Multiple Deeply Divergent Denisovan Ancestries in Papuans
Open accessAbstract
Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.
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?
Recent studies have shown the existence of genetic structure characterising the Indonesian archipelago, with Papuan-and thus, Denisovan-ancestry showing a marked west to east cline.
“Recent studies have shown the existence of genetic structure characterising the Indonesian archipelago, with Papuan—and thus, Denisovan—ancestry showing a marked west to east cline [6, 53].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [6]
Denisovan-like ancestry is the result of multiple introgression events from different source populations.
“We find support for the hypothesis that Denisovan-like ancestry is the result of multiple introgression events from different source populations (9, 10).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [10]
Prior studies have suggested that Denisovan-like haplotype blocks in humans have two or three distinct sources with different levels of divergence to the Denisovan genome, with the best-matching haplotype blocks in East Asia.
“Prior studies have suggested that Denisovan-like haplotype blocks in humans have two or three distinct sources with different levels of divergence to the Denisovan genome, with the best-matching haplotype blocks in East Asia (9, 10).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [10]
Denisovan components in Papuans exhibit deep divergence from the reference Altai Denisovan genome, providing evidence for multiple Denisovan introgression events across time and space.
“these components exhibit a deep divergence from the reference Altai Denisovan genome, providing strong evidence for the occurrence of multiple Denisovan introgression events across time and space [6, 7].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [6]
The filtering criteria ensure that only variants with a high likelihood of being truly introgressed are considered.
“While our analyses focus on a small subset of introgressed variants identified by [6], our filtering criteria ensure that we only consider variants with a high likelihood of being truly introgressed.”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [6]
Cites
Scikit-learn: Machine Learning in Python
Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Müller, A., Nothman, J., Louppe, G., et al. (2012) · arXiv · doi:10.48550/arxiv.1201.0490 · Cited by 71,016 · see citing works
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.1111/j.1558-5646.1984.tb05657.x · Cited by 18,909 · 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
Second-generation PLINK: rising to the challenge of larger and richer datasets
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015) · Gigascience · doi:10.1186/s13742-015-0047-8 · Cited by 12,709 · see citing works
Estimating F-Statistics for the Analysis of Population Structure
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.2307/2408641 · Cited by 11,023 · see citing works
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799 · see citing works
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248 · see citing works
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587 · see citing works
Statsmodels: Econometric and Statistical Modeling with Python
Seabold, S., & Perktold, J. (2010) · Proceedings of the Python in Science Conferences · doi:10.25080/majora-92bf1922-011 · Cited by 6,673 · see citing works
Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,283 · see citing works
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280 · see citing works
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,150 · see citing works
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438 · 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
Robust relationship inference in genome-wide association studies
Manichaikul, A., Mychaleckyj, J. C., Rich, S. S., Daly, K., Sale, M., & Chen, W.-M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq559 · Cited by 3,541 · 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
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
Self-citationA high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
Scaling accurate genetic variant discovery to tens of thousands of samplesPreprint
Poplin, R. E., Ruano-Rubio, V., DePristo, M. A., Fennell, T. J., Carneiro, M. O., der Auwera, G. A. V., Kling, D. E., Gauthier, L. D., Levy‐Moonshine, A., Roazen, D., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/201178 · Cited by 1,891 · 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
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
Self-citationNew fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens.
Hublin, J.-J., Ben-Ncer, A., Bailey, S. E., Freidline, S. E., Neubauer, S., Skinner, M. M., Bergmann, I., Le Cabec, A., Benazzi, S., Harvati, K., et al. (2017) · Nature · doi:10.1038/nature22336 · Cited by 1,347 · see citing works
Inference of Population Structure using Dense Haplotype Data
Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188 · see citing works
Self-citationA new small-bodied hominin from the Late Pleistocene of Flores, Indonesia.
