The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Open accessAbstract
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“It has been shown that Papuans and Indigenous Australians carry the largest amount of Denisovan introgression (∼1% to 5%), followed by East and South Asians (∼0.06% to 0.5%), and Indigenous Americans (∼0.05% to 0.4%) (Reich et al. 2010; Racimo et al. 2015; Mallick et al. 2016; Sankararaman et al. 2016; Browning et al. 2018).”
From The Human Accelerated Region HAR202 Controls NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Mallick et al. 2016
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“We caution, however, that our approach can artificially shorten haplotype block lengths (see Supplementary Methods and figs. S21 and S22), especially for populations such as Papuans and Australians that were absent from the 1000 Genomes Project panel (24) that was used for phasing (14).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [14]
The cited source says what the claim attributes to it.
In the citing paper
“Applying our approach to Neanderthal aSNPs segregating within present-day West Eurasians [31] replicates most of our findings, as well as previously reported signals including a depletion of Neanderthal variants within enhancer-like elements [12].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [31]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Self-citationPLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
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
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
Self-citationFast model-based estimation of ancestry in unrelated individuals
Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Self-citationPopulation Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
Self-citationA draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318
Self-citationAncient 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
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 201–300 of 1,002
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
Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe
Tříska, P., Chekanov, N., Степанов, В. А., Хуснутдинова, Э. К., Kumar, G. P. A., Akhmetova, V. R., Babalyan, K., Boulygina, E., Харьков, В. Н., Gubina, M. A., et al. (2017) · BMC Genetics · doi:10.1186/s12863-017-0578-3 · Cited by 99
Self-citationOne reference genome is not enough
Yang, X., Lee, W., Ye, K., & Lee, C. (2019) · Genome biology · doi:10.1186/s13059-019-1717-0 · Cited by 93
A comparison of humans and baboons suggests germline mutation rates do not track cell divisions
Wu, F. L., Strand, A. I., Cox, L. A., Ober, C., Wall, J. D., Moorjani, P., & Przeworski, M. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000838 · Cited by 91
Interpreting short tandem repeat variations in humans using mutational constraint
Gymrek, M., Willems, T., Reich, D., & Erlich, Y. (2017) · Nature Genetics · doi:10.1038/ng.3952 · Cited by 99
Self-citationPopulation 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 93
Self-citationEarly presence of Homo sapiens in Southeast Asia by 86–68 kyr at Tam Pà Ling, Northern Laos
Freidline, S. E., Westaway, K., Joannes‐Boyau, R., Duringer, P., Ponche, J., Morley, M. W., Hernandez, V., McAllister-Hayward, M. S., McColl, H., Zanolli, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38715-y · Cited by 100
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
Cultural evolution of genetic heritability
Uchiyama, R., Spicer, R., & Muthukrishna, M. (2021) · Behavioral and Brain Sciences · doi:10.1017/s0140525x21000893 · Cited by 103
Archaic hominin introgression into modern human genomes
Gökçümen, Ö. (2019) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23951 · Cited by 92
Fan, S., Spence, J. P., Feng, Y., Hansen, M. E. B., Terhorst, J., Beltrame, M. H., Ranciaro, A., Hirbo, J. B., Beggs, W. R., Thomas, N., et al. (2023) · Cell · doi:10.1016/j.cell.2023.01.042 · Cited by 97
