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

BackgroundPopulation 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 FindingsWe evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ∼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 ∼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.
ConclusionsWe 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.

研究背景
群体历史可通过群体遗传祖先（genetic ancestry）得以反映：通过线粒体DNA（mitochondrial DNA，mtDNA）与Y染色体非重组区（non-recombining portion of the Y chromosome，NRY）捕获的基因组变异，可区分性别特异性的基因混合过程。由于近期混血群体（如非裔美国人）中个体间的基因混合程度存在差异，遗传祖先可能会对遗传关联研究造成影响。
主要研究结果
本研究评估了塞内加尔人，以及来自费城的欧裔美国人和非裔美国人的遗传祖先。塞内加尔人的线粒体DNA中约含12%的U单倍型（haplotype，U6与U5b1b单倍型，在北非较为常见），而其NRY单倍型仅属于单倍群（haplogroup）E。在费城群体中，我们观察到不同程度的基因混合：非裔美国人的线粒体DNA与NRY分别有9%~10%和约31%源自欧洲血统，但这一现象并未在欧裔美国人的mtDNA与NRY基因库中呈现镜像结果——欧裔美国人的非欧洲来源mtDNA占比不足7%，非欧洲来源NRY占比不足2%。此外，费城非裔美国人的祖先成分中存在不足2%的美洲原住民贡献；结合mtDNA与NRY估算得到的基因混合程度，与常染色体遗传数据（autosomal genetic data）推导的混合结果一致。为进一步解析上述估算结果，我们结合美洲不同人口群体的背景对样本进行了分析。
研究结论
本研究发现，源自非洲的群体在整个美洲范围内均存在性别偏向性的基因混合（sex-biased admixture）现象：欧洲男性持续对其产生影响，而美洲原住民女性则主要对加勒比地区与南美洲的群体造成贡献。欧洲血统群体中存在较高比例的非欧洲女性祖先成分，这一特征与伊比利亚殖民时期的历史记录高度吻合。本研究数据表明，基因组数据与美洲殖民的历史记录具有良好的相关性。