Genome-wide patterns of population structure and admixture in West Africans and African Americans
Open accessAbstract
Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans ( n = 365) and individuals with ancestry from West Africa ( n = 203 from 12 populations) and Europe ( n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th–75th percentiles: 11.6–27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.
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More recent studies using high-density genotype data provide reliable individual ancestry estimates, illustrate large variability in African and European ancestry proportions at an individual level, and detect low proportions of Native American ancestry.
“More recent studies that utilized high-density genotype data provide reliable individual ancestry estimates, illustrate the large variability in African and European ancestry proportions at an individual level, and are able to detect low proportions of Native American ancestry.3–11”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [9]
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Experimental — accuracy not yet measuredEstimates of ancestry on the X chromosome have been shown to have higher African ancestry in African Americans.
“In particular, estimates of ancestry on the X chromosome have been shown to have higher African ancestry in African Americans.9”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [9]
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Cites
The Structure of Haplotype Blocks in the Human Genome
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. (2002) · Science · doi:10.1126/science.1069424 · Cited by 5,863 · see citing works
Convergent adaptation of human lactase persistence in Africa and Europe
Tishkoff, S. A., Reed, F. A., Ranciaro, A., Voight, B. F., Babbitt, C. C., Silverman, J. S., Powell, K., Mortensen, H. M., Hirbo, J. B., Osman, M., et al. (2007) · Nature Genetics · doi:10.1038/ng1946 · Cited by 1,615 · see citing works
Self-citationThe Genetic Structure and History of Africans and African Americans
Tishkoff, S. A., Reed, F. A., Friedlaender, F. R., Ehret, C., Ranciaro, A., Froment, A., Hirbo, J. B., Awomoyi, A. A., Bodo, J.-M., Doumbo, O., et al. (2009) · Science · doi:10.1126/science.1172257 · Cited by 1,573 · see citing works
Self-citationEstimating African American Admixture Proportions by Use of Population-Specific Alleles
Parra, E. J., Marcini, A., Akey, J., Martinson, J., Batzer, M. A., Cooper, R., Forrester, T., Allison, D. B., Deka, R., Ferrell, R. E., et al. (1998) · The American Journal of Human Genetics · doi:10.1086/302148 · Cited by 771 · see citing works
Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins
Tishkoff, S. A., Dietzsch, E., Speed, W., Pakstis, A. J., Kidd, J. R., Cheung, K., Bonné-Tamir, B., Santachiara-Benerecetti, A. S., Moral, P., Krings, M., et al. (1996) · Science · doi:10.1126/science.271.5254.1380 · Cited by 587 · see citing works
Self-citationCorrelation between Genetic and Geographic Structure in Europe
Lao, O., Lu, T. T., Nothnagel, M., Junge, O., Freitag-Wolf, S., Caliebe, A., Balascakova, M., Bertranpetit, J., Bindoff, L. A., Comas, D., et al. (2008) · Current Biology · doi:10.1016/j.cub.2008.07.049 · Cited by 503 · see citing works
Self-citationReed, T. E. (1969) · Science · doi:10.1126/science.165.3895.762 · Cited by 319 · see citing works
Nelson, M. R., Bryc, K., King, K. S., Indap, A., Boyko, A. R., Novembre, J., Briley, L. P., Maruyama, Y., Waterworth, D. M., Waeber, G., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.08.005 · Cited by 293 · see citing works
Self-citationShipwrecks and founder effects: Divergent demographic histories reflected in Caribbean mtDNA
Salas, A., Richards, M., Lareu, M., Sobrino, B., Silva, S., Matamoros, M., Macaulay, V., & Carracedo, Á. (2005) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20117 · Cited by 63 · see citing works
Flagged first, then by citations
Research works printed but not linked: 5
- [24]Nelis M, et al. (2009) Genetic structure of Europeans: A view from the North-East. PLoS One 4(5):e5472.
- [27]Lovejoy PE (2000) Transformations in Slavery (Cambridge Univ Press, New York).
- [30]Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2(12):e190.
- [42]Tian C, et al. (2008) Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 4(1):e4. Am J Hum Genet 81(1):626 -633.
- [44]Hall GM (2005) Slavery and African Ethnicities in the Americas: Restoring the Links (Univ North Carolina Press, Chapel Hill, NC).