Self-citationThe study of human Y chromosome variation through ancient DNA
Kivisild, T. (2017) · Human Genetics · doi:10.1007/s00439-017-1773-z · Cited by 93
Self-citationLocalization of adaptive variants in human genomes using averaged one-dependence estimation
Sugden, L. A., Atkinson, E. G., Fischer, A. P., Rong, S., Henn, B. M., & Ramachandran, S. (2018) · Nature Communications · doi:10.1038/s41467-018-03100-7 · Cited by 91
Self-citationA Comprehensive Map of Genetic Variation in the World’s Largest Ethnic Group—Han Chinese
Chiang, C. W. K., Mangul, S., Robles, C. R., Kretzschmar, W. W., Cai, N., Kendler, K. S., Sankararam, S., & Flint, J. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy170 · Cited by 89
PGG.Han: the Han Chinese genome database and analysis platform
Gao, Y., Zhang, C., Yuan, L., Ling, Y., Wang, X., Liu, C., Pan, Y., Zhang, X., Ma, X., Wang, Y., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz829 · Cited by 87
De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations
Wong, K. H. Y., Levy‐Sakin, M., & Kwok, P. (2018) · Nature Communications · doi:10.1038/s41467-018-05513-w · Cited by 86
Papuan mitochondrial genomes and the settlement of Sahul
Pedro, N., Brucato, N., Fernandes, V., André, M., Saag, L., Pomat, W., Besse, C., Boland, A., Deleuze, J.-F., Clarkson, C., et al. (2020) · Journal of Human Genetics · doi:10.1038/s10038-020-0781-3 · Cited by 48
Self-citationYost, C. L., Jackson, L. J., Stone, J. R., & Cohen, A. S. (2018) · Journal of Human Evolution · doi:10.1016/j.jhevol.2017.11.005 · Cited by 92
Jeong, C., Witonsky, D., Basnyat, B., Neupane, M., Beall, C. M., Childs, G. H., Craig, S. R., Novembre, J., & Rienzo, A. D. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007650 · Cited by 88
Self-citationThe 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 88
How to Be a Biological Racial Realist
Spencer, Q. (2019) · Oxford University Press eBooks · doi:10.1093/oso/9780190610173.003.0004 · Cited by 85
de la Puente, M., Phillips, C., Xavier, C., Amigo, J., Carracedo, Á., Parson, W., & Lareu, M. V. (2019) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2019.102213 · Cited by 85
Bantu-speaker migration and admixture in southern Africa
Choudhury, A., Sengupta, D., Ramsay, M., & Schlebusch, C. M. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa274 · Cited by 85
Sirak, K. A., Fernandes, D., Lipson, M., Mallick, S., Mah, M., Olalde, Í., Ringbauer, H., Rohland, N., Hadden, C. S., Harney, É., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27356-8 · Cited by 85
Self-citationAncient genomes from the last three millennia support multiple human dispersals into Wallacea
Oliveira, S., Nägele, K., Carlhoff, S., Pugach, I., Koesbardiati, T., Hübner, A., Meyer, M., Oktaviana, A. A., Takenaka, M., Katagiri, C., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01775-2 · Cited by 91
Immune diversity sheds light on missing variation in worldwide genetic diversity panels
Abi‐Rached, L., Gouret, P., Yeh, J.-H., Cristofaro, J. D., Pontarotti, P., Picard, C., & Paganini, J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0206512 · Cited by 84
Wu, S., Ou, T., Xing, N., Jiang, L., Wan, S., Wang, C., Zhang, X., Yang, F., Huang, Y. F., & Cai, Z. (2019) · Nature Communications · doi:10.1038/s41467-019-08576-5 · Cited by 87
Genome structural variation in human evolution
Hollox, E. J., Zuccherato, L. W., & Tucci, S. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.06.015 · Cited by 93
Stable population structure in Europe since the Iron Age, despite high mobility
Antonio, M. L., Weiß, C. L., Gao, Z., Sawyer, S., Oberreiter, V., Moots, H. M., Spence, J. P., Cheronet, O., Zagorc, B., Praxmarer, E., et al. (2023) · eLife · doi:10.7554/elife.79714 · Cited by 90
Self-citationRecurrent 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 94
