Within-Africa Ancestry from W/WC Africa vs. SW/WC Bantu to the populations of America such that the contribution of W/WC Africa is the greatest in Cuba (79% vs. 21%) and the Caribbean (75% vs. 25%), less in the United States (68% vs. 32%) and Philadelphia (59% vs. 41%), and even less in Brazil (41% vs. 45%), although Colombia does not follow this C.N.S trend (63% vs. 28%). In addition, Brazil and Colombia show significant contribution from SE Africa (14% and 10%, respectively). We proceeded to investigate in greater depth which regions of Africa contribute to American admixture in order to explain this Central-North-South variation. We assessed the contribution of the geographically, linguistically, and ethnically defined groups within these large African regions to each admixed American population (Table S6 in File S3). Figure 3b depicts both the colonial powers in the Americas and Africa as well as the genetically defined regions within Africa that contributed to the pool of mtDNAs in the Americas (see Table S7 in File S3 for simplified relative contribution of African regions to the admixed populations of the Americas as represented in Figure 3b). When we traced the former colonies of Africa that contributed to genetic ancestry in former colonies in the Americas, we observed that the colonial systems and genetic marker data are related. A clear example is formerly Portuguese Brazil, where most of the regions contributing to the pool of African-Brazilians were drawn from former Portuguese colonies in Africa (see Text S1 in File S3 for summary of the historical context). Because we are ultimately interested in capturing individual ancestry, we further investigated whether the diverse within-Africa ancestry can be captured by a set of AIMs suitable for estimating continental ancestry. We selected samples that had no more than 5% of European ancestry and used multidimensional scaling (MDS) analysis to evaluate differential clustering of West African Senegalese and Philadelphia African Americans, the latter having approximately 20% West African ancestry on average (Figure S7 in File S3). As previously described when using a different set of European-African AIMs [46], we did not see any separation of these 2 clusters, suggesting that the within-Africa ancestry is not captured by markers which were selected for high informative value in predicting European-African ancestry. Therefore, while the currently used method of selecting AIMs is not designed to or capable of detecting the different African sources, mtDNA Figure 3. African regions contributing to the populations of the Americas. (a) Left: proportion of W/WC Africa contributing to the mtDNA pools of North (N, USA), Central (C, Caribbean), and South (S, Brazil) America as reported by Salas et al. [3]. Right: the proportion of W/WC, SW/WC Bantu and SE Africa contributing to mtDNAs in comparative populations of America analyzed in this paper (‘‘Stefflova’’). The relative contributions of these large African regions agree with Salas et al. [3], except for the Brazilian sample that displays significant input from SE Africa as well, which may have been included in WC portion by Salas et al. (b) Within-Africa mtDNA variation of admixed populations of Americas within the context of the colonial system. Maps are colored, depicting the relevant British (brown), French (light gray), Portuguese (blue), and Spanish (green) colonies in the Americas around 1763 and Africa and overlaid with pie charts depicting the relative proportions of mtDNA variation in the pool of African-derived mtDNAs of USA, Philadelphia, Caribbean, Cuba, Colombia, and Brazil derived from corresponding regions of W/WC, SW/WC Bantu, and SE Africa. Enrichment of American variation from source African colonies is particularly visible on Brazil and Philadelphia that have drawn most of their variation from Portuguese or British colonies. (*Note: GB = Guinea Bissau; SL = Sierra Leone; Seneg = Senegal, Senegam. = Senegambia; B = Bight, Eq. = Equatorial.) doi:10.1371/journal.pone.0014495.g003 PLoS ONE | www.plosone.org 5 January 2011 | Volume 6 | Issue 1 | e14495