Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania
Open accessAbstract
Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.
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Cites
LeCun, Y., Bengio, Y., & Hinton, G. (2015) · Nature · doi:10.1038/nature14539 · Cited by 84,126 · see citing works
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works
Markov Chain Monte Carlo in Practice
Gilks, W. R., Richardson, S. T., & Spiegelhalter, D. J. (1995) · Chapman & Hall/CRC eBooks · doi:10.1201/b14835 · Cited by 7,927 · see citing works
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
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
Ancient Admixture in Human History
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848 · see citing works
Inference of human population history from individual whole-genome sequences
Li, H., & Durbin, R. (2011) · Nature · doi:10.1038/nature10231 · Cited by 2,590 · 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
Genetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991 · see citing works
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
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · see citing works
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584 · see citing works
Robust Demographic Inference from Genomic and SNP Data
Excoffier, L., Dupanloup, I., Huerta‐Sánchez, E., Sousa, V. C., & Foll, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003905 · Cited by 1,434 · see citing works
The genetic history of Ice Age Europe
Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., et al. (2016) · Nature · doi:10.1038/nature17993 · Cited by 959 · see citing works
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 aboriginal Australian genome reveals separate human dispersals into Asia
Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., et al. (2011) · Science · doi:10.1126/science.1211177 · Cited by 787 · see citing works
Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock
Soares, P. A., Ermini, L., Thomson, N., Mormina, M., Rito, T., Röhl, A., Salas, A., Oppenheimer, S., Macaulay, V. A., & Richards, M. B. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.05.001 · Cited by 736 · 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
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
A genomic history of Aboriginal Australia
Malaspinas, A.-S., Westaway, M. C., Muller, C., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., et al. (2016) · Nature · doi:10.1038/nature18299 · Cited by 650 · see citing works
Approximate Bayesian Computation
Sunnåker, M., Busetto, A. G., Numminen, E., Corander, J., Foll, M., & Dessimoz, C. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002803 · Cited by 622 · see citing works
Ancient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature · doi:10.1038/nature16544 · Cited by 577 · see citing works
The genome of the offspring of a Neanderthal mother and a Denisovan father
Slon, V., Mafessoni, F., Vernot, B., de Filippo, C., Grote, S., Viola, B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0455-x · Cited by 536 · see citing works
Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
Schlebusch, C. M., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., Munters, A. R., Vicente, M., Steyn, M., Soodyall, H., et al. (2017) · Science · doi:10.1126/science.aao6266 · Cited by 519 · see citing works
Fenner, J. N. (2005) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20188 · Cited by 508 · see citing works
ABC as a flexible framework to estimate demography over space and time: some cons, many pros
Bertorelle, G., Benazzo, A., & Mona, S. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04690.x · Cited by 465 · 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
Genomic analyses inform on migration events during the peopling of Eurasia