Hsieh, P., Vollger, M. R., Dang, V., Porubskỳ, D., Baker, C. A., Cantsilieris, S., Hoekzema, K., Lewis, A. P., Munson, K. M., Sorensen, M., et al. (2019) · Science · doi:10.1126/science.aax2083 · Cited by 86
Applying f 4 ‐statistics and admixture graphs: Theory and examples
Lipson, M. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13230 · Cited by 82
Self-citationArora, K. S., Tran, T. N., Kemel, Y. M., Mehine, M. M., Liu, Y. L., Nandakumar, S., Smith, S. A., Brannon, A. R., Ostrovnaya, I., Stopsack, K. H., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0312 · Cited by 77
Differences in the rare variant spectrum among human populations
Mathieson, I., & Reich, D. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006581 · Cited by 80
Self-citationThe 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 92
Self-citationThe 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 81
The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex
Brites, D., & Gagneux, S. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-64371-7_1 · Cited by 88
Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories
Beichman, A. C., Phung, T. N., & Lohmueller, K. E. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.300259 · Cited by 75
Inference of complex population histories using whole-genome sequences from multiple populations
Steinrücken, M., Kamm, J., Spence, J. P., & Song, Y. S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1905060116 · Cited by 81
Self-citationA genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals
Silva, M. S. D., Oliveira, M., Vieira, D., Brandão, A., Rito, T., Pereira, J. B., Fraser, R. M., Hudson, B., Gandini, F., Edwards, C. J., et al. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0936-9 · Cited by 83
The complete and fully-phased diploid genome of a male Han Chinese
Yang, C., Zhou, Y., Song, Y., Wu, D., Zeng, Y., Nie, L., Liu, P., Zhang, S., Chen, G., Xu, J., et al. (2023) · Cell Research · doi:10.1038/s41422-023-00849-5 · Cited by 83
Self-citationA deep population reference panel of tandem repeat variation
Jam, H. Z., Li, Y., DeVito, R., Mousavi, N., Ma, N., Lujumba, I., Adam, Y., Maksimov, M., Huang, B. B., Dolzhenko, E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42278-3 · Cited by 75
Self-citationsnpAD: an ancient DNA genotype caller
Prüfer, K. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty507 · Cited by 78
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 79
Self-citationDenisovan, 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
Neanderthal-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
Differentiated demographic histories and local adaptations between Sherpas and Tibetans
Zhang, C., Lü, Y., Feng, Q., Wang, X., Lou, H., Liu, J., Ning, Z., Yuan, K., Wang, Y., Zhou, Y., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1242-y · Cited by 80
Sanchez, T., Cury, J., Charpiat, G., & Jay, F. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13224 · Cited by 89
Genome interpretation using in silico predictors of variant impact
Katsonis, P., Wilhelm, K. O., Williams, A. M., & Lichtarge, O. (2022) · Human Genetics · doi:10.1007/s00439-022-02457-6 · Cited by 86
HUPAN: a pan-genome analysis pipeline for human genomes
Duan, Z., Qiao, Y., Lu, J., Lu, H., Zhang, W., Yan, F., Sun, C., Hu, Z., Zhang, Z., Li, G., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1751-y · Cited by 75
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 75
African-specific molecular taxonomy of prostate cancer
Jaratlerdsiri, W., Jiang, J., Gong, T., Patrick, S. M., Willet, C. E., Chew, T., Lyons, R. J., Haynes, A., Pasqualim, G., Louw, M., et al. (2022) · Nature · doi:10.1038/s41586-022-05154-6 · Cited by 75
Lamb, H. F., Bates, R., Bryant, C., Davies, S. J., Huws, D. G., Marshall, M., Roberts, H. M., & Toland, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-19601-w · Cited by 76
Kumar, V., & Campbell, R. (2022) · doi:10.1093/oso/9780197600122.001.0001 · Cited by 79
The functional and evolutionary impacts of human-specific deletions in conserved elements
