Guinea-Bissau/Sierra Leone region (29%), SE Africa (13.6%), and Nigeria, Niger, Cameroon (12.3%) (Figure 3b). In concordance with these genomic estimates, assessment from the historical record suggests these regions contributed ,50-60% (Angola/ Gabon/Equatorial Guinea), 20–25% (Upper Guinea, comprising mainly Guinea Bissau to Sierra Leone), 10–15% (SE Africa) and 10-18% (Bight of Benin) [45]. While the Portuguese had colonies both in Africa and the Americas, Spain lacked the same presence, holding a virtual monopoly in the Americas and almost no colonies in Africa. As a result, we expected to observe significant heterogeneity in African ancestral sources between Spanish colonies in the Americas – mainly between the mainland and islands, populated in different time periods [45]. For example, Colombia carries the signature of both the very early (Guinea-Bissau (63%), Kongo-Angola (27%, represented by Gabon/Equatorial Guinea)) and late (SE Africa (10%)) Portuguese/Spanish slave sources. In contrast, the majority of slaves were brought to Cuba at the end of the 18th and beginning of the 19th centuries. These individuals originated primarily from the Bight of Benin, Biafra, and Western Guinea [45] (see Figure S6 in File S3 for map), represented by genomic ancestry from Nigeria/Niger/Cameroon (37%), Cameroon Bantu (21%), and Guinea Bissau/Senegal/Sierra Leone/Mali (42%), respectively. A different distribution of African ancestry was observed in Philadelphia, a former British colony. The ancestry of African Americans from Philadelphia draws its mtDNAs mainly from the Bight of Biafra and Benin regions (37% Nigeria-Niger-Cameroon and 15% Cameroon Bantu in Philadelphia compared to 25% and 14% in the US overall, respectively). Ancestry from Guinea Bissau-Mali-Senegal-Sierra Leone predominates in other United States African American populations compared to Philadelphia alone (43% vs. 22%). Despite the differences in coverage and sampling, this pattern may be attributed to a significant contribution of slaves from British colonies in Africa to the British-controlled Philadelphia region compared to a more diverse contribution to other parts of the United States from French, Spanish, and Dutch colonies. Additional possible contributing factors include the different periods of the slave trade influencing the Philadelphian population compared to the other parts of the United States. However, these remain tentative conclusions since we cannot rule out a contribution from sampling bias. Another example of these differences is the Gullah/Geechee populations from South Carolina/Georgia that have .78% of their source from the Guinea Bissau-Mali-Senegal-Sierra Leone region (data not shown), corresponding to the ‘‘Rice coast’’ around Sierra Leone that was the major source of slaves drawn by the United States in the later period of the slave trade [21], [45]. Our data also included evaluation of the Caribbean islands of Dominica, Grenada, St. Kitts, St. Lucia, St. Vincent, and Trinidad. The majority of slaves were brought to these islands during the boom of sugar trading at the end of the 18th and beginning of the 19th centuries. The observed mtDNA variation reflects the multiple colonial powers that controlled these islands, with possible unique composition of within-Africa ancestry for each island. Limitations of our study Our database and analyses have several limitations. First, there remains limited data from W/WC Africa, where the published literature does not cover Ivory and Gold Coasts. Thus, the analysis of genotype data is limited by the available published data. Also, our data suggest that genetic variation captured by the mtDNA genotypes (HVS I/II and part of the coding region) may not, Within-Africa Ancestry despite the effort invested in defining a large set of haplotypes, contain sufficient information to accurately separate many genetically similar ethnic groups, especially those within West Africa. Second, mtDNA is a single locus that can inform us only about group maternal ancestry and needs to be complemented with study of NRY and AIMs. While NRY analysis is complicated by limited resolution and coverage of the published data in Africa as well as Bantu speakers’ migrations [50], additional detailed AIMs studies are on their way to help inform these analyses [40], [42], [44], especially once a more thorough coverage of African variation is in place. Conclusion We have dissected the ancestry of African-descended Americans at the level of continental and within-Africa ancestry. Our detailed analysis of the African mtDNA landscape helped us, for the first time, to identify the maternal ancestry of African-descended populations to the several (6–7) regions within W/WC, SW/WC and SE Africa. We estimated the contribution of each of these African regions to the American populations and linked this variation with historical records. Our results suggest that the distribution and identity of within-Africa ancestral contributions to groups of African descent in the Americas correspond to colonial histories and slave trade routes. The present analysis of genetic variation implies that African populations contributed differently to distinct populations of the New World, suggesting that the assumption of genetic homogeneity of African ancestry within the Americas is not necessarily valid. In addition, the selection of ancestral markers, including AIMs selected to account for continental or European vs. African admixture only, may not be adequate to detect or control for the heterogeneity in African source populations. This has significance for epidemiology studies using self-identified race as a proxy for ancestry in association studies, since this term does not capture the genetic admixture both on the continental level (as shown previously) but also on the within-Africa level. Materials and Methods Database We have collected marker data to evaluate the continental (i.e., European, Asian, Native American, and African) and within- African ancestry. We have assembled extensive databases of published mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) genotype and haplotype information from world populations linked to geography, language (obtained from http://www.ethnologue.com/) and ethnicity information. This database includes ,13,800 mtDNA sequences (File S1) and ,9,050 NRY haplogroup affiliations (File S2) with a strong focus on including comprehensive African data. We have also included admixed populations of the Americas, mainly those that were self- identified as having primarily African ancestry (here designated as African-descended Americans) but also some mixed or predom- inantly white populations. The mtDNA database is a comprehensive compilation of the relevant literature that could be used for a deep phylogenetic analysis. For a list of publications and detailed breakdown of African and American populations included in the mtDNA database see File S3 (Table S1, Text S1 and References S1). For the NRY database, we assembled multiple sample sets typed for NRY single nucleotide polymorphisms (SNPs), focusing mainly on those publications that genotyped the phylogenetic relation- ships with similar or greater depth as in our dataset (see Table S2 in File S3 for the list of publications included). We limited our PLoS ONE | www.plosone.org 7 January 2011 | Volume 6 | Issue 1 | e14495