Pagani, L., Lawson, D. J., Jagoda, E., Mörseburg, A., Eriksson, A., Mitt, M., Clemente, F., Hudjashov, G., DeGiorgio, M., Saag, L., et al. (2016) · Nature · doi:10.1038/nature19792 · Cited by 447 · see citing works
Reconstructing Prehistoric African Population Structure
Skoglund, P., Thompson, J. C., Prendergast, M. E., Mittnik, A., Sirak, K. A., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Peltzer, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.049 · Cited by 410 · 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
U-series and ESR analyses of bones and teeth relating to the human burials from Skhul
Grün, R., Stringer, C., McDermott, F., Nathan, R., Porat, N., Robertson, S., Taylor, L., Mortimer, G., Eggins, S., & McCulloch, M. (2005) · Journal of Human Evolution · doi:10.1016/j.jhevol.2005.04.006 · Cited by 338 · see citing works
The phenotypic legacy of admixture between modern humans and Neandertals
Simonti, C. N., Vernot, B., Bastarache, L., Bottinger, E., Carrell, D. S., Chisholm, R. L., Crosslin, D. R., Hebbring, S. J., Jarvik, G. P., Kullo, I. J., et al. (2016) · Science · doi:10.1126/science.aad2149 · Cited by 330 · see citing works
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
Posth, C., Wißing, C., Kitagawa, K., Pagani, L., van Holstein, L. A., Racimo, F., Wehrberger, K., Conard, N. J., Kind, C.-J., Bocherens, H., et al. (2017) · Nature Communications · doi:10.1038/ncomms16046 · Cited by 311 · see citing works
Ancestral Origins and Genetic History of Tibetan Highlanders
Lu, D., Lou, H., Yuan, K., Wang, X., Wang, Y., Zhang, C., Lü, Y., Yang, X. W., Deng, L., Zhou, Y., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.07.002 · Cited by 272 · see citing works
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
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
CpG Island Mapping by Epigenome Prediction
Bock, C., Walter, J., Paulsen, M., & Lengauer, T. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030110 · Cited by 190 · see citing works
Boitard, S., Rodríguez, W., Jay, F., Mona, S., & Austerlitz, F. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005877 · Cited by 190 · 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
Mondal, M., Casals, F., Xu, T., Dall'Olio, G. M., Pybus, M., Netea, M. G., Comas, D., Laayouni, H., Li, Q., Majumder, P. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3621 · Cited by 149 · see citing works
Self-citationHsieh, 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
Learning Summary Statistic for Approximate Bayesian Computation via Deep Neural Network
Wong, W. H., Jiang, B., Wu, T.-Y., & Zheng, C. (2017) · Statistica Sinica · doi:10.5705/ss.202015.0340 · Cited by 103 · see citing works
Lapierre, M., Lambert, A., & Achaz, G. (2017) · Genetics · doi:10.1534/genetics.116.192708 · Cited by 91 · see citing works
The Genomic Formation of South and Central AsiaPreprint
Narasimhan, V. M., Patterson, N. J., Moorjani, P., Lazaridis, I., Lipson, M., Mallick, S., Rohland, N., Bernardos, R. L., Kim, A. M., Nakatsuka, N. J., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/292581 · Cited by 85 · 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
Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes
Lipson, M., Loh, P., Sankararaman, S., Patterson, N. J., Berger, B., & Reich, D. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005550 · Cited by 67 · see citing works
Lukić, S., & Hey, J. (2012) · Genetics · doi:10.1534/genetics.112.141846 · Cited by 65 · see citing works
Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing
Wall, J. D. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.04.002 · Cited by 27 · see citing works
Flagged first, then by citations
1 of the 51 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- [22]Prangle, D. in Handbook of Approximate Bayesian Computation (ABC) (eds Sisson, S. A., Fan, Y. & Beaumont, B.) 320 (Taylor & Francis, Abingdon, 2108).
