Multiple episodes of interbreeding between Neanderthal and modern humans
Open accessAbstract
Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the 'dilution' hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.
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?
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 [7]
The Discussion supports multiple pulses of Neanderthal admixture into Europeans, but says only that the contributing Neanderthal population or populations were relatively closely related; it does not establish a single source population. The Abstract also says a simple single-admixture model does not fit the data, so the paper does not support the claim's allowance for just one pulse. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThese observations suggest that the population-specific haplotype blocks may be the result of more recent population-specific Neanderthal admixture.
“These observations suggest that the population-specific haplotype blocks may be the result of more recent population-specific Neanderthal admixture, as has recently been suggested (26–28, 30).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [30]
When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins (Neanderthals and Denisovans), DNA of archaic ancestry integrated into the genomes of anatomically modern humans.
“When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans.”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Villanea and Schraiber 2019
When AMH migrated into Eurasia, they interbred with archaic hominins, initially with Neanderthals around 60 ka and later with Denisovans.
“When AMH migrated into Eurasia, they interbred with the archaic hominins that were native to the continent, initially with Neanderthals (Green et al. 2010; Villanea and Schraiber 2019) around 60 ka (Sankararaman et al. 2012; Skoglund and Mathieson 2018) and later with Denisovans (Jacobs et al. 2019).”
From Archaic Introgression Shaped Human Circadian Traits (2023) · cites this paper as Villanea and Schraiber 2019
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
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
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
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
Self-citationThe 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
Genomic insights into the origin of farming in the ancient Near East
Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al. (2016) · Nature · doi:10.1038/nature19310 · Cited by 955 · 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
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
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
Kelleher, J., Etheridge, A. M., & McVean, G. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004842 · Cited by 660 · see citing works
A recent bottleneck of Y chromosome diversity coincides with a global change in culturePreprint
Karmin, M., Karmin, M., Kivisild, T., Sayres, M. A. W., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A.-M., Mägi, R., Mitt, M., et al. (2015) · Genome Research · doi:10.1101/gr.186684.114 · Cited by 468 · see citing works
The 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
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-citationScaling Learning Algorithms toward AI
Bengio, Y., & LeCun, Y. (2007) · The MIT Press eBooks · doi:10.7551/mitpress/7496.003.0016 · Cited by 457 · see citing works
Supervised Machine Learning for Population Genetics: A New Paradigm
Schrider, D. R., & Kern, A. D. (2018) · Trends in Genetics · doi:10.1016/j.tig.2017.12.005 · Cited by 453 · 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
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
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
Poznik, G. D., Xue, Y., Mendez, F. L., Willems, T., Massaia, A., Wilson, M. A., Ayub, Q., McCarthy, S., Narechania, A., Kashin, S., et al. (2016) · Nature Genetics · doi:10.1038/ng.3559 · Cited by 318 · see citing works
The landscape of recombination in African Americans
Hinch, A. G., Tandon, A., Patterson, N. J., Song, Y., Rohland, N., Palmer, C. D., Chen, G. K., Wang, K., Buxbaum, S. G., Akylbekova, E. L., et al. (2011) · Nature · doi:10.1038/nature10336 · Cited by 315 · 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
The deleterious mutation load is insensitive to recent population history.
