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

Date Published: November 25, 2009

Publisher: Public Library of Science

Author(s): Klara Stefflova, Matthew C. Dulik, Athma A. Pai, Amy H. Walker, Charnita M. Zeigler-Johnson, Serigne M. Gueye, Theodore G. Schurr, Timothy R. Rebbeck, John Relethford. http://doi.org/10.1371/journal.pone.0007842

Abstract: 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.

Partial Text: Populations of the present-day Americas were shaped by diverse incoming groups and their intermixing. Although the number of the Native Americans was greatly reduced due to conflict and disease they, together with the early arriving Europeans and surviving Africans brought to the Americas during the massive African Diaspora, all left their genetic imprint in multiple admixed populations. Later, several other immigrant groups from around the World (e.g. Asian populations) and increasingly common admixture among the existing groups further amplified the admixed character of this continent. This complicated ancestry and admixture is reflected in an individual’s genetic background. While recognizing that each individual is genetically unique, it is still common in epidemiology to categorize people into a few self-identified races (SIRE) that partly reflect the complicated history of each group, yet fail to predict the extent of the contribution from each parental population to different SIRE groups [1].

First, we deeply typed both mtDNA and NRY in Philadelphian African Americans and European Americans. We also typed the same markers in a group of Senegalese in order to gain insight into the detailed composition of one of the founding populations (e.g. the presence of “Eurasian” haplotypes) instead of relying on less well characterized published data. We then proceeded to phylogenetically analyze these haplotypes in parallel with admixture analysis using ADMIX, exploring the possible founding populations. Based on these analyses, we focused further on analysis using three founding populations (K = 3 was also corroborated by our STRUCTURE analysis using autosomal AIMs).

We have characterized the mitochondrial DNA (mtDNA) and non-recombining portion of Y-chromosome (NRY) variation in a sample from Senegal as well as two major groups of Philadelphians: self-identified European Americans and African Americans. These two groups comprise over 88% of the Philadelphian population (45% and 43.2%, respectively, according to the 2000 U.S. Census). We found mainly African haplogroups in the Senegalese sample, with the exception of 12.2% of Senegalese (3 Wolof, 2 Fulbe, and 1 Sahalle) carrying U6 and U5b1b mtDNA haplogroups that, although haplogroup U is of Eurasian origin, can be found throughout North Africa as a result of an ancient migration back to Africa. In Philadelphian African Americans, we observed a significant European admixture (mtDNA>9% and NRY>31%) as well as a small (<2%) contribution from Native Americans. To calculate the corresponding autosomal ancestry of self-identified African Americans, accounting for both maternal and paternal contributions, we used our data to compute mAUTO = ½ mmtDNA + ½ mNRY[5], which was estimated to be: 78.4% African, 20.1% European, and 1.5% Native American. These calculated estimates seem to accurately reflect the autosomal group admixture, based on typing a small subset of samples using autosomal AIMs (n = 31, 74.4% African, 23.7% European, and 1.9% SE Asian/Native American, Table S4). Also, these estimates parallel previous reports, although our estimates suggest a higher European contribution, especially compared to the 12.7–13.8% autosomal and 2.8–11% low resolution maternal European ancestry found in a sample from Philadelphia reported by Parra et al. [9]. For example, European contribution to NRY, autosomes, and mtDNA was estimated to be 28.46%, 19.99%, and 8.51%, respectively, in African Americans from Pittsburg, Chicago, Baltimore and North Carolina [5], or autosomal ancestry of African Americans from NY state was estimated to be 83% African, 15% European and 2% Native American [1]. Source: http://doi.org/10.1371/journal.pone.0007842

 

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