Brown, P., Sutikna, T., Morwood, M. J., Soejono, R. P., Jatmiko, Wayhu Saptomo, E., & Awe Due, R. (2004) · Nature · doi:10.1038/nature02999 · Cited by 1,075 · see citing works
Stratigraphic placement and age of modern humans from Kibish, Ethiopia
McDougall, I., Brown, F. H., & Fleagle, J. G. (2005) · Nature · doi:10.1038/nature03258 · Cited by 1,023 · see citing works
Robust and scalable inference of population history from hundreds of unphased whole genomes
Terhorst, J., Kamm, J., & Song, Y. S. (2016) · Nature Genetics · doi:10.1038/ng.3748 · Cited by 950 · see citing works
RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference
Maples, B. K., Gravel, S., Kenny, E. E., & Bustamante, C. D. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.020 · Cited by 900 · see citing works
The timing and spatiotemporal patterning of Neanderthal disappearance
Higham, T., Douka, K., Wood, R. E., Ramsey, C. B., Brock, F., Basell, L., Camps, M., Valbuena, Á. A., Preysler, J. B., Ruíz, C. B., et al. (2014) · Nature · doi:10.1038/nature13621 · Cited by 898 · 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
Hofreiter, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.23.4793 · Cited by 684 · see citing works
Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania
Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.09.005 · Cited by 656 · see citing works
Self-citationA 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
Self-citationSensitive detection of chromosomal segments of distinct ancestry in admixed populations
Price, A. L., Tandon, A., Patterson, N., Barnes, K. C., Rafaels, N., Ruczinski, I., Beaty, T. H., Mathias, R., Reich, D., & Myers, S. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000519 · Cited by 539 · see citing works
The shaping of modern human immune systems by multiregional admixture with archaic humans
Abi-Rached, L., Jobin, M. J., Kulkarni, S., McWhinnie, A., Dalva, K., Gragert, L., Babrzadeh, F., Gharizadeh, B., Luo, M., Plummer, F. A., et al. (2011) · Science · doi:10.1126/science.1209202 · Cited by 537 · see citing works
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
The prehistoric peopling of Southeast Asia
McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J. V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente Castro, C., et al. (2018) · Science · doi:10.1126/science.aat3628 · Cited by 517 · 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
Widespread 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
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
Self-citationBarker, G., Barton, H. J., Bird, M. I., Daly, P., Datan, I., Dykes, A. P., Farr, L., Gilbertson, D. D., Harrisson, B., Hunt, C. O., et al. (2006) · Journal of Human Evolution · doi:10.1016/j.jhevol.2006.08.011 · Cited by 438 · see citing works
Ancient genomes document multiple waves of migration in Southeast Asian prehistory
Lipson, M., Cheronet, O., Mallick, S., Rohland, N., Oxenham, M. F., Pietrusewsky, M., Pryce, T. O., Willis, A., Matsumura, H., Buckley, H. R., et al. (2018) · Science · doi:10.1126/science.aat3188 · Cited by 420 · see citing works
Genomic insights into the peopling of the Southwest Pacific
Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., Clark, G. R., Reepmeyer, C., Petchey, F., Fernandes, D., et al. (2016) · Nature · doi:10.1038/nature19844 · Cited by 414 · see citing works
Self-citationHaplotype Estimation Using Sequencing Reads
Delaneau, O., Howie, B., Cox, A. J., Zagury, J., & Marchini, J. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.09.002 · Cited by 396 · 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
On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure
Ferrer-Admetlla, A., Liang, M., Korneliussen, T. S., & Nielsen, R. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu077 · Cited by 362 · see citing works
The genetic structure of Pacific Islanders
Friedlaender, J. S., Friedlaender, F. R., Reed, F. A., Kidd, K. K., Kidd, J. R., Chambers, G. K., Lea, R. A., Loo, J.-H., Koki, G., Hodgson, J. A., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.0040019 · Cited by 359 · see citing works
Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia
Sutikna, T., Tocheri, M. W., Morwood, M. J., Saptomo, E. W., Jatmiko, Awe, R. D., Wasisto, S., Westaway, K. E., Aubert, M., Li, B., et al. (2016) · Nature · doi:10.1038/nature17179 · Cited by 330 · see citing works
Genomic structure in Europeans dating back at least 36,200 years
Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., et al. (2014) · Science · doi:10.1126/science.aaa0114 · Cited by 315 · see citing works
Population Genetics Models of Local Ancestry
Gravel, S. (2012) · Genetics · doi:10.1534/genetics.112.139808 · Cited by 311 · see citing works
Genetic evidence for archaic admixture in Africa
Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C., & Wall, J. D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109300108 · Cited by 304 · see citing works
Papuan Pasts: Cultural, linguistic and biological histories of Papuan-speaking peoples
Pawley, A., Attenborough, R., Golson, J., & Hide, R. L. (2005) · ANU Open Research (Australian National University) · doi:10.15144/pl-572 · Cited by 303 · see citing works
Estimating the mutation load in human genomes
Henn, B. M., Botigué, L. R., Bustamante, C. D., Clark, A. G., & Gravel, S. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3931 · Cited by 281 · see citing works
Possible Ancestral Structure in Human Populations
Plagnol, V., & Wall, J. D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020105 · Cited by 275 · see citing works
The Global Origins and Development of Seafaring
Callaghan, R. T. (2011) · The Journal of Island and Coastal Archaeology · doi:10.1080/15564894.2011.582072 · Cited by 273 · 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
When did <i>Homo sapiens</i> first reach Southeast Asia and Sahul?
O’Connell, J. F., Allen, J., Williams, M. A. J., Williams, A. N., Turney, C. S. M., Spooner, N. A., Kamminga, J., Brown, G., & Cooper, A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1808385115 · Cited by 236 · see citing works
Geographic variation in human mitochondrial DNA from Papua New Guinea.