Cited by
Sorted by citations
fastsimcoal2 : demographic inference under complex evolutionary scenarios
Excoffier, L., Marchi, N., Marques, D. A., Matthey‐Doret, R., Gouy, A., & Sousa, V. C. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab468 · Cited by 431 · see citing works
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
Deep learning as a tool for ecology and evolution
Borowiec, M. L., Dikow, R. B., Frandsen, P. B., McKeeken, A. J., Valentini, G., & White, A. E. (2022) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13901 · Cited by 264 · see citing works
Collin, F.-D., Durif, G., Raynal, L., Lombaert, É., Gautier, M., Vitalis, R., Marin, J., & Estoup, A. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13413 · Cited by 184 · 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
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
Ghost Lineages Highly Influence the Interpretation of Introgression Tests
Tricou, T., Tannier, É., & de Vienne, D. M. (2022) · Systematic Biology · doi:10.1093/sysbio/syac011 · Cited by 110 · see citing works
Genome of a middle Holocene hunter-gatherer from Wallacea
Carlhoff, S., Duli, A., Nägele, K., Nur, M., Skov, L., Sumantri, I., Oktaviana, A. A., Hakim, B., Burhan, B., Syahdar, F. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03823-6 · Cited by 104 · see citing works
Deep Learning for Voltammetric Sensing in a Living Animal Brain
Xue, Y., Ji, W., Jiang, Y. Y., Yu, P., & Mao, L. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202109170 · Cited by 103 · see citing works
Ghost Introgression: Spooky Gene Flow in the Distant Past
Ottenburghs, J. (2020) · BioEssays · doi:10.1002/bies.202000012 · Cited by 98 · 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
Lorente-Galdos, B., Lao, O., Serra-Vidal, G., Santpere, G., Kuderna, L. F. K., Arauna, L. R., Fadhlaoui-Zid, K., Pimenoff, V. N., Soodyall, H., Zalloua, P., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1684-5 · Cited by 77 · see citing works
Yang, F., Zuo, R., & Kreuzer, O. P. (2024) · Earth-Science Reviews · doi:10.1016/j.earscirev.2024.104941 · Cited by 90 · see citing works
The genomic history of the Aegean palatial civilizations
Clemente, F., Unterländer, M., Dolgova, O., Amorim, C. E. G., Coroado-Santos, F., Neuenschwander, S., Ganiatsou, E., Dávalos, D. I. C., Anchieri, L., Michaud, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.039 · Cited by 77 · 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
Inference of natural selection from ancient DNA
Dehasque, M., Ávila‐Arcos, M. C., Díez‐del‐Molino, D., Fumagalli, M., Guschanski, K., Lorenzen, E. D., Malaspinas, A., Marquès‐Bonet, T., Martin, M. D., Murray, G. G. R., et al. (2020) · Evolution Letters · doi:10.1002/evl3.165 · Cited by 70 · 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 68 · see citing works
Teixeira, J. C., Jacobs, G. S., Stringer, C., Tuke, J., Hudjashov, G., Purnomo, G. A., Sudoyo, H., Cox, M. P., Tobler, R., Turney, C. S. M., et al. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01408-0 · Cited by 51 · see citing works
Barnett, R., Westbury, M. V., Sandoval‐Velasco, M., Vieira, F. G., Jeon, S., Zazula, G. D., Martin, M. D., Ho, S. Y. W., Mather, N., Gopalakrishnan, S., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.09.051 · Cited by 51 · see citing works
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0
Yuan, K., Ni, X., Liu, C., Pan, Y., Deng, L., Zhang, R., Gao, Y., Ge, X., Liu, J., Ma, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26503-5 · Cited by 42 · see citing works
Inferring archaic introgression from hominin genetic data
Gopalan, S., Atkinson, E. G., Buck, L. T., Weaver, T. D., & Henn, B. M. (2021) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21895 · Cited by 37 · see citing works
Congruent evolutionary responses of European steppe biota to late Quaternary climate change
Kirschner, P., Perez, M. F., Záveská, E., Sanmartín, I., Marquer, L., Schlick-Steiner, B. C., Álvarez, N., Arthofer, W., Frajman, B., Gamisch, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29267-8 · Cited by 37 · see citing works
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528 · Cited by 35 · 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
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
A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions
Loewenthal, G., Rapoport, D., Avram, O., Moshe, A., Wygoda, E., Itzkovitch, A., Israeli, O., Azouri, D., Cartwright, R. A., Mayrose, I., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab266 · Cited by 30 · see citing works
Modeling colorectal cancer evolution
Niida, A., Mimori, K., Shibata, T., & Miyano, S. (2021) · Journal of Human Genetics · doi:10.1038/s10038-021-00930-0 · Cited by 27 · see citing works
Toward a clearer view into human prehistory
