Genome-Wide Patterns of Population Structure and Admixture in West Africans and African Americans

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 01/2010; 107(2):786-91. DOI: 10.1073/pnas.0909559107
Source: PubMed


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study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

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Available from: Matthew R Nelson, Jan 07, 2014
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    • "The superior preservation of the two African individuals (125 and 165) from the urban discard deposit burial site and resistance of their genetic signals to restriction of the data set to reads with showing deaminations encouraged investigation of their origins at a finer detail, showing affinity with Bantu-speaking groups and Western African Mandenka and Yoruba populations, as expected from historical records. A previous study18 has shown that African chromosomal segments in African-American individuals were most similar to Niger-Kordofanian-speaking populations such as those included here. Here, we did not achieve sufficient resolution in PCA and ADMIXTURE to distinguish between Bantu and non-Bantu Niger-Kordofanian populations. "
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