Stoneking, M., Jorde, L. B., Bhatia, K., & Wilson, A. C. (1990) · Genetics · doi:10.1093/genetics/124.3.717 · Cited by 209 · see citing works
Self-citationPhysiological and Genetic Adaptations to Diving in Sea Nomads
Ilardo, M. A., Moltke, I., Korneliussen, T. S., Cheng, J. Y., Stern, A. J., Racimo, F., Damgaard, P. D. B., Sikora, M., Seguin‐Orlando, A., Rasmussen, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.054 · Cited by 200 · see citing works
Complex Patterns of Admixture across the Indonesian Archipelago
Hudjashov, G., Karafet, T. M., Lawson, D. J., Downey, S., Savina, O., Sudoyo, H., Lansing, J. S., Hammer, M. F., & Cox, M. P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx196 · Cited by 191 · see citing works
Self-citationAncestry-specific recent effective population size in the Americas
Browning, S. R., Browning, B. L., Daviglus, M. L., Durazo-Arvizu, R. A., Schneiderman, N., Kaplan, R. C., & Laurie, C. C. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007385 · Cited by 187 · see citing works
Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments
Gittelman, R. M., Schraiber, J. G., Vernot, B., Mikacenic, C., Wurfel, M. M., & Akey, J. M. (2016) · Current Biology · doi:10.1016/j.cub.2016.10.041 · Cited by 181 · see citing works
Earliest known hominin activity in the Philippines by 709 thousand years ago
Ingicco, T., van den Bergh, G. D., Jago-on, C., Bahain, J., Chacón, M. G., Amano, N., Forestier, H., King, C., Manalo, K., Nomade, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0072-8 · Cited by 155 · see citing works
35,000-year-old sites in the rainforests of West New Britain, Papua New Guinea
Pavlides, C., & Gosden, C. (1994) · Antiquity · doi:10.1017/s0003598x00047104 · 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-citationA working model of the deep relationships of diverse modern human genetic lineages outside of Africa
Lipson, M., & Reich, D. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw293 · Cited by 145 · see citing works
Detecting ancient admixture and estimating demographic parameters in multiple human populations.
Wall, J., Lohmueller, K., & Plagnol, V. (2009) · Molecular biology and evolution · doi:10.1093/molbev/msp096 · Cited by 141 · see citing works
Detecting archaic introgression using an unadmixed outgroup
Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, M. H., & Durbin, R. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007641 · Cited by 125 · see citing works
Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species
Alves, T. D., Mairal, J., & Blum, M. G. B. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy126 · Cited by 123 · see citing works
The Lengths of Admixture Tracts
Liang, M., & Nielsen, R. (2014) · Genetics · doi:10.1534/genetics.114.162362 · Cited by 122 · see citing works
A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea
Bergström, A., Oppenheimer, S., Mentzer, A. J., Auckland, K., Robson, K., Attenborough, R., Alpers, M. P., Koki, G., Pomat, W. S., Siba, P., et al. (2017) · Science · doi:10.1126/science.aan3842 · Cited by 111 · see citing works
Novel human vomeronasal receptor-like genes reveal species-specific families
Rodríguez, I., & Mombaerts, P. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00909-0 · Cited by 103 · see citing works
Jinam, T. A., Phipps, M. E., Aghakhanian, F., Majumder, P. P., Datar, F., Stoneking, M., Sawai, H., Nishida, N., Tokunaga, K., Kawamura, S., et al. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx118 · Cited by 103 · see citing works
Self-citationArchaic adaptive introgression in <i>TBX15/WARS2</i>
Racimo, F., Gokhman, D., Fumagalli, M., Ko, A., Hansen, T., Moltke, I., Albrechtsen, A., Carmel, L., Huerta-Sánchez, E., & Nielsen, R. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw283 · Cited by 101 · see citing works
Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., et al. (2018) · Science · doi:10.1126/science.aar8486 · Cited by 97 · see citing works
Self-citationNarasimhan, V. M., Rahbari, R., Scally, A., Wüster, A., Mason, D., Xue, Y., Wright, J., Trembath, R. C., Maher, E. R., van Heel, D. A., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00323-y · Cited by 89 · see citing works
Yokoyama, Y., Falguères, C., Sémah, F., Jacob, T., & Grün, R. (2008) · Journal of Human Evolution · doi:10.1016/j.jhevol.2008.01.006 · Cited by 80 · see citing works