Xue, J. R., Mackay-Smith, A., Mouri, K., García, M. F., Dong, M. X., Akers, J. F., Noble, M., Li, X., Lindblad‐Toh, K., Karlsson, E. K., et al. (2023) · Science · doi:10.1126/science.abn2253 · Cited by 79
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 75
Recurrent evolution and selection shape structural diversity at the amylase locus
Bolognini, D., Halgren, A. S., Lou, R. N., Raveane, A., Rocha, J. L., Guarracino, A., Soranzo, N., Chin, C.-S., Garrison, E. P., & Sudmant, P. H. (2024) · Nature · doi:10.1038/s41586-024-07911-1 · Cited by 88
Phillips, C., Amigo, J., Tillmar, A. O., Peck, M. A., de la Puente, M., Ruiz-Ramírez, J., Bittner, F., Idrizbegović, S., Wang, Y., Parsons, T. J., et al. (2020) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2020.102232 · Cited by 74
The genomic history of the Middle East
Almarri, M. A., Haber, M., Lootah, R. A., Hallast, P., Turki, S. H. A., Martin, H. C., Xue, Y., & Tyler‐Smith, C. (2021) · Cell · doi:10.1016/j.cell.2021.07.013 · Cited by 75
Self-citationGopalan, S., Berl, R. E. W., Myrick, J. W., Garfield, Z. H., Reynolds, A. W., Bafens, B. K., Belbin, G. M., Mastoras, M., Williams, C., Daya, M., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.02.050 · Cited by 74
Self-citationContrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations
Kutanan, W., Kampuansai, J., Srikummool, M., Brunelli, A., Ghirotto, S., Arias, L., Macholdt, E., Hübner, A., Schröder, R., & Stoneking, M. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz083 · Cited by 68
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
Self-citationPapua 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 72
Self-citationPopulation Histories and Genomic Diversity of South American Natives
Silva, M. A. C. E., Ferraz, T., Couto-Silva, C. M., Lemes, R. B., Nunes, K., Comas, D., & Hünemeier, T. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab339 · Cited by 75
Self-citationTwenty years of the Human Genome Diversity Project
Aneli, S., Birolo, G., & Matullo, G. (2022) · Green Energy and Sustainability · doi:10.47248/hpgg2202040005 · Cited by 73
Clarifying distinct models of modern human origins in Africa
Henn, B. M., Steele, T. E., & Weaver, T. D. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.10.003 · Cited by 71
Self-citationDeng, L., Zhang, C., Yuan, K., Gao, Y., Pan, Y., Ge, X., He, Y., Yuan, Y., Lü, Y., Zhang, X., et al. (2019) · National Science Review · doi:10.1093/nsr/nwz108 · Cited by 72
Xavier, C., de la Puente, M., Mosquera-Miguel, A., Freire-Aradas, A., Kalamara, V., Vidaki, A., Gross, T., Revoir, A., Pośpiech, E., Kartasińska, E., et al. (2020) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2020.102336 · Cited by 67
MONI: A Pangenomic Index for Finding Maximal Exact Matches
Rossi, M., Oliva, M., Langmead, B., Gagie, T., & Boucher, C. A. (2022) · Journal of Computational Biology · doi:10.1089/cmb.2021.0290 · Cited by 72
Genomics of rare genetic diseases—experiences from India
Sivasubbu, S., & Scaria, V. (2019) · Human Genomics · doi:10.1186/s40246-019-0215-5 · Cited by 75
MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations
Phillips, C., McNevin, D. B., Kídd, K. K., Lagace, R. E., Wootton, S., de la Puente, M., Freire-Aradas, A., Mosquera‐Miguel, A., Eduardoff, M., Gross, T. E., et al. (2019) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2019.06.022 · Cited by 69
Widespread somatic L1 retrotransposition in normal colorectal epithelium
Nam, C. H., Youk, J., Kim, J. Y., Lim, J., Park, J. W., Oh, S. A., Lee, H. J., Won, H., Won, H., Lee, D.-S., et al. (2023) · Nature · doi:10.1038/s41586-023-06046-z · Cited by 71
Outstanding questions in the study of archaic hominin admixture
Wolf, A. B., & Akey, J. M. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007349 · Cited by 68
Diversity in non-repetitive human sequences not found in the reference genome
