, F. F., Mokhtar, S. S., et al. (2018) · Human Genetics · doi:10.1007/s00439-018-1869-0 · Cited by 41 · see citing works
Out of Africa and into Asia: Fossil and genetic evidence on modern human origins and dispersals
Reyes‐Centeno, H. (2016) · Quaternary International · doi:10.1016/j.quaint.2015.11.063 · Cited by 40 · see citing works
Hominin interbreeding and the evolution of human variation
Ko, K. H. (2016) · Journal of Biological Research - Thessaloniki · doi:10.1186/s40709-016-0054-7 · Cited by 40 · see citing works
Harris, A. M., & DeGiorgio, M. (2017) · Human Biology · doi:10.13110/humanbiology.89.1.02 · Cited by 30 · see citing works
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 33 · see citing works
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 · see citing works
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 33 · see citing works
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 29 · see citing works
“These signals of admixture can also be indicative of selection (Tang et al. 2007), past demographic events (Vernot and Akey 2015; Wang et al. 2020), and even disease susceptibility (Rudan 2006; Mautz et al. 2019), demonstrating the value of analyzing admixed individuals.”
BackgroundArchaic 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 28 · see citing works
Evolution, systematics, and the unnatural history of mitochondrial DNA
Schwartz, J. H. (2021) · Mitochondrial DNA Part A · doi:10.1080/24701394.2021.1899165 · Cited by 27 · see citing works
Inferences of African evolutionary history from genomic data
Beltrame, M. H., Rubel, M., & Tishkoff, S. A. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.10.002 · Cited by 26 · see citing works
Were Neanderthals and Homo sapiens ‘good species’?
Meneganzin, A., & Bernardi, M. (2023) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2023.107975 · Cited by 27 · see citing works
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 26 · see citing works
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 23 · see citing works
A Genomic View of the Pleistocene Population History of Asia
Sikora, M. (2017) · Current Anthropology · doi:10.1086/694422 · Cited by 24 · see citing works
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 24 · see citing works
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 22 · see citing works
Sellayah, D. (2019) · Journal of the Endocrine Society · doi:10.1210/js.2018-00363 · Cited by 21 · see citing works
Taskent, O., Lin, Y. L., Patramanis, I., Pavlidis, P., & Gokcumen, O. (2020) · Genetics · doi:10.1534/genetics.120.303167 · Cited by 20 · see citing works
Dispersals Out of Africa and Back to Africa: Modern origins in North Africa
Garcea, E. A. A. (2016) · Quaternary International · doi:10.1016/j.quaint.2016.02.024 · Cited by 20 · see citing works
An evolutionary medicine perspective on Neandertal extinction
Sullivan, A., de Manuel, M., Marquès‐Bonet, T., & Perry, G. H. (2016) · Journal of Human Evolution · doi:10.1016/j.jhevol.2017.03.004 · Cited by 22 · see citing works
Introgression Makes Waves in Inferred Histories of Effective Population Size
Hawks, J. D. (2017) · Human Biology · doi:10.13110/humanbiology.89.1.04 · Cited by 18 · see citing works
Fourcade, T., Goñi, M. F. S., Lahaye, C., Rossignol, L., & Philippe, A. (2022) · Quaternary Research · doi:10.1017/qua.2022.21 · Cited by 17 · see citing works
An Extended Admixture Pulse Model Reveals the Limitations to Human–Neandertal Introgression Dating
Iasi, L. N. M., Ringbauer, H., & Peter, B. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab210 · Cited by 15 · see citing works
Archaic hominin admixture and its consequences for modern humans
Tagore, D., & Akey, J. M. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102280 · Cited by 13 · see citing works
Self-citationThe contribution of ancient hominin genomes from Siberia to our understanding of human evolution
Pääbo, S. (2015) · Herald of the Russian Academy of Sciences · doi:10.1134/s1019331615050081 · Cited by 13 · see citing works
Past human expansions shaped the spatial pattern of Neanderthal ancestry
Quilodrán, C. S., Rio, J., Tsoupas, A., & Currat, M. (2023) · Science Advances · doi:10.1126/sciadv.adg9817 · Cited by 12 · see citing works
Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations
Yermakovich, D., André, M., Brucato, N., Kariwiga, J., Leavesley, M., Pankratov, V., Mondal, M., Ricaut, F.-X., & Dannemann, M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2405889121 · Cited by 12 · see citing works
First Peoples in a New World: Populating Ice Age America
Meltzer, D. J. (2021) · Cited by 12 · see citing works
The genetic structure of the world’s first farmersPreprint
