Within-Africa Ancestry Figure 2. Multidimensional Scaling Plot of African mtDNA variation. (a) MDS plot of mtDNA variation within Africa. Africa was divided based on geography combined in a few cases with ethnicity (in the case of Pygmy hunter gatherers and Bantu speakers). SAMOVA was used to eliminate the following outlier groups: West Pygmy (Cameroon, C.A.R., and Gabon), Khoisan speakers (South Africa and Botswana), East Pygmy group Mbuti (D.R.C.), and Moroccan sample (mainly Berbers from North Africa). After removing outliers, the remaining states were divided using SAMOVA into 4 groups: WC/SW Bantu speakers from Angola, Cameroon, Gabon and Equatorial Guinea, E/SE sample from Kenya and Mozambique Bantu speakers, NE/E sample from Egypt, Sudan, Eritrea, Ethiopia, and Somalia, and W/WC countries after excluding Bantu speakers and Pygmy hunter-gatherers. The MDS plot parameters and AMOVA results are listed in the left bottom corner. When all 24 populations are considered, 18.7% of variation is between these 24 groups. When the populations are grouped into 8 groups, 20.43% of total variation is captured between these groups and 1.72% within these groups. (b) MDS plot showing the mtDNA variation-based genetic distances between African populations after the outliers (West and East Pygmy, Khoisan speakers and North Africans, outside of lighter insert in a) were excluded from the calculations. This plot shows the general structure of the remaining regions (with highlighted W/WC clustering) and their relationship to the admixed African American populations, depicted using only the African portion of their ancestry. doi:10.1371/journal.pone.0014495.g002 In contrast, the founding population of Sa˜o Tome´ e Pr´ıncipe is drawn from both SW/WC Bantu (40–46%, mainly from Gabon/ Equatorial Guinea and Angola) and West Africa (54–60%). The West African portion is drawn from the same populations as seen in Cabo Verde, or possibly from the population of Cabo Verde itself [45]. However, the available data do not cover the Ivory and Gold Coast that may be represented by this source. Our results, based on genetic variation, are consistent with the most likely source populations based on geographical proximity and historical records. The strong relationship between genetic variation, geography, and historical record supports the hypothesis that the admixture analysis used here is a reasonable approach for predicting within-Africa ancestry. African-derived populations in the Americas. Guided by admixture coefficients obtained from ADMIX, we found that only W/WC Africa, SW/WC Bantu, and SE Africa contributed significantly to the genetic ancestry of admixed Americans (Figure 3a). There is a varying ratio between contributions PLoS ONE | www.plosone.org 4 January 2011 | Volume 6 | Issue 1 | e14495