Linden, M. V. (2019) · Science · doi:10.1126/science.aaw8020 · Cited by 27 · see citing works
Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species
Zhang, W.-P., Ding, Y.-Z., Cao, Y., Li, P., Yang, Y., Pang, X.-X., Bai, W., & Zhang, D.-Y. (2024) · The Plant Journal · doi:10.1111/tpj.16859 · Cited by 22 · see citing works
Componentwise approximate Bayesian computation via Gibbs-like steps
Clarté, G., Robert, C. P., Ryder, R., & Stoehr, J. (2020) · Biometrika · doi:10.1093/biomet/asaa090 · Cited by 24 · see citing works
Perez, M. F., Bonatelli, I. A. S., Romeiro‐Brito, M., Franco, F. F., Taylor, N. P., ZAPPI, D. C., & Moraes, E. M. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13534 · Cited by 22 · see citing works
Hominin diversity in East Asia during the Middle Pleistocene: A premolar endostructural perspective
Pan, L., Dumoncel, J., Mazurier, A., & Zanolli, C. (2020) · Journal of Human Evolution · doi:10.1016/j.jhevol.2020.102888 · Cited by 22 · see citing works
Martín‐Perea, D., Courtenay, L. A., Domingo, M. S., & Morales, J. (2020) · PeerJ · doi:10.7717/peerj.8767 · 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
Chromosome‐scale inference of hybrid speciation and admixture with convolutional neural networks
Blischak, P. D., Barker, M. S., & Gutenkunst, R. N. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13355 · Cited by 19 · see citing works
Deep Learning for Voltammetric Sensing in a Living Animal Brain
Xue, Y., Ji, W., Jiang, Y. Y., Yu, P., & Mao, L. (2021) · Angewandte Chemie · doi:10.1002/ange.202109170 · Cited by 17 · see citing works
von Thaden, A., Cocchiararo, B., Mueller, S. A., Reiners, T. E., Reinert, K., Tuchscherer, I., Janke, A., & Nowak, C. (2021) · Ecology and Evolution · doi:10.1002/ece3.8385 · Cited by 15 · see citing works
Skeletal remains of a Pleistocene modern human (Homo sapiens) from Sulawesi
Brumm, A., Bulbeck, D., Hakim, B., Burhan, B., Oktaviana, A. A., Sumantri, I., Zhao, J., Aubert, M., Sardi, R., McGahan, D. P., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0257273 · Cited by 16 · see citing works
Shock wave hydrodynamics of nano-carbons
Chinke, S. L., Sandhu, I. S., Bhave, T. M., & Alegaonkar, P. S. (2021) · Materials Chemistry and Physics · doi:10.1016/j.matchemphys.2021.124337 · Cited by 15 · see citing works
Ebdon, S., Laetsch, D. R., Vila, R., Baird, S. J. E., & Lohse, K. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011655 · Cited by 15 · see citing works
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Schroeder, L. (2020) · American Anthropologist · doi:10.1111/aman.13410 · Cited by 13 · see citing works
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Self-citationVaill, M., Kawanishi, K., Varki, N. M., Gagneux, P., & Varki, A. P. (2023) · Physiological Reviews · doi:10.1152/physrev.00040.2021 · Cited by 13 · see citing works
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Self-citationTran, 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
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Musker, S. D., Pirie, M. D., & Nürk, N. M. (2024) · Molecular Ecology · doi:10.1111/mec.17505 · Cited by 10 · see citing works
Perez, M. F., & Gascuel, O. (2025) · Systematic Biology · doi:10.1093/sysbio/syaf082 · 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
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Kulkarni, S., Krell, M. M., Nabarro, S., & Moritz, C. A. (2022) · ACM Journal on Emerging Technologies in Computing Systems · doi:10.1145/3471188 · Cited by 9 · see citing works
Satta, Y., Zheng, W., Nishiyama, K. V., Iwasaki, R. L., Hayakawa, T., Fujito, N. T., & Takahata, N. (2019) · Genes & Genetic Systems · doi:10.1266/ggs.19-00012 · Cited by 9 · see citing works
Serradell, J. M., Lorenzo-Salazar, J. M., Flores, C., Lao, Ó., & Comas, D. (2024) · Genome biology · doi:10.1186/s13059-024-03341-4 · Cited by 8 · see citing works
Population genomics advances in frontier ethnic minorities in China
Chen, H., & Xu, S. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2659-2 · Cited by 7 · see citing works
A History of Humanity: The Evolution of the Human System
Manning, P. M. (2020) · Cited by 7 · see citing works
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Taufik, L., Teixeira, J. C., Llamas, B., Sudoyo, H., Tobler, R., & Purnomo, G. A. (2022) · Genes · doi:10.3390/genes13122373 · Cited by 6 · see citing works
Quelin, A., Austerlitz, F., & Jay, F. (2025) · Heredity · doi:10.1038/s41437-025-00773-x · Cited by 5 · see citing works
Guez, J., Achaz, G., Bienvenu, F., Cury, J., Toupance, B., Heyer, É., Jay, F., & Austerlitz, F. (2023) · Genetics · doi:10.1093/genetics/iyad007 · Cited by 5 · 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
Early male and female footprints of modern humans across Eurasia and Australasia.