Cox, M. P., Karafet, T. M., Lansing, J. S., Sudoyo, H., & Hammer, M. F. (2010) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2009.2041 · Cited by 60 · see citing works
Self-citationHayakawa, A., Leonard, D. M., Murphy, S. T., Hayes, S. J., Soto, M. C., Fogarty, K., Standley, C., Bellve, K., Lambright, D., Mello, C., et al. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0508832103 · Cited by 58 · see citing works
Swadling, P., & Hide, R. L. (2005) · ANU Open Research (Australian National University) · Cited by 47 · see citing works
Isoform-specific Regulation of Akt Signaling by the Endosomal Protein WDFY2
Walz, H. A., Shi, X., Chouinard, M., Bue, C. A., Navaroli, D. M., Hayakawa, A., Zhou, Q. L., Nadler, J., Leonard, D. M., & Corvera, S. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.110536 · Cited by 42 · see citing works
Akt‐ and Foxo1‐interacting WD‐repeat‐FYVE protein promotes adipogenesis
Fritzius, T., & Moelling, K. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.67 · Cited by 36 · see citing works
A test for ancient selective sweeps and an application to candidate sites in modern humans
Racimo, F., Kuhlwilm, M., & Slatkin, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu255 · Cited by 30 · see citing works
Coalescent simulation in continuous space
Kelleher, J., Barton, N., & Etheridge, A. M. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt067 · Cited by 30 · 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
Pleistocene Migration and Colonization in the Indo-Pacific region
O’Connor, S. (2010) · ANU Open Research (Australian National University) · Cited by 21 · see citing works
Offline: Indonesia—unravelling the mystery of a nation
Horton, R. C. (2016) · The Lancet · doi:10.1016/s0140-6736(16)00544-4 · Cited by 14 · see citing works
Yasukochi, Y., & Ohashi, J. (2016) · Immunogenetics · doi:10.1007/s00251-016-0952-8 · Cited by 9 · see citing works
Henningsson, S., Hovey, D., Vass, K., Walum, H., Sandnabba, K., Santtila, P., Jern, P., & Westberg, L. (2017) · Translational Psychiatry · doi:10.1038/tp.2017.70 · Cited by 8 · see citing works
No evidence for unknown archaic ancestry in South Asia
Skoglund, P., Mallick, S., Patterson, N., & Reich, D. (2018) · Nature Genetics · doi:10.1038/s41588-018-0097-9 · Cited by 8 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Insights into human genetic variation and population history from 929 diverse genomes
Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020 · see citing works
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
Pan-genomics in the human genome era
Sherman, R. M., & Salzberg, S. L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0210-7 · Cited by 364 · see citing works
Kaufman, D. A., & Himmelmann, N. P. (2024) · Oxford University Press eBooks · doi:10.1093/oso/9780198807353.003.0042 · Cited by 263 · see citing works
Genomic insights into population history and biological adaptation in Oceania
Choin, J., Mendoza-Revilla, J., Arauna, L. R., Cuadros-Espinoza, S., Cassar, O., Larena, M., Ko, A. M.-S., Harmant, C., Laurent, R., Verdu, P., et al. (2021) · Nature · doi:10.1038/s41586-021-03236-5 · Cited by 208 · see citing works
Self-citationA community-maintained standard library of population genetic models
Adrion, J. R., Cole, C. B., Dukler, N., Galloway, J., Gladstein, A. L., Gower, G., Kyriazis, C. C., Ragsdale, A. P., Tsambos, G., Baumdicker, F., et al. (2020) · eLife · doi:10.7554/elife.54967 · Cited by 206 · see citing works
A unified genealogy of modern and ancient genomes
Wohns, A. W., Wong, Y., Jeffery, B., Akbari, A., Mallick, S., Pinhasi, R., Patterson, N. J., Reich, D., Kelleher, J., & McVean, G. (2022) · Science · doi:10.1126/science.abi8264 · Cited by 182 · see citing works
Last appearance of Homo erectus at Ngandong, Java, 117,000–108,000 years ago
Rizal, Y., Westaway, K. E., Zaim, Y., van den Bergh, G. D., Bettis, E. A., Morwood, M. J., Huffman, O. F., Grün, R., Joannes-Boyau, R., Bailey, R. M., et al. (2020) · Nature · doi:10.1038/s41586-019-1863-2 · Cited by 165 · see citing works
Climate effects on archaic human habitats and species successions
Timmermann, A., Yun, K., Raia, P., Ruan, J., Mondanaro, A., Zeller, E., Zollikofer, C. P. E., de León, M. S. P., Lemmon, D., Willeit, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04600-9 · Cited by 163 · see citing works
Ancient DNA from Guam and the peopling of the Pacific