Kehr, B., Helgadóttir, A., Melsted, P., Jónsson, H., Helgason, H., Jónasdóttir, A., Jónasdóttir, Á., Sigurðsson, Á., Gylfason, A., Halldorsson, G. H., et al. (2017) · Nature Genetics · doi:10.1038/ng.3801 · Cited by 68
Distinct genetic variation and heterogeneity of the Iranian population
Mehrjoo, Z., Fattahi, Z., Beheshtian, M., Mohseni, M., Poustchi, H., Ardalani, F., Jalalvand, K., Arzhangi, S., Mohammadi, Z., Khoshbakht, S., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008385 · Cited by 70
Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies
Speidel, L., Cassidy, L. M., Davies, R. W., Hellenthal, G., Skoglund, P., & Myers, S. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab174 · Cited by 78
Self-citationHuman Colonization of Asia in the Late Pleistocene
Bae, C. J., Douka, K., & Petraglia, M. D. (2017) · Current Anthropology · doi:10.1086/694420 · Cited by 66
Haber, M., Jones, A., Connell, B., Asan, Arciero, E., Yang, H., Thomas, M., Xue, Y., & Tyler‐Smith, C. (2019) · Genetics · doi:10.1534/genetics.119.302368 · Cited by 68
Self-citationGenomic Insights Into the Demographic History of the Southern Chinese
Huang, X., Xia, Z., Bin, X., He, G., Guo, J., Adnan, A., Yin, L., Huang, Y., Zhao, J., Yi-dong, Y., et al. (2022) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2022.853391 · Cited by 80
Characterization of genome-wide STR variation in 6487 human genomes
Shi, Y., Niu, Y., Zhang, P., Luo, H., Liu, S., Zhang, S., Wang, J., Li, Y., Liu, X., Song, T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37690-8 · Cited by 70
Insights into Modern Human Prehistory Using Ancient Genomes
Yang, M. A., & Fu, Q. (2018) · Trends in Genetics · doi:10.1016/j.tig.2017.11.008 · Cited by 66
Self-citationGouy, A., & Excoffier, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz306 · Cited by 63
Population structure and the evolution of Homo sapiens in Africa
Klein, R. G. (2019) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21788 · Cited by 67
A variant-centric perspective on geographic patterns of human allele frequency variation
Biddanda, A., Rice, D. P., & Novembre, J. (2020) · eLife · doi:10.7554/elife.60107 · Cited by 67
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 67
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 75
Self-citationWang, L.-X., Lü, Y., Zhang, C., Wei, L., Yan, S. L., Huang, Y., Wang, C., Mallick, S., Wen, S., Li, J., et al. (2018) · Molecular Genetics and Genomics · doi:10.1007/s00438-018-1461-2 · Cited by 65
Self-citationCultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia
Arias, L., Schröder, R., Hübner, A., Barreto, G., Stoneking, M., & Pakendorf, B. (2018) · Molecular Biology and Evolution · doi:10.1101/347336 · Cited by 63
Japan considered from the hypothesis of farmer/language spread
de Boer, E. M., Yang, M. A., Kawagoe, A., & Barnes, G. L. (2020) · Evolutionary Human Sciences · doi:10.1017/ehs.2020.7 · Cited by 61
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Lu, T.-Y. T., Munson, K. M., Lewis, A. P., Zhu, Q., Tallon, L. J., Devine, S. E., Lee, C., Eichler, E. E., & Chaisson, M. (2021) · Nature Communications · doi:10.1038/s41467-021-24378-0 · Cited by 60
Inference and applications of ancestral recombination graphs
Nielsen, R., Vaughn, A. H., & Deng, Y. K. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00772-4 · Cited by 82
Practical guide for managing large-scale human genome data in research
Tanjo, T., Kawai, Y., Tokunaga, K., Ogasawara, O., & Nagasaki, M. (2021) · Journal of Human Genetics · doi:10.1038/s10038-020-00862-1 · Cited by 62
Johansson, P. A., Brattås, P. L., Douse, C. H., Hsieh, P., Adami, A., Pontis, J., Grassi, D. A., Garza, R., Sozzi, E., Cataldo, L. R., et al. (2021) · Cell stem cell · doi:10.1016/j.stem.2021.09.008 · Cited by 64
Ancient human DNA recovered from a Palaeolithic pendant
Essel, E., Zavala, E. I., Schulz‐Kornas, E., Kozlikin, M. B., Fewlass, H., Vernot, B., Shunkov, M. V., Derevianko, A. P., Douka, K., Barnes, I., et al. (2023) · Nature · doi:10.1038/s41586-023-06035-2 · Cited by 63