Cabrera, V. M. (2024) · Medical Research Archives · doi:10.18103/mra.v12i8.5552 · Cited by 3 · see citing works
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Mondal, M., André, M., Pathak, A. K., Brucato, N., Ricaut, F., Metspalu, M., & Eriksson, A. (2025) · Nature Communications · doi:10.1038/s41467-025-61661-w · Cited by 4 · see citing works
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Homola, J. J., Robinson, J. D., Kanefsky, J., Stott, W., Whelan, G., & Scribner, K. T. (2021) · Journal of Great Lakes Research · doi:10.1016/j.jglr.2021.08.008 · Cited by 4 · see citing works
Maceda, I., & Lao, Ó. (2021) · Genes · doi:10.3390/genes13010044 · Cited by 4 · see citing works
Maceda, I., Álvarez‐Álvarez, M. M., Athanasiadis, G. I., Tonda, R., Camps, J., Beltrán, S., Camps, A., Fàbrega, J., Felisart, J., Grané, J., et al. (2021) · European Journal of Human Genetics · doi:10.1038/s41431-021-00875-0 · Cited by 3 · see citing works
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Svetec, N., Lee, U., & Zhao, L. (2026) · Trends in Genetics · doi:10.1016/j.tig.2026.01.013 · Cited by 2 · see citing works
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Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.003 · Cited by 2 · see citing works
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Matisoo-Smith, E. A., & Gosling, A. L. (2021) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780190095611.013.11 · Cited by 2 · see citing works
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Kulkarni, S., & Moritz, C. A. (2023) · IEEE Transactions on Parallel and Distributed Systems · doi:10.1109/tpds.2023.3238045 · Cited by 2 · see citing works
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Diederich, N. J., Brüne, M., Allen, J. S., Bender, N., Bruner, E., Changeux, J., Calì, C., Dolgova, O., Grünewald, A., Konopka, G., et al. (2025) · Annals of Neurology · doi:10.1002/ana.78030 · Cited by 1 · see citing works
Norman, K., O’Connor, S., & Bird, M. I. (2021) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780190095611.013.8 · Cited by 1 · see citing works
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Smith, T. (2022) · BioCosmos · doi:10.2478/biocosmos-2022-0003 · Cited by 1 · see citing works
Plaza, F., & Araya, H. (2024) · Progress In Oceanography · doi:10.1016/j.pocean.2023.103190 · Cited by 1 · see citing works
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Dolgova, O., & Lao, Ó. (2024) · doi:10.1093/med/9780197676592.003.0007 · Cited by 1 · see citing works
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Witt, K. E., & Villanea, F. A. (2024) · American Journal of Biological Anthropology · doi:10.1002/ajpa.70010 · Cited by 1 · see citing works
Inferring state‐dependent diversification rates using approximate Bayesian computation
Xie, S., Valente, L., & Etienne, R. S. (2026) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70240 · Cited by 1 · see citing works
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Guimarães, S. W. F., & Silva Hilton, P. (2020) · Anthropological Review · doi:10.2478/anre-2020-0008 · Cited by 1 · see citing works
Bocicor, M. I., Szuhai, I.-M., Pop, E.-L., & Mircea, I.-G. (2020) · International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC) · doi:10.1109/synasc51798.2020.00036 · Cited by 1 · see citing works
Using image-based haplotype alignments to map global adaptation of SARS-CoV-2Preprint
Ouellette, T. W., Shaw, J., & Awadalla, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.13.426571 · Cited by 1 · see citing works