Pugach, I., Hübner, A., Hung, H., Meyer, M., Carson, M. T., & Stoneking, M. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022112118 · Cited by 145 · see citing works
Self-citationAspects of human physical and behavioural evolution during the last 1 million years
Galway‐Witham, J., Cole, J., & Stringer, C. B. (2019) · Journal of Quaternary Science · doi:10.1002/jqs.3137 · 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
Hubisz, M. J., Williams, A. L., & Siepel, A. (2020) · PLOS Genetics · doi:10.1371/journal.pgen.1008895 · Cited by 130 · 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
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
The history and evolution of the Denisovan- <i>EPAS1</i> haplotype in Tibetans
Zhang, X., Witt, K. E., Bañuelos, M. M., Ko, A., Yuan, K., Xu, S., Nielsen, R., & Huerta-Sanchez, E. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2020803118 · Cited by 105 · 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
Human occupation of northern India spans the Toba super-eruption ~74,000 years ago
Clarkson, C., Harris, C., Li, B., Neudorf, C. M., Roberts, R. G., Lane, C. S., Norman, K., Pal, J., Jones, S., Shipton, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14668-4 · Cited by 97 · 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
Population Structure, Stratification, and Introgression of Human Structural Variation
Almarri, M. A., Bergström, A., Prado-Martinez, J., Yang, F., Fu, B., Dunham, A. S., Chen, Y., Hurles, M. E., Tyler‐Smith, C., & Xue, Y. (2020) · Cell · doi:10.1016/j.cell.2020.05.024 · Cited by 92 · 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
Climatic windows for human migration out of Africa in the past 300,000 years
Beyer, R. M., Krapp, M., Eriksson, A., & Manica, A. (2021) · Nature Communications · doi:10.1038/s41467-021-24779-1 · Cited by 91 · see citing works
A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos
Demeter, F., Zanolli, C., Westaway, K., Joannes-boyau, R. C., Duringer, P., Morley, M. W., Welker, F., Rüther, P. L., Skinner, M. M., McColl, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29923-z · Cited by 90 · see citing works
Papuan mitochondrial genomes and the settlement of Sahul
Pedro, N., Brucato, N., Fernandes, V., André, M., Saag, L., Pomat, W. S., Besse, C., Boland, A., Deleuze, J., Clarkson, C., et al. (2020) · Journal of Human Genetics · doi:10.1038/s10038-020-0781-3 · Cited by 89 · see citing works
Self-citationPleistocene Water Crossings and Adaptive Flexibility Within the Homo Genus
Gaffney, D. (2020) · Journal of Archaeological Research · doi:10.1007/s10814-020-09149-7 · Cited by 89 · see citing works
Zwyns, N., Paine, C. H., Bolorbat, T., Talamo, S., Fitzsimmons, K. E., Gantumur, A., Lkhundev, G., Одсурэн, Д., Flas, D., Dogandžić, T., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-47972-1 · Cited by 88 · see citing works
The languages of Halmahera and West New Guinea
Gasser, E., Arnold, L., & Kamholz, D. (2024) · Oxford University Press eBooks · doi:10.1093/oso/9780198807353.003.0037 · Cited by 86 · 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
Sun, X., Wen, S., Lu, C.-Q., Zhou, B.-Y., Curnoe, D., Lu, H., Li, H., Wang, W., Cheng, H., Yi, S.-W., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2019158118 · Cited by 78 · see citing works
Colson, P., Fournier, P., Delerce, J., Million, M., Bedotto, M., Houhamdi, L., Yahi, N., Bayette, J., Levasseur, A., Fantini, J., et al. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27789 · Cited by 76 · see citing works
Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity
Zammit, N. W., Siggs, O. M., Gray, P. E., Horikawa, K., Langley, D. B., Walters, S. N., Daley, S. R., Loetsch, C., Warren, J., Yap, J. Y., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0492-0 · Cited by 80 · see citing works
Self-citationNeanderthal-Denisovan ancestors interbred with a distantly related hominin
Rogers, A. R., Harris, N. S., & Achenbach, A. A. (2020) · Science Advances · doi:10.1126/sciadv.aay5483 · Cited by 77 · see citing works
Purnomo, G. A., Mitchell, K. J., O’Connor, S., Kealy, S., Taufik, L., Schiller, S., Rohrlach, A. B., Cooper, A., Llamas, B., Sudoyo, H., et al. (2021) · Genes · doi:10.3390/genes12070965 · Cited by 76 · see citing works
Self-citationMiddle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave
Xia, H., Zhang, D., Wang, J., Fagernäs, Z., Li, T., Li, Y., Yao, J., Lin, D., Troché, G., Smith, G. M., et al. (2024) · Nature · doi:10.1038/s41586-024-07612-9 · Cited by 77 · see citing works
Indigenous Australian genomes show deep structure and rich novel variation
Silcocks, M., Farlow, A., Hermes, A., Tsambos, G., Patel, H. R., Huebner, S., Baynam, G. S., Jenkins, M. R., Vukcevic, D., Easteal, S., et al. (2023) · Nature · doi:10.1038/s41586-023-06831-w · Cited by 73 · see citing works
A different paradigm for the initial colonisation of Sahul
Allen, J., & O’Connell, J. F. (2020) · Archaeology in Oceania/Archæology & physical anthropology in Oceania · doi:10.1002/arco.5207 · Cited by 73 · see citing works
Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul
Brucato, N., André, M., Tsang, R., Saag, L., Kariwiga, J., Sesuki, K., Beni, T., Pomat, W. S., Muke, J., Meyer, V., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab238 · Cited by 71 · see citing works
Self-citationBrzozowska, M. M., Havula, E., Allen, R., & Cox, M. P. (2019) · Reviews in Endocrine and Metabolic Disorders · doi:10.1007/s11154-019-09505-z · Cited by 70 · see citing works
Self-citationTwo-stage mid-Brunhes climate transition and mid-Pleistocene human diversification
Ao, H., Rohling, E. J., Stringer, C. B., Roberts, A. P., Dekkers, M. J., Dupont‐Nivet, G., Yu, J., Liu, Q., Zhang, P., Liu, Z., et al. (2020) · Earth-Science Reviews · doi:10.1016/j.earscirev.2020.103354 · Cited by 66 · see citing works
Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages
Karmin, M., Flores, R., Saag, L., Hudjashov, G., Brucato, N., Darusallam, C. C., Larena, M., Endicott, P., Jakobsson, M., Lansing, J. S., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac045 · Cited by 65 · see citing works
Self-citationMore 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
Human evolutionary history in Eastern Eurasia using insights from ancient DNA
Zhang, M., & Fu, Q. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.06.009 · Cited by 61 · 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
The genetic changes that shaped Neandertals, Denisovans, and modern humans
Zeberg, H., Jakobsson, M., & Pääbo, S. (2024) · Cell · doi:10.1016/j.cell.2023.12.029 · Cited by 60 · see citing works
Mattes, V., & Schwaiger, T. (2024) · Oxford University Press eBooks · doi:10.1093/oso/9780198807353.003.0045 · Cited by 59 · see citing works
Gil, D. (2020) · Typological studies in language · doi:10.1075/tsl.129.03gil · Cited by 58 · see citing works
Reconstruction of the Austronesian Diaspora in the Era of Genomics
Chambers, G. K., & Edinur, H. A. (2021) · Human Biology · doi:10.1353/hub.2017.0096 · Cited by 58 · see citing works
Human dispersal and plant processing in the Pacific 55 000–50 000 years ago
Gaffney, D., Tanudirjo, D. A., Djami, E. N. I., Mas’ud, Z., Macap, A. R., Russell, T., Dailom, M., Ray, Y., Higham, T., Bradshaw, F., et al. (2024) · Antiquity · doi:10.15184/aqy.2024.83 · Cited by 56 · see citing works
A male Denisovan mandible from Pleistocene Taiwan
Tsutaya, T., Sawafuji, R., Taurozzi, A. J., Fagernäs, Z., Patramanis, I., Troché, G., Mackie, M., Gakuhari, T., Oota, H., Tsai, C., et al. (2025) · Science · doi:10.1126/science.ads3888 · Cited by 57 · 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
Self-citationThe earliest Denisovans and their cultural adaptation
Brown, S., Massilani, D., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Stoessel, A., Jope-Street, B., Meyer, M., Kelso, J. F., Pääbo, S., et al. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01581-2 · Cited by 55 · see citing works
Natri, H. M., Bobowik, K. S., Kusuma, P., Crenna Darusallam, C., Jacobs, G. S., Hudjashov, G., Lansing, J. S., Sudoyo, H., Banovich, N. E., Cox, M. P., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008749 · Cited by 48 · see citing works
Self-citationThe genetic origins and impacts of historical Papuan migrations into Wallacea
Purnomo, G. A., Kealy, S., O’Connor, S., Schapper, A., Shaw, B., Llamas, B., Teixeira, J. C., Sudoyo, H., & Tobler, R. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2412355121 · Cited by 48 · see citing works
Self-citationDenisovan introgression has shaped the immune system of present-day Papuans
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46 · see citing works
“To account for this while enriching for variants of putative evolutionary interest we applied a series of filtering steps to our starting list of 8,337,067 SNPs [5].”