Lazaridis, I., Nadel, D., Rollefson, G. O., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K. A., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/059311 · Cited by 12 · see citing works
Midfacial Morphology and Neandertal–Modern Human Interbreeding
Churchill, S. E., Keys, K., & Ross, A. H. (2022) · Biology · doi:10.3390/biology11081163 · Cited by 11 · see citing works
Further consideration of the curvature of the Neandertal Femur
Chapman, T. J., Sholukha, V. A., Semal, P., Louryan, S., & Jan, S. V. S. (2017) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23334 · Cited by 9 · see citing works
IBD Sharing between Africans, Neandertals, and Denisovans
Povysil, G., & Hochreiter, S. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw234 · Cited by 9 · see citing works
The Search for Ice Age Americans
Meltzer, D. J. (2021) · Cambridge University Press eBooks · doi:10.1017/9781108632867.005 · Cited by 9 · see citing works
RNA viruses drove adaptive introgressions between Neanderthals and modern humansPreprint
Enard, D., & Petrov, D. A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/120477 · Cited by 9 · see citing works
Smith, O., & Gilbert, M. T. P. (2018) · Population genomics · doi:10.1007/13836_2018_17 · Cited by 7 · see citing works
AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data
Schaefer, N. K., Shapiro, B., & Green, R. E. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1613-0 · Cited by 7 · see citing works
Vernot, B., & Pääbo, S. (2018) · Cell · doi:10.1016/j.cell.2018.03.023 · Cited by 7 · see citing works
Self-citationLan, T., & Lindqvist, C. (2018) · Population genomics · doi:10.1007/13836_2017_7 · Cited by 6 · see citing works
Prat, S., Péan, S., Crépin, L., Puaud, S. J., Drucker, D. G., Lázničková‐Galetová, M., van der Plicht, J., Valladas, H., Verna, C., Patou‐Mathis, M., et al. (2018) · Bulletins et Mémoires de la Société d anthropologie de Paris · doi:10.3166/bmsap-2018-0032 · Cited by 6 · see citing works
A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens
Funato, N., Heliövaara, A., & Boeckx, C. A. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.03.012 · Cited by 5 · see citing works
Conceiving of “Them” When Before There Was Only “Us”
Chang, M. L., & Nowell, A. (2020) · Springer eBooks · doi:10.1007/978-3-030-36350-5_13 · Cited by 5 · see citing works
Underrepresented Populations at the Archaic Introgression Frontier
Villanea, F. A., & Witt, K. E. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.821170 · Cited by 5 · see citing works
Bosman, A. M., & Harvati, K. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23844 · Cited by 5 · see citing works
A field theoretic approach to non-equilibrium population genetics in the strong selection regimePreprint
Balick, D. J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.16.524324 · Cited by 5 · see citing works
Archaic adaptive introgression in modern human reproductive genes
Kendall, C., Nooranikhojasteh, A., Parra, E. J., Schillaci, M. A., & Viola, B. (2025) · Communications Biology · doi:10.1038/s42003-025-08682-9 · Cited by 6 · see citing works
Santo, L. N. D., Quilodrán, C. S., & Currat, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad252 · Cited by 4 · see citing works
Applications of Bayesian Skyline Plots and Approximate Bayesian Computation for Human Demography
Villanea, F. A., Kitchen, A., & Kemp, B. M. (2019) · Human Biology · doi:10.13110/humanbiology.91.4.04 · Cited by 4 · see citing works
Palaeogenetics: Dirt, what is it good for? Everything
Linderholm, A. E. (2021) · Current Biology · doi:10.1016/j.cub.2021.06.074 · Cited by 4 · see citing works
A new approach to exploratory data analysis in hominin phylogenetic reconstruction
Gautney, J. R. (2023) · Journal of Human Evolution · doi:10.1016/j.jhevol.2023.103412 · Cited by 3 · see citing works
- Authors
- Vernot, B., & Akey, J. M.
- Affiliations
- University of Washington (US)
- Corresponding author
- Vernot, Benjamin
- Akey, Joshua M.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2015-03
- Volume
- 96
- Issue
- 3
- Pages
- 448-453
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC4375686
- OpenAlex
- W2056921607
- Cited by
- 149
- References
- 19
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 11 · 2023: 10 · 2022: 8 · 2021: 30 · 2020: 9 · 2019: 6 · 2018: 19 · 2017: 15 · 2016: 26 · 2015: 6
- FWCI
- 92.10
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM110068)
- 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 diversity and population structure
- Keywords
- purifying selection, demographic history, gene flow
- MeSH terms
- Animals, Genetics, Population, Humans, Models, Genetic, Genome, White People, Asian People, 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