Simons, Y. B., Turchin, M. C., Pritchard, J. K., & Sella, G. (2014) · Nature Genetics · doi:10.1038/ng.2896 · Cited by 279 · 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
Ancient 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
Deep Learning for Population Genetic Inference
Sheehan, S., & Song, Y. S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004845 · Cited by 245 · see citing works
Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation
Jouganous, J., Long, W., Ragsdale, A. P., & Gravel, S. (2017) · Genetics · doi:10.1534/genetics.117.200493 · Cited by 240 · 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
Do, R., Balick, D. J., Li, H., Adzhubei, I. A., Sunyaev, S. R., & Reich, D. (2015) · Nature Genetics · doi:10.1038/ng.3186 · Cited by 208 · see citing works
S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning
Schrider, D. R., & Kern, A. D. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005928 · Cited by 184 · see citing works
Efficiently Inferring the Demographic History of Many Populations With Allele Count Data
Kamm, J., Terhorst, J., Durbin, R. M., & Song, Y. S. (2019) · Journal of the American Statistical Association · doi:10.1080/01621459.2019.1635482 · Cited by 161 · 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
Learning Natural Selection from the Site Frequency Spectrum
Ronen, R., Udpa, N., Halperin, E., & Bafna, V. (2013) · Genetics · doi:10.1534/genetics.113.152587 · Cited by 109 · see citing works
Early 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
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
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
Flow-Based Network Analysis of the Caenorhabditis elegans Connectome
Bacik, K. A., Schaub, M. T., Beguerisse-Díaz, M., Billeh, Y. N., & Barahona, M. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005055 · Cited by 67 · see citing works
Efficiently inferring the demographic history of many populations with allele count dataPreprint
Kamm, J., Terhorst, J., Durbin, R. M., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/287268 · Cited by 37 · see citing works
Mafessoni, F., & Prüfer, K. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1716918114 · Cited by 28 · see citing works
Reply to Mafessoni and Prüfer: Inferences with and without singleton site patterns
Rogers, A. R., Bohlender, R. J., & Huff, C. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717085114 · Cited by 7 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Origins 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
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
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
Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France
Slimak, L., Zanolli, C., Higham, T., Frouin, M., Schwenninger, J., Arnold, L. J., Demuro, M., Douka, K., Mercier, N., Guèrin, G., et al. (2022) · Science Advances · doi:10.1126/sciadv.abj9496 · Cited by 224 · see citing works
The evolution and changing ecology of the African hominid oral microbiome
Yates, J. A. F., Velsko, I. M., Aron, F., Posth, C., Hofman, C. A., Austin, R. M., Parker, C., Mann, A. E., Nägele, K., Arthur, K. W., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021655118 · Cited by 176 · see citing works
Insights into human history from the first decade of ancient human genomics
Liu, Y., Mao, X., Krause, J., & Fu, Q. (2021) · Science · doi:10.1126/science.abi8202 · Cited by 163 · see citing works
Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning
Maasch, J. R. M. A., Torres, M. D. T., Melo, M. C. R., & de la Fuente‐Núñez, C. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.07.001 · Cited by 156 · 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
Using hominin introgression to trace modern human dispersals
Teixeira, J. C., & Cooper, A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1904824116 · Cited by 136 · 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
Predicting geographic location from genetic variation with deep neural networks
Battey, C. J., Ralph, P. L., & Kern, A. D. (2020) · eLife · doi:10.7554/elife.54507 · Cited by 121 · 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
Beyond Reproductive Isolation: Demographic Controls on the Speciation Process
Harvey, M. G., Singhal, S., & Rabosky, D. (2019) · Annual Review of Ecology, Evolution and Systematics · doi:10.1146/annurev-ecolsys-110218-024701 · Cited by 98 · see citing works
Models of archaic admixture and recent history from two-locus statistics
Ragsdale, A. P., & Gravel, S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008204 · Cited by 94 · see citing works
Detecting adaptive introgression in human evolution using convolutional neural networks
Gower, G., Picazo, P. I., Fumagalli, M., & Racimo, F. (2021) · eLife · doi:10.7554/elife.64669 · Cited by 95 · see citing works
Philippine Ayta possess the highest level of Denisovan ancestry in the world
Larena, M., McKenna, J., Sanchez-Quinto, F., Bernhardsson, C., Ebeo, C., Reyes, R., Casel, O., Huang, J.-Y., Hagada, K. P., Guilay, D., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.07.022 · Cited by 93 · see citing works
Archaic hominin introgression into modern human genomes
Gökçümen, Ö. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23951 · Cited by 91 · see citing works
Deep Learning in Population Genetics
Korfmann, K., Gaggiotti, O. E., & Fumagalli, M. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad008 · Cited by 87 · see citing works
Harmonizing hybridization dissonance in conservation
Quilodrán, C. S., Montoya‐Burgos, J. I., & Currat, M. (2020) · Communications Biology · doi:10.1038/s42003-020-1116-9 · Cited by 84 · 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
Timmermann, A. (2020) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2020.106331 · Cited by 84 · see citing works
d’Errico, F., Martí, À. P., Shipton, C., Vraux, E. L., Ndiema, E., Goldstein, S. T., Petraglia, M. D., & Boivin, N. L. (2020) · Journal of Human Evolution · doi:10.1016/j.jhevol.2019.102737 · Cited by 81 · 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
Resolving the “muddle in the middle”: The case for Homo bodoensis sp. nov.