InfluentialSelf-citationLiu, Y.-C., Hunter-Anderson, R. L., Cheronet, O., Eakin, J., Camacho, F. A., Pietrusewsky, M., Rohland, N., Ioannidis, A. G., Athens, J. S., Douglas, M. T., et al. (2022) · Science · doi:10.1126/science.abm6536 · Cited by 42 · see citing works
Wang, M., Chen, H., Luo, L., Huang, Y., Duan, S., Yuan, H., Tang, R., Liu, C., & He, G. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.06.016 · Cited by 43 · see citing works
The evolutionary history of the human oral microbiota and its implications for modern health
Weyrich, L. S. (2020) · Periodontology 2000 · doi:10.1111/prd.12353 · Cited by 43 · 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
The genomic signatures of natural selection in admixed human populations
Cuadros-Espinoza, S., Laval, G., Quintana‐Murci, L., & Patin, É. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.02.011 · Cited by 40 · see citing works
Quinn, L. J. E., Whitfield, J. T., Alpers, M. P., Campbell, T., Hummerich, H., Pomat, W. S., Siba, P., Koki, G., Moltke, I., Collinge, J., et al. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.02.011 · Cited by 40 · 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
The Impact of Ancient Genome Studies in Archaeology
Gökçümen, Ö., & Frachetti, M. D. (2020) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-010220-074353 · Cited by 37 · see citing works
Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations
Zhang, P., Zhang, X., Zhang, X., Gao, X., Huerta‐Sánchez, E., & Zwyns, N. (2021) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2021.11.004 · Cited by 38 · see citing works
Further analyses of the structural organization of Homo luzonensis teeth: Evolutionary implications
Zanolli, C., Kaifu, Y., Pan, L., Xing, S., Mijares, A. S., Kullmer, O., Schrenk, F., Corny, J., Dizon, E., Robles, E., et al. (2022) · Journal of Human Evolution · doi:10.1016/j.jhevol.2021.103124 · Cited by 37 · see citing works
Past climate change effects on human evolution
Timmermann, A., Raia, P., Mondanaro, A., Zollikofer, C. P. E., de León, M. S. P., Zeller, E., & Yun, K. (2024) · Nature Reviews Earth & Environment · doi:10.1038/s43017-024-00584-4 · Cited by 38 · see citing works
Zhang, X., Kim, B., Lohmueller, K. E., & Huerta-Sánchez, E. (2020) · Genetics · doi:10.1534/genetics.120.303081 · Cited by 35 · see citing works
New insights into human immunity from ancient genomics
Kerner, G., Patin, É., & Quintana‐Murci, L. (2021) · Current Opinion in Immunology · doi:10.1016/j.coi.2021.04.006 · Cited by 34 · see citing works
Natri, H. M., Hudjashov, G., Jacobs, G., Kusuma, P., Saag, L., Darusallam, C. C., Metspalu, M., Sudoyo, H., Cox, M. P., Gallego Romero, I., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.11.017 · Cited by 33 · see citing works
Self-citationTournebize, R., & Chikhi, L. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02591-6 · Cited by 32 · 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
Climate shifts orchestrated hominin interbreeding events across Eurasia
Ruan, J., Timmermann, A., Raia, P., Yun, K., Zeller, E., Mondanaro, A., Febbraro, M. D., Lemmon, D., Castiglione, S., & Melchionna, M. (2023) · Science · doi:10.1126/science.add4459 · Cited by 32 · 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
Bergmann, I., Hublin, J., Gunz, P., & Freidline, S. E. (2021) · Journal of Human Evolution · doi:10.1016/j.jhevol.2021.103026 · Cited by 29 · see citing works
A history of multiple Denisovan introgression events in modern humans
Ongaro, L., & Huerta‐Sánchez, E. (2024) · Nature Genetics · doi:10.1038/s41588-024-01960-y · Cited by 31 · 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
Zhang, X., Kim, B., Singh, A., Sankararaman, S., Durvasula, A., & Lohmueller, K. E. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad001 · Cited by 29 · see citing works
Zilhão, J., d'Errico, F., Banks, W., & Teyssandier, N. (2024) · Quaternary Environments and Humans · doi:10.1016/j.qeh.2024.100037 · Cited by 28 · see citing works
Rong, S., Neil, C. R., Welch, A., Duan, C., Maguire, S., Meremikwu, I. C., Meyerson, M., Evans, B. J., & Fairbrother, W. G. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218308120 · Cited by 24 · see citing works
Langdon, Q. K., Groh, J. S., Aguillon, S. M., Powell, D. L., Gunn, T. R., Payne, C. Y., Baczenas, J. J., Donny, A. E., Dodge, T. O., Du, K., et al. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002742 · Cited by 24 · 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
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
Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels
André, M., Brucato, N., Hudjashov, G., Pankratov, V., Yermakovich, D., Montinaro, F., Kreevan, R., Kariwiga, J., Muke, J., Boland, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47735-1 · Cited by 25 · see citing works
Self-citationBlinkhorn, J., Achyuthan, H., Durcan, J. A., Roberts, P., & Ilgner, J. (2021) · Scientific Reports · doi:10.1038/s41598-021-98897-7 · Cited by 21 · see citing works