Self-citationGrugni, V., Raveane, A., Ongaro, L., Battaglia, V., Trombetta, B., Colombo, G., Capodiferro, M. R., Olivieri, A., Achilli, A., Perego, U. A., et al. (2019) · BMC Biology · doi:10.1186/s12915-018-0622-4 · Cited by 62
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 72
Archaic Hominin Populations in Asia before the Arrival of Modern Humans
Kaifu, Y. (2017) · Current Anthropology · doi:10.1086/694318 · Cited by 61
Nakatsuka, N. J., Luisi, P., Motti, J. M. B., Salemme, M., Santiago, F., del Campo, M. D. D., Vecchi, R. J., Espinosa‐Parrilla, Y., I, A. P., Adamski, N., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17656-w · Cited by 66
Self-citationSchäbitz, F., Asrat, A., Lamb, H. F., Cohen, A. S., Foerster, V., Duesing, W., Kaboth‐Bahr, S., Opitz, S., Viehberg, F., Vogelsang, R., et al. (2021) · Communications Earth & Environment · doi:10.1038/s43247-021-00195-7 · Cited by 60
High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation
Mulindwa, J., Noyes, H. A., Ilboudo, H., Pagani, L., Nyangiri, O. A., Kimuda, M. P., Ahouty, B., Asina, O. F., Ofon, E. A., Kamoto, K., et al. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.07.007 · Cited by 60
Metadata
- Authors
- Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., Skoglund, P., Lazaridis, I., Sankararaman, S., Fu, Q., Rohland, N., Renaud, G., Erlich, Y., Willems, T., Gallo, C., Spence, J. P., Song, Y. S., Poletti, G., Balloux, F., van Driem, G., de Knijff, P., Romero, I. G., Jha, A. R., Behar, D. M., Bravi, C. M., Capelli, C., Hervig, T., Moreno-Estrada, A., Posukh, O. L., Balanovska, E., Balanovsky, O., Karachanak-Yankova, S., Sahakyan, H., Toncheva, D., Yepiskoposyan, L., Tyler-Smith, C., Xue, Y., Abdullah, M. S., Ruiz-Linares, A., Beall, C. M., Di Rienzo, A., Jeong, C., Starikovskaya, E. B., Metspalu, E., Parik, J., Villems, R., Henn, B. M., Hodoglugil, U., Mahley, R., Sajantila, A., Stamatoyannopoulos, G., Wee, J. T. S., Khusainova, R., Khusnutdinova, E., Litvinov, S., Ayodo, G., Comas, D., Hammer, M. F., Kivisild, T., Klitz, W., Winkler, C. A., Labuda, D., Bamshad, M., Jorde, L. B., Tishkoff, S. A., Watkins, W. S., Metspalu, M., Dryomov, S., Sukernik, R., Singh, L., Thangaraj, K., Pääbo, S., Kelso, J., Patterson, N., & Reich, D.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- University of California, Berkeley (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- New York Genome Center (US)
- Universidad Peruana Cayetano Heredia (PE)
- University of Pennsylvania (US)
- Nanyang Technological University (SG)
- University of Chicago (US)
- Estonian Biocentre (EE)
- University of Oxford (GB)
- University of Bergen (NO)
- Russian Academy of Sciences (RU)
- Research Centre for Medical Genetics (RU)
- Moscow Institute of Physics and Technology (RU)
- Medical University of Sofia (BG)
- Institute of Molecular Biology (AM)
- Wellcome Sanger Institute (GB)
- Raja Isteri Pengiran Anak Saleha Hospital (BN)
- Case Western Reserve University (US)
- Estonian Academy of Sciences (EE)
- Stony Brook University (US)
- Gladstone Institutes (US)
- University of Helsinki (FI)
- University of Washington (US)
- National Cancer Centre Singapore (SG)
- Jaramogi Oginga Odinga University of Science and Technology (KE)
- Universitat Pompeu Fabra (ES)
- University of Arizona (US)
- University of Cambridge (GB)
- Frederick National Laboratory for Cancer Research (US)
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- University of Utah (US)
- Centre for Cellular and Molecular Biology (IN)
- Corresponding author
- Mallick, Swapan
- Reich, David
- ORCID
- Mallick, Swapan
- Li, Heng
- Lipson, Mark
- Mathieson, Iain
- Gymrek, Melissa
- Racimo, Fernando
- Zhao, Mengyao
- Skoglund, Pontus
- Lazaridis, Iosif
- Sankararaman, Sriram
- Fu, Qiaomei
- Rohland, Nadin
- Renaud, Gabriel
- Erlich, Yaniv
- Willems, Thomas
- Gallo, Carla
- Spence, Jeffrey P.