Roksandić, M., Radović, P., Wu, X., & Bae, C. J. (2021) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21929 · Cited by 76 · see citing works
Sanchez, T., Cury, J., Charpiat, G., & Jay, F. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13224 · Cited by 78 · see citing works
Greenbaum, G., Friesem, D. E., Hovers, E., Feldman, M. W., & Kolodny, O. (2018) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2018.12.011 · Cited by 74 · 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
Harnessing deep learning for population genetic inference
Huang, X., Rymbekova, A., Dolgova, O., Lao, Ó., & Kuhlwilm, M. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00636-3 · Cited by 65 · see citing works
Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans
Iasi, L. N. M., Chintalapati, M., Skov, L., Mesa, A. B., Hajdinjak, M., Peter, B. M., & Moorjani, P. (2024) · Science · doi:10.1126/science.adq3010 · Cited by 58 · see citing works
Lombard, M., & Högberg, A. (2021) · Journal of Archaeological Method and Theory · doi:10.1007/s10816-020-09502-6 · Cited by 59 · see citing works
Beyond binaries. Interrogating ancient DNA
Crellin, R. J., & Harris, O. J. T. (2020) · Archaeological Dialogues · doi:10.1017/s1380203820000082 · Cited by 59 · see citing works
Harvati, K., & Ackermann, R. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01875-z · Cited by 59 · see citing works
A Phylogenetic Networks perspective on reticulate human evolution
y Caparrós, M. Á. C., & Prat, S. (2021) · iScience · doi:10.1016/j.isci.2021.102359 · Cited by 50 · see citing works
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
Rinker, D. C., Simonti, C. N., McArthur, E., Shaw, D., Hodges, E., & Capra, J. A. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1261-z · Cited by 44 · see citing works
Key, A., Jarić, I., & Roberts, D. L. (2021) · Humanities and Social Sciences Communications · doi:10.1057/s41599-021-00735-8 · Cited by 45 · see citing works
Nubian Levallois technology associated with southernmost Neanderthals
Blinkhorn, J., Zanolli, C., Compton, T., Groucutt, H. S., Scerri, E. M. L., Crété, L., Stringer, C. B., Petraglia, M. D., & Blockley, S. P. E. (2021) · Scientific Reports · doi:10.1038/s41598-021-82257-6 · Cited by 43 · see citing works
Evolution of Homo in the Middle and Late Pleistocene
Harvati, K., & Reyes‐Centeno, H. (2022) · Journal of Human Evolution · doi:10.1016/j.jhevol.2022.103279 · Cited by 43 · see citing works
Greenbaum, G., Getz, W. M., Rosenberg, N. A., Feldman, M. W., Hovers, E., & Kolodny, O. (2019) · Nature Communications · doi:10.1038/s41467-019-12862-7 · Cited by 42 · see citing works
Coll Macià, M., Skov, L., Peter, B. M., & Schierup, M. H. (2021) · Nature Communications · doi:10.1038/s41467-021-25524-4 · Cited by 33 · 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
Self-citationThe 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
Ahsan, T., Urmi, N. J., & Sajib, A. A. (2020) · PLoS ONE · doi:10.1371/journal.pone.0228000 · Cited by 32 · see citing works
Darney, K., Lautz, L. S., Béchaux, C., Więcek, W., Testai, E., Amzal, B., & Dorne, J. L. C. M. (2021) · Environment International · doi:10.1016/j.envint.2021.106760 · Cited by 27 · see citing works
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 · see citing works
Parallels and discrepancies between non‐native species introductions and human migration
Ahmed, D. A., Sousa, R., Bortolus, A., Aldemir, C., Angeli, N. F., Błońska, D., Briski, E., Britton, J. R., Cano‐Barbacil, C., Clark‐Ginsberg, A., et al. (2025) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.70004 · Cited by 26 · see citing works