Tracing the Evolution of Human Immunity Through Ancient DNA
Patin, É., & Quintana‐Murci, L. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-082323-024638 · 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
Flemming, N. C. (2020) · The Journal of Island and Coastal Archaeology · doi:10.1080/15564894.2020.1781712 · Cited by 20 · see citing works
Archaic mitochondrial DNA inserts in modern day nuclear genomes
Bücking, R., Cox, M. P., Hudjashov, G., Saag, L., Sudoyo, H., & Stoneking, M. (2019) · BMC Genomics · doi:10.1186/s12864-019-6392-8 · Cited by 19 · see citing works
Self-citationReconstruction of the Austronesian Diaspora in the Era of Genomics
Chambers, G. K., & Edinur, H. A. (2020) · Human Biology · doi:10.13110/humanbiology.92.4.04 · Cited by 19 · see citing works
Kaifu, Y., Kurniawan, I., Yurnaldi, D., Setiawan, R., Setiyabudi, E., Insani, H., Takai, M., Nishioka, Y., Takahashi, A., Aziz, F., et al. (2022) · Journal of Human Evolution · doi:10.1016/j.jhevol.2021.103122 · Cited by 19 · see citing works
Rogers, N. M., Zammit, N. W., Nguyen-Ngo, D., Souilmi, Y., Minhas, N., Meijles, D. N., Self, E., Walters, S. N., Warren, J. A., Cultrone, D., et al. (2023) · Kidney International · doi:10.1016/j.kint.2023.02.030 · Cited by 19 · see citing works
sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S *
Huang, X., Kruisz, P., & Kuhlwilm, M. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac212 · Cited by 19 · see citing works
East and Southeast Asian hominin dispersal and evolution: A review
Sawafuji, R., Tsutaya, T., Takahata, N., Pedersen, M. W., & Ishida, H. (2024) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2024.108669 · Cited by 16 · 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
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
“The Eurasian environments where Neanderthals and Denisovans lived for several hundred thousand years are located at higher latitudes with more variable photoperiods than the landscape where AMH evolved before leaving Africa.”
BackgroundInfluentialIntrogressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates
Storz, J. F., & Signore, A. V. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.696484 · 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
Genomic evidence supports the “long chronology” for the peopling of Sahul
Gandini, F., Almeida, M., Foody, M. G. B., Nagle, N., Bergström, A., Olivieri, A., Rodrigues, S., Fichera, A., Oteo‐García, G., Torroni, A., et al. (2025) · Science Advances · doi:10.1126/sciadv.ady9493 · Cited by 13 · see citing works
- Authors
- Jacobs, G. S., Hudjashov, G., Saag, L., Kusuma, P., Darusallam, C. C., Lawson, D. J., Mondal, M., Pagani, L., Ricaut, F.-X., Stoneking, M., Metspalu, M., Sudoyo, H., Lansing, J. S., & Cox, M. P.
- Affiliations
- Nanyang Technological University (SG)
- Massey University (NZ)
- University of Tartu (EE)
- Eijkman Institute for Molecular Biology (ID)
- University of Bristol (GB)
- University of Padua (IT)
- Centre National de la Recherche Scientifique (FR)
- Max Planck Institute for Evolutionary Anthropology (DE)
- The University of Sydney (AU)
- Santa Fe Institute (US)
- Corresponding author
- Hudjashov, Georgi
- Cox, Murray P.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-05
- Volume
- 177
- Issue
- 4
- Pages
- 1010-1021.e32
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2923745223
- Cited by
- 346
- References
- 95
- Citations by year
- 2026: 27 · 2025: 31 · 2024: 104 · 2023: 22 · 2022: 37 · 2021: 63 · 2020: 43 · 2019: 18 · 2014: 1
- FWCI
- 185.42
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Explore Bristol Research (acceptedVersion, cc-by-nc-nd)
- HAL (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion, cc-by-nc-nd)
- Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
- Padua Research Archive (University of Padova) (submittedVersion, other-oa)
- Apollo
- Funders
- National Science Foundation (SES 0725470)
- Singapore Ministry of Education Tier II (MOE2015-T2-1-127)
- NTU Presidential Postdoctoral Fellowship
- Complexity Institute Individual Fellowship
- French ANR grant (ANR-14-CE31-0013-01)
- European Union grant through the European Regional Development Fund (2014-2020.4.01.15-0012)
- Royal Society of New Zealand Marsden (17-MAU-040)
- German Alexander von Humboldt Foundation fellowship
- Microsoft research grant for Azure cloud computing
- High Performance Computing Center, University of Tartu, Estonia
- 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
- Denisovans, Papuans, archaic introgression, Wallace's Line, Island Southeast Asia, New Guinea, Pleistocene, human dispersal out of Africa
- MeSH terms
- Genetic Introgression, Animals, Biological Evolution, Haplotypes, Humans, Indonesia, Genetic Variation, Hominidae, Genome, Human, Oceania, 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