- Song, Yun S.
- Poletti, Giovanni
- Romero, Irene Gallego
- Jha, Aashish R.
- Behar, Doron M.
- Capelli, Cristian
- Hervig, Tor
- Posukh, Olga L.
- Balanovska, Elena
- Karachanak-Yankova, Sena
- Sahakyan, Hovhannes
- Toncheva, Draga
- Yepiskoposyan, Levon
- Abdullah, M. Syafiq
- Beall, Cynthia M.
- Jeong, Choongwon
- Starikovskaya, Elena B.
- Metspalu, Ene
- Villems, Richard
- Henn, Brenna M.
- Mahley, Robert
- Sajantila, Antti
- Wee, Joseph T. S.
- Khusainova, Rita
- Litvinov, Sergey
- Ayodo, George
- Comas, David
- Hammer, Michael F.
- Kivisild, Toomas
- Winkler, Cheryl A.
- Labuda, Damian
- Bamshad, Michael
- Jorde, Lynn B.
- Tishkoff, Sarah A.
- Watkins, W. Scott
- Metspalu, Mait
- Sukernik, Rem
- Singh, Lalji
- Pääbo, Svante
- Kelso, Janet
- Patterson, Nick
- Reich, David
- Venue
- Nature
- Published
- 2016-09-21
- Volume
- 538
- Issue
- 7624
- Pages
- 201-206
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5161557
- OpenAlex
- W2522993044
- Cited by
- 1,584
- References
- 47
- Citations by year
- 2026: 100 · 2025: 187 · 2024: 188 · 2023: 155 · 2022: 189 · 2021: 179 · 2020: 173 · 2019: 152 · 2018: 142 · 2017: 104 · 2016: 10
- FWCI
- 109.87
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Universidad Peruana Cayetano Heredia Institutional Repository (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- BORIS (University Library Bern) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- RUNE (Research UNE) (submittedVersion)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- National Science Foundation (1153911, 0924726, 02543, 1032255)
- Wellcome Trust (098051)
- Simons Foundation Autism Research Initiative
- European Commission (15,16, 28,29)
- Russian Foundation for Basic Research (16-06-00364, 16-06-00303)
- Eesti Teadusagentuur (IUT24-1, IUT2-4)
- Max-Planck-Gesellschaft
- Vetenskapsrådet (16,17, 02543, 2014-453)
- Tartu Ülikool
- National Institutes of Health (5ul1tr001067-05, 16,17, 10,11, GM100233)
- Biotechnology and Biological Sciences Research Council (BB/H008802/1, BB/H008802/2)
- European Regional Development Fund (IUT24-1)
- National Human Genome Research Institute (R01HG006399)
- National Institute of General Medical Sciences (R01GM113657, R01GM059290, R01GM100233, R00GM111744, R01GM094402)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK104339)
- National Institute of Environmental Health Sciences (DP1ES022577)
- National Center for Advancing Translational Sciences (UL1-TR001067)
- FP7 Ideas: European Research Council (261213)
- 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
- human genetic variation, dispersal out of Africa, human ancestry, mutation rate, African populations, Aboriginal Australians, Papuans, Andamanese, Indigenous Australians, non-African populations
- MeSH terms
- Animals, Australia, Genetics, Population, Humans, New Guinea, Phylogeny, Species Specificity, Time Factors, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Genomics, Black People, Native Hawaiian or Other Pacific Islander, Racial Groups, History, Ancient, Neanderthals, Mutation Rate, Human Migration, Datasets as Topic
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