Ottenburghs, J., Honka, J., Müskens, G. J. D. M., & Ellegren, H. (2020) · Heredity · doi:10.1038/s41437-020-0322-z · Cited by 25 · see citing works
Paleogenomics of the prehistory of Europe: human migrations, domestication and disease
Serrano, J. G., Ordóñez, A. C., & Fregel, R. (2021) · Annals of Human Biology · doi:10.1080/03014460.2021.1942205 · Cited by 23 · see citing works
Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method
Folk, R. A., Gaynor, M. L., Engle‐Wrye, N. J., O’Meara, B. C., Soltis, P. S., Soltis, P. S., Guralnick, R., Smith, S. A., Grady, C. J., & Okuyama, Y. (2023) · Systematic Biology · doi:10.1093/sysbio/syad018 · Cited by 29 · 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
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 · 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
Self-citationNowell, A. (2023) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-052621-024752 · 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
The MUC19 gene: An evolutionary history of recurrent introgression and natural selection
Villanea, F. A., Peede, D., Kaufman, E. J., Añorve-Garibay, V., Chevy, E. T., Villa-Islas, V., Witt, K. E., Zeloni, R., Marnetto, D., Moorjani, P., et al. (2025) · Science · doi:10.1126/science.adl0882 · Cited by 21 · see citing works
Self-citationJöris, O., Neruda, P., Wiśniewski, A., & Weiß, M. (2022) · Journal of Paleolithic Archaeology · doi:10.1007/s41982-022-00126-8 · Cited by 20 · see citing works
Beyond reasonable doubt: reconsidering Neanderthal aesthetic capacity
Meneganzin, A., & Killin, A. (2024) · Phenomenology and the Cognitive Sciences · doi:10.1007/s11097-024-10003-0 · Cited by 19 · see citing works
Morphological and phylogeographic evidence for budding speciation: an example in hominins
Parins‐Fukuchi, C. (2021) · Biology Letters · doi:10.1098/rsbl.2020.0754 · Cited by 18 · see citing works
Pavón‐Vázquez, C. J., Brennan, I. G., & Keogh, J. S. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa102 · Cited by 18 · see citing works
Carvalho, M. M., & Bicho, N. (2021) · Journal of Quaternary Science · doi:10.1002/jqs.3350 · Cited by 18 · see citing works
Moving beyond the adaptationist paradigm for human evolution, and why it matters
Schroeder, L., & Ackermann, R. (2022) · Journal of Human Evolution · doi:10.1016/j.jhevol.2022.103296 · Cited by 17 · 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
Pomeroy, E. (2023) · Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · doi:10.1016/j.cbpa.2023.111420 · Cited by 16 · see citing works
Initial Upper Palaeolithic lithic industry at Cueva Millán in the hinterlands of Iberia
Sánchez‐Yustos, P., Marín-Arroyo, A. B., Arnold, L. J., Luque, L., Kehl, M., Sáez, J. A. L., Carrancho, Á., Demuro, M., Sanz‐Royo, A., Buckley, M., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-69913-3 · Cited by 16 · see citing works
Vahdati, A. R., Weissmann, J. D., Timmermann, A., de León, M. S. P., & Zollikofer, C. P. E. (2022) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2022.107391 · Cited by 18 · see citing works
Archaic Introgression Shaped Human Circadian Traits
Velazquez-Arcelay, K., Colbran, L. L., McArthur, E., Brand, C. M., Rinker, D. C., Siemann, J. K., McMahon, D. G., & Capra, J. A. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad203 · Cited by 18 · see citing works
“…AMH migrated into Eurasia, they interbred with the archaic hominins that were native to the continent, initially with Neanderthals (Green et al. 2010; Villanea and Schraiber 2019) around 60 ka (Sankararaman et al. 2012; Skoglund and Mathieson 2018) and later with Denisovans (Jacobs et al. 2019).”
