correlates with the average AIMs-based ancestry [1], [5], [7]. Also, unlike AIMs, these markers are powerful tools for predicting maternal/paternal population demographic processes [36–38] and have comprehensive published resources covering all populated continents. These studies of continental ancestry in the Americas conclude that individual admixture, and often group ancestry, varies extensively between geographically distinct groups united by the same ancestral label. The existing admixture frequently has a distinct gender bias, showing a larger contribution from European males and African/Native American females across multiple groups of the whole continent [5], [39], [40] (with the exception of European Americans [4], [7]). The Native American compo- nent that is generally small in North America [5] plays a significant role in Central and South America [39]. Focusing on African- derived populations, US African Americans were described to have a significant and variable proportion of individual European ancestry. While on average this European ancestry falls within the 15–25% range [1], [5], [15], regional differences were reported among some African American groups (the lowest level of European admixture (3.5%) was reported in Gullah Sea Islanders [41]). In Central and South America, in addition to varying European admixture, a variable Native American component adds to the ancestral complexity, making the populations of the Americas distinct from each other in their continental admixture. Our interest lies in the African component of this continental admixture. The contribution of African ancestry to American populations was previously investigated using historical resources as well as genetic markers, mainly mtDNA. These reports suggest that there are ancestral contributions from 2–3 large African regions: West (W), West-Central/South-West (WC/SW) [3], and possibly South-East (SE) Africa [6] and their proportion differs between North, Central and South America. This implies that continental admixture is not the only source of genetic differences between geographically distinct populations in the Americas of African ancestry, but within-Africa admixture may play a significant role as well. More recently, reports using autosomal markers and focusing on US African Americans have also been published. Bryc et al. investigated the ancestry of 365 US African Americans from across the United States and concluded that their ancestry is most similar to non-Bantu Niger Kordofanian-speaking populations of W/WC Africa based on analysis including 12 populations [40]. Zakharia et al. showed that the individual ancestry of 136 African Americans, investigated using 450,000 autosomal SNPs, is drawn mainly from West and West-Central Africa and, unlike the European component, this proportion is not very variable [42]. However, African variation was represented either by populations expected to contribute little to present-day US African Americans or by Yoruba, Mandenka, and Bantu – three populations representing the hundreds of populations of W/WC/SW Africa. While these AIMs-based studies have done a thorough analysis using current-day resources, they are limited by both their low within-Africa resolution that may reduce the complexity of the within-Africa component in African American ancestry as well as a narrow focus within the Americas. While it has been previously reported that the contribution of W and WC/SW African populations varies between African- descended populations from North, Central and South America [2], [3], there remains limited information about the underlying reasons for these differences. To address this, we first compre- hensively characterized African genetic diversity on the population level. Defining diverse African groups helped us to estimate with unprecedented resolution their contribution to admixed Within-Africa Ancestry African-descended American populations of North and South America, and the Caribbean. By using a systematic approach to understand the source of African ancestry we have shown that genetically distinct African populations contributed differently to the genetic pool of geographically distinct American populations of African descent. Interpretation of our results suggests how this genetic ancestry-based pattern reflects the different colonial history of each region. Results Continental Ancestry of African Americans mtDNA and NRY. Using comprehensive databases (File S1 and File S2) assembled from published mtDNA and NRY marker data, we have calculated the continental group admixture in American populations of primarily African ancestry sampled from Philadelphia, across the United States, the Caribbean, and Brazil (see Table S1 and Table S2 in File S3 for the list of populations and publications mined for mtDNA and NRY marker data, respectively). We confirmed that the previously described [4], [5], [7] European gender-specific admixture and a North-South gradient are present. European males, rather than females, are predominantly responsible for the European genomic contribu- tion to American populations of African descent and both Native American females and European males provided a greater con- tribution to South American (represented by Brazil) compared to US admixed populations (Figure 1, and Table S3 in File S3). Autosomal Ancestry Informative Markers (AIMs). To complement the group-specific information of uniparental (mtDNA and NRY) markers, we typed 175 autosomal AIMs (File S4) to estimate the continental individual admixture proportions in a larger set of Philadelphia African Americans (n = 331, Figure 1), Philadelphia European Americans (n = 728, Figure S1 in File S3), and Africans from Senegal (n = 205, Figure 1) (these include all of the Philadelphia samples subjected to mtDNA and NRY analysis). Consistent with historical records, we see substantial inter-individual variability in admixture in the African Americans, with estimated African ancestry ranging from 7% to ,100% (average 79.1%). In comparison, European ancestry in European Americans rarely dropped below 85%. Further, we compared the AIMs-based group ancestry estimates (obtained by averaging the individual ancestry estimates) with the estimates calculated here based on published mtDNA and NRY variation in all African-descended American groups (see Table S3 in File S3). We found that the African proportions of ancestry based on AIMs or averaged mtDNA and NRY estimates are correlated (Figure 1, and Table S4 in File S3) with the exception of Brazil, possibly because diversely admixed Afro- Brazilian populations were sampled for each marker. These results demonstrate that sub-Saharan African ancestry can easily be separated from European and Native American-Asian ancestry and that ancestry estimates based on mtDNA/NRY and AIMs are highly correlated if the populations are thoroughly sampled. Within-Africa Ancestry: Maternal Contribution MtDNA variation within Africa. In order to relate within- Africa genetic variation to admixed Americans of African descent, we first assessed the genetic similarity of African populations using published African mtDNA variation. We initially divided the African continent into geographical regions, using current African countries as independent units except in the case of the populations of Cameroon, Democratic Republic of Congo (D.R.C.), Central African Republic (C.A.R.), and Gabon, where ethnic affiliation was also considered and these countries were PLoS ONE | www.plosone.org 2 January 2011 | Volume 6 | Issue 1 | e14495