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The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
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Howie, B., Marchini, J., & Stephens, M. (2011) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.111.001198 · Cited by 966 · see citing works
Tracing the peopling of the world through genomics
Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728 · see citing works
Self-citationThe genetic ancestry of African Americans, Latinos, and European Americans across the United States
Bryc, K., Durand, E. Y., Macpherson, J. M., Reich, D., & Mountain, J. L. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.11.010 · Cited by 712 · see citing works
Self-citationGenetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z. A., Pacis, A., Dumaine, A., Grenier, J.-C., Freiman, A., Sams, A. J., Hebert, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.025 · Cited by 512 · see citing works
Hunter-gatherer genomic diversity suggests a southern African origin for modern humans
Henn, B. M., Gignoux, C. R., Jobin, M., Granka, J. M., Macpherson, J. M., Kidd, J. M., Rodríguez-Botigué, L., Ramachandran, S., Hon, L., Brisbin, A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017511108 · Cited by 502 · see citing works
Self-citationMiller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., Kim, H. L., Burhans, R. C., Drautz, D. I., Wittekindt, N. E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210506109 · Cited by 353 · see citing works
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Moreno-Estrada, A., Gravel, S., Zakharia, F., McCauley, J. L., Byrnes, J. K., Gignoux, C. R., Ortiz-Tello, P. A., Martínez, R. J., Hedges, D. J., Morris, R. W., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003925 · Cited by 327 · see citing works
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Altmäe, S., Esteban, F. J., Stavreus-Evers, A., Simón, C., Giudice, L., Lessey, B. A., Horcajadas, J. A., Macklon, N. S., D'Hooghe, T., Campoy, C., et al. (2014) · Human Reproduction Update · doi:10.1093/humupd/dmt048 · Cited by 151 · see citing works
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Kidd, J. M., Gravel, S., Byrnes, J., Moreno-Estrada, A., Musharoff, S., Bryc, K., Degenhardt, J. D., Brisbin, A., Sheth, V., Chen, R., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.08.025 · Cited by 95 · see citing works
Self-citationMaglo, K. N., Mersha, T. B., & Martin, L. J. (2016) · Frontiers in Genetics · doi:10.3389/fgene.2016.00022 · Cited by 106 · see citing works
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Fujimura, J. H., Bolnick, D. A., Rajagopalan, R., Kaufman, J. S., Lewontin, R. C., Duster, T., Ossorio, P., & Marks, J. (2014) · Sociological Theory · doi:10.1177/0735275114551611 · Cited by 76 · see citing works
- Authors
- Bryc, K., Auton, A., Nelson, M. R., Oksenberg, J. R., Hauser, S. L., Williams, S., Froment, A., Bodo, J.-M., Wambebe, C., Tishkoff, S. A., & Bustamante, C. D.
- Affiliations
- Cornell University (US)
- GlaxoSmithKline (United States) (US)
- University of California, San Francisco (US)
- Vanderbilt University (US)
- Muséum national d'Histoire naturelle (FR)
- Ministry of Scientific Research and Innovation (CM)
- International Biomedical Research in Africa, Abuja, Nigeria; and
- University of Pennsylvania (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2009-12-22
- Volume
- 107
- Issue
- 2
- Pages
- 786-791
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2818934
- OpenAlex
- W2051864455
- Cited by
- 455
- References
- 9
- Citations by year
- 2026: 10 · 2025: 15 · 2024: 12 · 2023: 19 · 2022: 15 · 2021: 21 · 2020: 21 · 2019: 29 · 2018: 30 · 2017: 37 · 2016: 34 · 2015: 43 · 2014: 35 · 2013: 31 · 2012: 41
- FWCI
- 19.78
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0196183, 0827436, 0552486)
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM083606, R01GM076637, 1R01GM83606)
- National Institute of Neurological Disorders and Stroke (R01NS046297)
- National Institute of Environmental Health Sciences (DP1ES022577)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- population structure, genetic admixture, African Americans, West Africans, European ancestry, African ancestry, Bantu expansion, sex-biased gene flow, X chromosome, transatlantic slave trade, African diaspora, European populations
- MeSH terms
- Africa, Western, Algorithms, Black or African American, Ethnicity, Europe, Female, Genetic Markers, Geography, Humans, Language, Male, United States, Genetic Variation, Africa South of the Sahara, Black People, Genome-Wide Association Study
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