Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage
Open accessAbstract
Although analysis of modern and ancient genomes showed that Neanderthals contributed genetic material to the ancestors of extant human populations, when and where Neanderthals interacted with modern human populations remain exciting... The time, extent, and genomic effect of the introgressions from archaic humans into ancestors of extant human populations remain some of the most exciting venues of population genetics research in the past decade. Several studies have shown population-specific signatures of introgression events from Neanderthals, Denisovans, and potentially other unknown hominin populations in different human groups. Moreover, it was shown that these introgression events may have contributed to phenotypic variation in extant humans, with biomedical and evolutionary consequences. In this study, we present a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and show that they can be traced back to multiple introgression events. In parallel, we document hundreds of deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.
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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
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
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
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
Letunic, I., & Bork, P. (2016) · Nucleic Acids Res. · doi:10.1093/nar/gkw290 · Cited by 4,851 · 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
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
An integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354 · 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
Origins and functional impact of copy number variation in the human genome
The Wellcome Trust Case Control Consortium, Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T. D., Barnes, C., et al. (2010) · Nature · doi:10.1038/nature08516 · Cited by 1,970 · 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
The genomic landscape of Neanderthal ancestry in present-day humans
Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014) · Nature · doi:10.1038/nature12961 · Cited by 1,107 · see citing works
Genomic insights into the origin of farming in the ancient Near East
Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al. (2016) · Nature · doi:10.1038/nature19310 · Cited by 955 · see citing works
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
An atlas of genetic associations in UK Biobank
Canela‐Xandri, O., Rawlik, K., & Tenesa, A. (2018) · Nature Genetics · doi:10.1038/s41588-018-0248-z · Cited by 657 · see citing works
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
Kelleher, J., Etheridge, A. M., & McVean, G. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004842 · Cited by 628 · 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
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
The Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419 · see citing works
Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe
Currat, M., & Excoffier, L. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020421 · Cited by 376 · see citing works
Reconstructing the genetic history of late Neanderthals
Hajdinjak, M., Fu, Q., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Skoglund, P., Narasimham, V., Rougier, H., Crèvecoeur, I., et al. (2018) · Nature · doi:10.1038/nature26151 · Cited by 258 · see citing works
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Chen, L., Wolf, A. B., Fu, W., Li, L., & Akey, J. M. (2020) · Cell · doi:10.1016/j.cell.2020.01.012 · Cited by 254 · see citing works
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
Limits of long-term selection against Neandertal introgression
Petr, M., Pääbo, S., Kelso, J., & Vernot, B. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814338116 · Cited by 211 · see citing works
Moorjani, P., Sankararaman, S., Fu, Q., Przeworski, M., Patterson, N. J., & Reich, D. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514696113 · Cited by 201 · see citing works
Multiple episodes of interbreeding between Neanderthal and modern humans
Villanea, F. A., & Schraiber, J. G. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0735-8 · Cited by 192 · see citing works
Recovering signals of ghost archaic introgression in African populations
Durvasula, A., & Sankararaman, S. (2020) · Science Advances · doi:10.1126/sciadv.aax5097 · Cited by 158 · see citing works
Complex History of Admixture between Modern Humans and Neandertals
Vernot, B., & Akey, J. M. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.01.006 · Cited by 149 · see citing works
Mondal, M., Bertranpetit, J., & Lao, O. (2019) · Nature Communications · doi:10.1038/s41467-018-08089-7 · Cited by 124 · 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
Kim, B. Y., & Lohmueller, K. E. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.029 · Cited by 82 · see citing works
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 · see citing works
Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation
Xu, D., Pavlidis, P., Taşkent, R. Ö., Alachiotis, N., Flanagan, C., DeGiorgio, M., Blekhman, R., Rühl, S., & Gökçümen, Ö. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx206 · Cited by 62 · see citing works
Self-citationThe Evolution and Functional Impact of Human Deletion Variants Shared with Archaic Hominin Genomes
Lin, Y., Pavlidis, P., Karakoç, E., Ajay, J., & Gökçümen, Ö. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu405 · Cited by 46 · see citing works
Self-citationVariation and Functional Impact of Neanderthal Ancestry in Western Asia
Taşkent, R. Ö., Alioğlu, D., Fer, E., Dönertaş, H. M., Somel, M., & Gökçümen, Ö. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx216 · Cited by 18 · see citing works
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Quantifying the contribution of Neanderthal introgression to the heritability of complex traits
McArthur, E., Rinker, D. C., & Capra, J. A. (2021) · Nature Communications · doi:10.1038/s41467-021-24582-y · Cited by 71 · 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
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
Balancing selection on genomic deletion polymorphisms in humans
Aqil, A., Speidel, L., Pavlidis, P., & Gökçümen, Ö. (2023) · eLife · doi:10.7554/elife.79111 · Cited by 28 · see citing works
Self-citationKoller, D., Wendt, F. R., Pathak, G. A., De Lillo, A., De Angelis, F., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2022) · BMC Biology · doi:10.1186/s12915-022-01449-2 · Cited by 27 · see citing works
“Leveraging data generated from large-scale GWAS conducted in Biobank Japan (BBJ) [29, 30], we analyzed the genetic background of individuals of East Asian descent (EAS).”
BackgroundInfluentialApportioning 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
Andirkó, A., Moriano, J., Vitriolo, A., Kuhlwilm, M., Testa, G., & Boeckx, C. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-13589-0 · Cited by 16 · see citing works
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Santo, L. N. D., Quilodrán, C. S., & Currat, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad252 · Cited by 4 · see citing works
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Koller, D., Wendt, F., Pathak, G., Lillo, A. D., Angelis, F. D., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2021) · bioRxiv · doi:10.1101/2021.08.12.456138 · Cited by 4 · see citing works
Wroblewski, T. H., Witt, K. E., Lee, S., Malhi, R. S., Peede, D., Huerta‐Sánchez, E., Villanea, F. A., & Claw, K. G. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad222 · Cited by 3 · see citing works
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- Authors
- Taskent, O., Lin, Y. L., Patramanis, I., Pavlidis, P., & Gokcumen, O.
- Affiliations
- Department of Biological Sciences , State University of New York at Buffalo, New York 14260
- University of Chicago (US)
- Foundation for Research and Technology Hellas (GR)
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-06-01
- Volume
- 215
- Issue
- 2
- Pages
- 497-509
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC7268982
- OpenAlex
- W3014184378
- Cited by
- 20
- References
- 36
- Citations by year
- 2024: 2 · 2023: 5 · 2022: 5 · 2021: 7 · 2020: 1
- FWCI
- 16.95
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- creativecommons.org/licenses/by/4.0/ (vor, 224 d)
- Locations
- Genetics (publishedVersion, public-domain)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Commons - University of South Florida (University of South Florida) (submittedVersion)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Neanderthal introgression, Denisovans, deletion polymorphism, East Asian ancestry, human genetic variation
- MeSH terms
- Animals, Genetics, Population, Haplotypes, Humans, Phenotype, Polymorphism, Genetic, Russia, Selection, Genetic, Hominidae, Genome, Human, Neanderthals
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