Genome-wide patterns of population structure and admixture in West Africans and African Americans

Katarzyna Bryc, Adam Auton, Matthew R. Nelson, Jorge R. Oksenberg, Stephen L. Hauser, Scott Williams, Alain Froment, Jean Marie Bodo, Charles Wambebe, Sarah A. Tishkoff, Carlos D. Bustamante

Research output: Contribution to journalArticle

280 Citations (Scopus)

Abstract

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study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

Original languageEnglish (US)
Pages (from-to)786-791
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number2
DOIs
StatePublished - 2010
Externally publishedYes

Fingerprint

African Americans
Genome
Population
Slaves
Niger
Western Africa
Gene Flow
X Chromosome
Language
History
Genotype

Keywords

  • Africa
  • Human genomics
  • Population genetics

ASJC Scopus subject areas

  • General

Cite this

Genome-wide patterns of population structure and admixture in West Africans and African Americans. / Bryc, Katarzyna; Auton, Adam; Nelson, Matthew R.; Oksenberg, Jorge R.; Hauser, Stephen L.; Williams, Scott; Froment, Alain; Bodo, Jean Marie; Wambebe, Charles; Tishkoff, Sarah A.; Bustamante, Carlos D.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 107, No. 2, 2010, p. 786-791.

Research output: Contribution to journalArticle

Bryc, K, Auton, A, Nelson, MR, Oksenberg, JR, Hauser, SL, Williams, S, Froment, A, Bodo, JM, Wambebe, C, Tishkoff, SA & Bustamante, CD 2010, 'Genome-wide patterns of population structure and admixture in West Africans and African Americans', Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 2, pp. 786-791. https://doi.org/10.1073/pnas.0909559107
Bryc, Katarzyna ; Auton, Adam ; Nelson, Matthew R. ; Oksenberg, Jorge R. ; Hauser, Stephen L. ; Williams, Scott ; Froment, Alain ; Bodo, Jean Marie ; Wambebe, Charles ; Tishkoff, Sarah A. ; Bustamante, Carlos D. / Genome-wide patterns of population structure and admixture in West Africans and African Americans. In: Proceedings of the National Academy of Sciences of the United States of America. 2010 ; Vol. 107, No. 2. pp. 786-791.
@article{e3d2b93d7dc94599967392fd8313bb39,
title = "Genome-wide patterns of population structure and admixture in West Africans and African Americans",
abstract = "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.",
keywords = "Africa, Human genomics, Population genetics",
author = "Katarzyna Bryc and Adam Auton and Nelson, {Matthew R.} and Oksenberg, {Jorge R.} and Hauser, {Stephen L.} and Scott Williams and Alain Froment and Bodo, {Jean Marie} and Charles Wambebe and Tishkoff, {Sarah A.} and Bustamante, {Carlos D.}",
year = "2010",
doi = "10.1073/pnas.0909559107",
language = "English (US)",
volume = "107",
pages = "786--791",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "2",

}

TY - JOUR

T1 - Genome-wide patterns of population structure and admixture in West Africans and African Americans

AU - Bryc, Katarzyna

AU - Auton, Adam

AU - Nelson, Matthew R.

AU - Oksenberg, Jorge R.

AU - Hauser, Stephen L.

AU - Williams, Scott

AU - Froment, Alain

AU - Bodo, Jean Marie

AU - Wambebe, Charles

AU - Tishkoff, Sarah A.

AU - Bustamante, Carlos D.

PY - 2010

Y1 - 2010

N2 - 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.

AB - 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.

KW - Africa

KW - Human genomics

KW - Population genetics

UR - http://www.scopus.com/inward/record.url?scp=76249102674&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=76249102674&partnerID=8YFLogxK

U2 - 10.1073/pnas.0909559107

DO - 10.1073/pnas.0909559107

M3 - Article

VL - 107

SP - 786

EP - 791

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 2

ER -