BackgroundAn amphibian species pushed out of Britain by a moving hybrid zone
Arntzen, J. W. (2019) · Molecular Ecology · doi:10.1111/mec.15285 · Cited by 15 · see citing works
de Oliveira, E. A., Perez, M. F., Bertollo, L. A. C., Gestich, C. C., Ráb, P., Ezaz, T., de Souza, F. H. S., Viana, P. F., Feldberg, E., de Oliveira, E. H. C., et al. (2020) · Ecography · doi:10.1111/ecog.04874 · Cited by 15 · 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
Weber, G. W., Hershkovitz, I., Gunz, P., Neubauer, S., Ayalon, A., Latimer, B., Bar‐Matthews, M., Yasur, G., Barzilai, O., & May, H. (2019) · Quaternary International · doi:10.1016/j.quaint.2019.10.009 · Cited by 14 · see citing works
The arrival of Homo sapiens in the Near East and Europe
Picin, A., Moroni, A., & Benazzi, S. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-821428-2.00021-4 · Cited by 14 · see citing works
Nugent, C. M., Kess, T., Langille, B. L., Beck, S. V., Duffy, S., Messmer, A., Smith, N. C. P., Lehnert, S. J., Wringe, B. F., Kent, M., et al. (2024) · Journal of Biogeography · doi:10.1111/jbi.14852 · Cited by 14 · see citing works
Schroeder, L. (2020) · American Anthropologist · doi:10.1111/aman.13410 · Cited by 13 · see citing works
ABO Genetic Variation in Neanderthals and Denisovans
Villanea, F. A., Huerta‐Sánchez, E., & Fox, K. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab109 · Cited by 14 · see citing works
Self-citationEstimating population split times and migration rates from historical effective population sizesPreprint
Shchur, V., Brandt, D. Y. C., Il'ina, A. V., & Nielsen, R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.17.496540 · Cited by 15 · 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
Nugent, C. M., Kess, T., Brachmann, M. K., Langille, B. L., Holborn, M. K., Beck, S. V., Smith, N. C. P., Duffy, S., Lehnert, S. J., Wringe, B. F., et al. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13811 · Cited by 12 · see citing works
Reinscheid, R. K., Mafessoni, F., Lüttjohann, A., Jüngling, K., Pape, H., & Schulz, S. (2021) · Peptides · doi:10.1016/j.peptides.2021.170506 · Cited by 12 · see citing works
Blinkhorn, J., Groucutt, H. S., Scerri, E. M. L., Petraglia, M. D., & Blockley, S. P. E. (2021) · Scientific Reports · doi:10.1038/s41598-021-90744-z · Cited by 12 · see citing works
Archaic introgression and the distribution of shared variation under stabilizing selection
Ragsdale, A. P. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011623 · Cited by 11 · see citing works
Kuzmin, Y. V., Slavinsky, V. S., Цыбанков, А. А., & Keates, S. G. (2021) · Journal of Archaeological Research · doi:10.1007/s10814-021-09164-2 · Cited by 11 · see citing works
Revisiting the out of Africa event with a deep-learning approach
Montinaro, F., Pankratov, V., Yelmen, B., Pagani, L., & Mondal, M. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.09.006 · Cited by 11 · 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
Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneckPreprint
Rinker, D. C., Simonti, C., McArthur, E., Shaw, D. M., Hodges, E. C., & Capra, J. A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/533257 · Cited by 11 · see citing works
Tran, L., Sun, C. K., Struck, T. J., Sajan, M., & Gutenkunst, R. N. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae077 · Cited by 10 · see citing works
Brand, C. M., White, F. J., Rogers, A. R., & Webster, T. H. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2200858119 · Cited by 10 · see citing works
