Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation
Open accessAbstract
To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Evidence for super-archaic introgression into the ancestors of the Altai Denisovans and, possibly, Andamanese populations suggests that viable reproduction between super-archaic hominins and more derived hominins may have been possible.
“Evidence for super-archaic introgression into the ancestors of the Altai Denisovans 30 and, possibly, Andamanese populations 31-33 , suggests that viable reproduction may actually have been possible, though further evaluation of these hypotheses at present is not possible given the available data.”
From Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture (2021) · 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.
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 · see citing works
PLINK: 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 · see citing works
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 · see citing works
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,008 · see citing works
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
Tajima, F. (1989) · Genetics · doi:10.1093/genetics/123.3.585 · Cited by 13,991 · 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
Fast 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 · see citing works
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · 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
Statistical tests of neutrality of mutations.
Fu, Y., & Li, W. (1993) · Genetics · doi:10.1093/genetics/133.3.693 · Cited by 4,051 · 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
The History and Geography of Human Genes
Cavalli-Sforza, L. L., Menozzi, P., & Piazza, A. (2018) · Princeton University Press eBooks · doi:10.2307/j.ctv301gjp · Cited by 3,175 · see citing works
A Map of Recent Positive Selection in the Human Genome
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,912 · 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 population splits and mixtures from genome-wide allele frequency data
Pickrell, J. K., & Pritchard, J. K. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002967 · Cited by 2,731 · 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
Genome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131 · see citing works
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106 · 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
Massive migration from the steppe was a source for Indo-European languages in Europe
Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940 · 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
A linear complexity phasing method for thousands of genomes
Delaneau, O., Marchini, J., & Zagury, J.-F. (2012) · Nature Methods · doi:10.1038/nmeth.1785 · Cited by 1,850 · see citing works
Hitchhiking Under Positive Darwinian Selection
Fay, J. C., & Wu, C.-I. (2000) · Genetics · doi:10.1093/genetics/155.3.1405 · Cited by 1,819 · see citing works
Reconstructing Indian population history
Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L. (2009) · Nature · doi:10.1038/nature08365 · Cited by 1,674 · see citing works
Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
Self-citationHuman Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays
Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010) · Science · doi:10.1126/science.1181498 · Cited by 1,212 · see citing works
Inferring human population size and separation history from multiple genome sequences
Schiffels, S., & Durbin, R. M. (2014) · Nature Genetics · doi:10.1038/ng.3015 · Cited by 1,051 · see citing works
Genomic scans for selective sweeps using SNP dataPreprint
Nielsen, R., Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G., & Bustamante, C. D. (2005) · Genome Research · doi:10.1101/gr.4252305 · Cited by 1,024 · see citing works
The Genetic Association Database
Becker, K. G., Barnes, K. C., Bright, T. J., & Wang, S. A. (2004) · Nature Genetics · doi:10.1038/ng0504-431 · Cited by 971 · see citing works
Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., et al. (2014) · Nature · doi:10.1038/nature12736 · Cited by 963 · see citing works
Great ape genetic diversity and population history
Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdós, B., Veeramah, K. R., Woerner, A. E., O’Connor, T. D., Santpere, G., et al. (2013) · Nature · doi:10.1038/nature12228 · Cited by 873 · see citing works
Self-citationAn 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
Demographic history and rare allele sharing among human populations
Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G., Clark, A. G., Yu, F., Gibbs, R. A., The 1000 Genomes Project, Bustamante, C. D., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019276108 · Cited by 625 · see citing works
Calibrating a coalescent simulation of human genome sequence variation
Schaffner, S. F., Foo, C., Gabriel, S., Reich, D., Daly, M. J., & Altshuler, D. (2005) · Genome Research · doi:10.1101/gr.3709305 · Cited by 616 · see citing works
Resurrecting Surviving Neandertal Lineages from Modern Human Genomes
Vernot, B., & Akey, J. M. (2014) · Science · doi:10.1126/science.1245938 · Cited by 562 · see citing works
Delaneau, O., Marchini, J., McVean, G., Donnelly, P., Lunter, G. A., Marchini, J., Myers, S., Hinch, A. G., Iqbal, Z., Mathieson, I., et al. (2014) · Nature Communications · doi:10.1038/ncomms4934 · Cited by 395 · see citing works
Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde, I., Allentoft, M. E., Sánchez-Quinto, F., Santpere, G., Chiang, C. W. K., DeGiorgio, M., Prado-Martinez, J., Rodríguez, J. A., Rasmussen, S., Quilez, J., et al. (2014) · Nature · doi:10.1038/nature12960 · Cited by 360 · see citing works
Self-citationGlobal diversity, population stratification, and selection of human copy-number variation
Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., et al. (2015) · Science · doi:10.1126/science.aab3761 · Cited by 345 · see citing works
Self-citationLatest Homo erectus of Java: Potential Contemporaneity with Homo sapiens in Southeast Asia
Swisher, C. C., Rink, W. J., Antón, S. C., Schwarcz, H. P., Curtis, G. H., Suprijo, A., & Widiasmoro (1996) · Science · doi:10.1126/science.274.5294.1870 · Cited by 323 · 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
Basu, A., Sarkar-Roy, N., & Majumder, P. P. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1513197113 · Cited by 213 · see citing works
Self-citationHeight-reducing variants and selection for short stature in Sardinia
Żołędziewska, M., The Understanding Society Scientific Group, Sidore, C., Chiang, C. W. K., Sanna, S., Mulas, A., Steri, M., Busonero, F., Marcus, J. H., Marongiu, M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3403 · Cited by 98 · see citing works
The Andaman Islanders: A Study in Social Anthropology
Brown, A. R. (2018) · Medical Entomology and Zoology · Cited by 93 · see citing works
Pybus, M., Luisi, P., Dall’Olio, G. M., Uzkudun, M., Laayouni, H., Bertranpetit, J., & Engelken, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv493 · Cited by 83 · see citing works
Self-citationOn the Geographical Distribution of the Chief Modifications of Mankind
Huxley, T. H. (1870) · The Journal of the Ethnological Society of London (1869-1870) · doi:10.2307/3014371 · Cited by 72 · see citing works
Primate brains, the ‘island rule’ and the evolution of Homo floresiensis
Montgomery, S. H. (2013) · Journal of Human Evolution · doi:10.1016/j.jhevol.2013.08.006 · Cited by 42 · see citing works
Population and genomic lessons from genetic analysis of two Indian populations
Juyal, G., Mondal, M., Luisi, P., Laayouni, H., Sood, A., Midha, V., Heutink, P., Bertranpetit, J., Thelma, B. K., & Casals, F. (2014) · Human Genetics · doi:10.1007/s00439-014-1462-0 · Cited by 29 · see citing works
Self-citationIs Great Andamanese genealogically and typologically distinct from Onge and Jarawa?
