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Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas

Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, Gueye SM, Schurr TG, Rebbeck TR - PLoS ONE (2009)

Bottom Line: We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America.The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization.These data suggest that genomic data correlate well with historical records of colonization in the Americas.

Affiliation: Department of Biostatistics and Epidemiology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America. Klara.Stefflova@cancer.org.uk

ABSTRACT

Background: Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans.

Principal findings: We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of approximately 12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9-10% mtDNAs and approximately 31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is <2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas.

Conclusions: We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.

Y chromosome phylogenetic tree.NRY tree haplogroups observed in Philadelphia and Senegal data with typed SNPs indicated on each branch. Associated with each branch is the number of samples observed for each haplogroup in the pool of African Americans (AA, n = 199), European Americans (EA, n = 190), and Senegalese (Af, n = 33). We have omitted from the NRY tree M148 SNP designating E1b1b1a3a (formerly E3b1a). One EA sample belonging to this haplogroup was added to E1b1b1 (#). One EA sample was 12f2a* (Hg J) but was grouped with J1 (*) because of space constraints. The raw data can be found in File S1.
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pone-0007842-g002: Y chromosome phylogenetic tree.NRY tree haplogroups observed in Philadelphia and Senegal data with typed SNPs indicated on each branch. Associated with each branch is the number of samples observed for each haplogroup in the pool of African Americans (AA, n = 199), European Americans (EA, n = 190), and Senegalese (Af, n = 33). We have omitted from the NRY tree M148 SNP designating E1b1b1a3a (formerly E3b1a). One EA sample belonging to this haplogroup was added to E1b1b1 (#). One EA sample was 12f2a* (Hg J) but was grouped with J1 (*) because of space constraints. The raw data can be found in File S1.

Mentions: For NRY, the samples were typed using pre-designed TaqMan assays in combination with multiplex fragment analysis and RFLP (Figure 2). The SNPs are listed in Table S3 (see also References S1) together with the haplogroup designation established by the Y-Chromosome Consortium in 2002 [18] and revised in Karafet et al. 2008 [19]. Both mtDNA, NRY variation and ethnicity information is listed in File S1.

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Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas

Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, Gueye SM, Schurr TG, Rebbeck TR - PLoS ONE (2009)

Y chromosome phylogenetic tree.NRY tree haplogroups observed in Philadelphia and Senegal data with typed SNPs indicated on each branch. Associated with each branch is the number of samples observed for each haplogroup in the pool of African Americans (AA, n = 199), European Americans (EA, n = 190), and Senegalese (Af, n = 33). We have omitted from the NRY tree M148 SNP designating E1b1b1a3a (formerly E3b1a). One EA sample belonging to this haplogroup was added to E1b1b1 (#). One EA sample was 12f2a* (Hg J) but was grouped with J1 (*) because of space constraints. The raw data can be found in File S1.
© Copyright Policy
pone-0007842-g002: Y chromosome phylogenetic tree.NRY tree haplogroups observed in Philadelphia and Senegal data with typed SNPs indicated on each branch. Associated with each branch is the number of samples observed for each haplogroup in the pool of African Americans (AA, n = 199), European Americans (EA, n = 190), and Senegalese (Af, n = 33). We have omitted from the NRY tree M148 SNP designating E1b1b1a3a (formerly E3b1a). One EA sample belonging to this haplogroup was added to E1b1b1 (#). One EA sample was 12f2a* (Hg J) but was grouped with J1 (*) because of space constraints. The raw data can be found in File S1.
Mentions: For NRY, the samples were typed using pre-designed TaqMan assays in combination with multiplex fragment analysis and RFLP (Figure 2). The SNPs are listed in Table S3 (see also References S1) together with the haplogroup designation established by the Y-Chromosome Consortium in 2002 [18] and revised in Karafet et al. 2008 [19]. Both mtDNA, NRY variation and ethnicity information is listed in File S1.

Bottom Line: We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America.The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization.These data suggest that genomic data correlate well with historical records of colonization in the Americas.

Affiliation: Department of Biostatistics and Epidemiology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America. Klara.Stefflova@cancer.org.uk

ABSTRACT

Background:

Background: Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans.

Principal findings: We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of approximately 12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9-10% mtDNAs and approximately 31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is <2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas.

Conclusions: We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.

View Similar Images In: Results  - Collection
View Article: Pubmed Central -  PubMed
Show All Figures - Show MeSH
getmorefigures.php?pmc=2776971&rFormat=json&query=null&req=5