Integrating sex-bias into studies of archaic introgression on chromosome X
Chevy, E. T., Huerta‐Sánchez, E., & Ramachandran, S. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010399 · Cited by 10 · see citing works
Methods for detecting introgressed archaic sequences
Sankararaman, S. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.026 · Cited by 10 · see citing works
Genomic determinants of speciationPreprint
Cong, Q., Zhang, J., & Grishin, N. V. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/837666 · Cited by 10 · see citing works
Frahm, E., & Tryon, C. A. (2019) · Journal of Archaeological Science Reports · doi:10.1016/j.jasrep.2019.102060 · Cited by 9 · see citing works
Weissbrod, L., & Weinstein‐Evron, M. (2020) · Journal of Human Evolution · doi:10.1016/j.jhevol.2020.102833 · Cited by 9 · see citing works
Malik, S. A. (2023) · Religions · doi:10.3390/rel14010095 · Cited by 9 · see citing works
Excavating new facts from ancient Hepatitis B virus sequences
Datta, S. (2020) · Virology · doi:10.1016/j.virol.2020.08.002 · Cited by 10 · see citing works
Mugharet el'Aliya: Affinities of an enigmatic north African Aterian maxillary fragment
Röding, C., Stringer, C. B., Lacruz, R. S., & Harvati, K. (2022) · American Journal of Biological Anthropology · doi:10.1002/ajpa.24642 · Cited by 8 · see citing works
Greer, C., Bhakta, H., Ghanem, L., Refai, F. H., Linn, E., & Avella, M. (2020) · Human Reproduction · doi:10.1093/humrep/deaa347 · Cited by 8 · see citing works
Neanderthals: Anatomy, genes, and evolution
Rosas, A., Bastir, M., & García‐Tabernero, A. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-821428-2.00007-x · Cited by 8 · see citing works
Why Are Some Snakes More Terrifying and What Is Behind the Fear?
Frynta, D., Janovcová, M., Elmi, H. S. A., Štolhoferová, I., Rudolfová, V., Rexová, K., Sommer, D., Král, D., Berti, D. A., Landová, E., et al. (2025) · Animals · doi:10.3390/ani15050731 · Cited by 7 · see citing works
Ghosts of extinct apes: genomic insights into African hominid evolution
Foley, R., & Lahr, M. M. (2024) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2023.12.009 · Cited by 7 · see citing works
Encounters with archaic hominins
Mafessoni, F. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0729-6 · Cited by 7 · see citing works
The Hominin Fossil Record from Greece
Harvati, K. (2021) · Springer eBooks · doi:10.1007/978-3-030-68398-6_19 · Cited by 7 · see citing works
Genetics in the X-Men film franchise: mutants as allegories of difference
Grimsted, S. R., Krizner, K. G., Porter, C. D., & Clayton, J. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2023.1331905 · Cited by 7 · see citing works
- Authors
- Villanea, F. A., & Schraiber, J. G.
- Affiliations
- Temple University (US)
- Corresponding author
- Schraiber, Joshua G.
- Venue
- Nature Ecology & Evolution
- Published
- 2018-11-26
- Volume
- 3
- Issue
- 1
- Pages
- 39-44
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC6309227
- OpenAlex
- W2900471700
- Cited by
- 192
- References
- 36
- Citations by year
- 2026: 18 · 2025: 12 · 2024: 21 · 2023: 32 · 2022: 28 · 2021: 39 · 2020: 28 · 2019: 12 · 2018: 2
- FWCI
- 85.66
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R35GM124745)
- 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
- Neanderthal admixture, Neanderthal ancestry, gene flow, demographic models, human migration out of Africa
- MeSH terms
- Animals, Humans, Hybridization, Genetic, Models, Theoretical, Genome, Human, 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