Musker, S. D., Pirie, M. D., & Nürk, N. M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.19.549682 · Cited by 1 · see citing works
Tracing the Neanderthal–Modern Human hybrid zone using paleogenomic dataPreprint
Santo, L. N. D., Quilodrán, C. S., Cerrito, P., & Currat, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.06.697899 · Cited by 1 · see citing works
A ‘Denisovan’ genetic history of recent human evolutionPreprint
Teixeira, J. C., & Cooper, A. (2019) · doi:10.7287/peerj.preprints.27526v1
Human origin and migration deciphered from a novel genomic footprints of mitochondrial sequencesPreprint
Mahapatra, A., & Mukherjee, J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/848341
Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast AsiaPreprint
Teixeira, J. C., Jacobs, G. S., Stringer, C. B., Tuke, J., Hudjashov, G., Purnomo, G. A., Sudoyo, H., Cox, M. P., Tobler, R., TURNEY, C. S. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.24.219048
Improving Approximate Bayesian Computation with Pre-judgment Rule
Wang, Y., Yu, X., Qin, P., Chai, R., & Qiao, G. (2020) · Communications in computer and information science · doi:10.1007/978-981-15-7981-3_15
Society: Network versus Hierarchy
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.007
From Global Networks to Capitalism
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.009
Efficient State-space Exploration in Massively Parallel Simulation Based InferencePreprint
Kulkarni, S., & Moritz, C. A. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2106.15508
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.002
Epidemiological Parameter Sensitivity In Covid-19 Dynamics And EstimationPreprint
Bhadana, J., & Singh, R. K. B. (2021) · Research Square · doi:10.21203/rs.3.rs-985686/v1
An etiology of human modernity
Bednarik, R. G. (2021) · Anthropological Review · doi:10.2478/anre-2021-0020
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.008
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.004
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.001
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.010
Manning, P. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108784528.015
- Authors
- Mondal, M., Bertranpetit, J., & Lao, O.
- Affiliations
- University of Tartu (EE)
- Universitat Pompeu Fabra (ES)
- Corresponding author
- Bertranpetit, Jaume
- Venue
- Nature Communications
- Published
- 2019-01-16
- Volume
- 10
- Issue
- 1
- Pages
- 246-246
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6335398
- OpenAlex
- W2909640254
- Cited by
- 124
- References
- 51
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 11 · 2023: 9 · 2022: 15 · 2021: 29 · 2020: 38 · 2019: 9
- FWCI
- 13.59
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
- Funders
- Centres de Recerca de Catalunya
- European Commission (2014‐2020, 2020 ‘, 2014-2020.4.01.16-0030)
- Generalitat de Catalunya (GRC 2017 SGR 937, 2017-SGR, MDM-2014-0370)
- Ministerio de Asuntos Económicos y Transformación Digital, Gobierno de España (RYC-2013-14797, MDM-2014-0370, BFU2015-68759-P)
- Instituto de Salud Carlos III (MDM-2014-0370, 2014/2020)
- European Regional Development Fund (BFU2016, 2014-2020’, 2014-2020.4.01.16-0030, MDM-2014-0370, 14797, BFU2016-77961-P)
- Agencia Estatal de Investigación (MDM-2014-0370, BFU2016-77961-P)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- archaic introgression, Neanderthal introgression, Denisovan introgression, approximate Bayesian computation, dispersal out of Africa, human evolution
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