Abbi, A. (2008) · Language Sciences · doi:10.1016/j.langsci.2008.02.002 · Cited by 17 · see citing works
Molnar, S. (2015) · Routledge eBooks · doi:10.4324/9781315663975 · Cited by 6 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [12]12. throughput sequencing data. Nucleic Acids Res. 38, e164 (2010). 444 <!-- image --> b <!-- image --> <!-- image --> a FRN(W) <!-- image --> b DAI(W) <!-- image --> <!-- image -->
Cited by
Sorted by citations
Human occupation of northern Australia by 65,000 years ago
Clarkson, C., Jacobs, Z., Marwick, B., Fullagar, R., Wallis, L., Smith, M., Roberts, R. G., Hayes, E., Lowe, K., Carah, X., et al. (2017) · Nature · doi:10.1038/nature22968 · Cited by 1,185 · see citing works
On the origin of modern humans: Asian perspectives
Bae, C. J., Douka, K., & Petraglia, M. D. (2017) · Science · doi:10.1126/science.aai9067 · Cited by 471 · see citing works
Multiple Deeply Divergent Denisovan Ancestries in Papuans
Jacobs, G. S., Hudjashov, G., Saag, L., Kusuma, P., Darusallam, C. C., Lawson, D. J., Mondal, M., Pagani, L., Ricaut, F.-X., Stoneking, M., et al. (2019) · Cell · doi:10.1016/j.cell.2019.02.035 · Cited by 346 · see citing works
Self-citationDetecting 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
Mondal, M., Bertranpetit, J., & Lao, O. (2019) · Nature Communications · doi:10.1038/s41467-018-08089-7 · Cited by 124 · see citing works
Self-citationJinam, 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-citationPhilippine 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
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
Evolutionary and medical consequences of archaic introgression into modern human genomes
Dolgova, O., & Lao, O. (2018) · Genes · doi:10.3390/genes9070358 · Cited by 34 · see citing works
Reply to ‘No evidence for unknown archaic ancestry in South Asia’
Mondal, M., Casals, F., Majumder, P. P., & Bertranpetit, J. (2018) · Nature Genetics · doi:10.1038/s41588-018-0280-z · Cited by 8 · see citing works
Self-citationNo 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
- Authors
- Mondal, M., Casals, F., Xu, T., Dall'Olio, G. M., Pybus, M., Netea, M. G., Comas, D., Laayouni, H., Li, Q., Majumder, P. P., & Bertranpetit, J.
- Affiliations
- Universitat Pompeu Fabra (ES)
- BGI Group (China) (CN)
- Radboud University Medical Center (NL)
- Universitat Autònoma de Barcelona (ES)
- National Institute of Biomedical Genomics (IN)
- Corresponding author
- Majumder, Partha P
- Bertranpetit, Jaume
- ORCID
- Venue
- Nature Genetics
- Published
- 2016-07-25
- Volume
- 48
- Issue
- 9
- Pages
- 1066-1070
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2476899933
- Cited by
- 149
- References
- 51
- Citations by year
- 2026: 7 · 2025: 17 · 2024: 10 · 2023: 6 · 2022: 15 · 2021: 24 · 2020: 15 · 2019: 14 · 2018: 23 · 2017: 16 · 2016: 2
- FWCI
- 14.79
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (acceptedVersion, other-oa)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- 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
- Andamanese, human migration out of Africa, body size, short stature, morphological adaptation, population genomics, South Asian populations, Southeast Asian populations, Out of Africa hypothesis
- MeSH terms
- Adaptation, Physiological, Asia, Genetic Markers, Genetics, Population, Humans, Phenotype, Selection, Genetic, Genetic Variation, Asian People, Genome-Wide Association Study, Human Migration
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
