consideration of these datasets because shallower NRY typing significantly reduces the resolution that could be achieved using the combined dataset. In all ancestry estimates, we used the phylogenetic relationship between haplotype data thoroughly characterized for both mtDNA and NRY. Specifically for mtDNA, 429 pan-continental mtDNA haplotype motifs were defined based on the variation within the mtDNA database. Of these, approximately 5,800 African individuals (including admixed individuals from Cabo Verde and Sa˜o Tome´ e Pr´ıncipe) from 10 geographic regions, 13 language families, 33 countries, and 143 populations were used to capture 304 haplotypes that represent variation within Africa. These data were used to map the group ancestry of African Americans to smaller regions of Africa. Population comparisons Arlequin 3.11 [53] was used to estimate genetic distances utilizing the phylogenetic relationship defined by 429 FASTA- formatted mtDNA haplotypes, assuming Tamura and Nei’s [54] model for nucleotide substitution. Analysis of molecular variance (AMOVA) [55] was used to assess the between group and within- population variation for each step. SAMOVA 1.0 software [43], combining AMOVA with geographical information, was used to explore the clustering of geographic regions or ethnic groups of the whole and W/WC Africa based on the genetic variation. Autosomal AIMs We typed 175 AIMs (File S4) for 331 self-identified African Americans and 728 European Americans from Philadelphia, and 205 Senegalese using an Illumina Golden Gate Platform. The individuals from Philadelphia were ascertained between 1995 and 2007 as part of a prostate cancer case-control study, with cases identified through Urologic Oncology Clinics at multiple hospitals of the University of Pennsylvania Health System (UPHS) and controls being men attending UPHS general medicine clinics. The individuals from Senegal were identified and ascertained from university and hospital populations in Dakar, Senegal. All study subjects from US and Senegal provided written informed consent for participation in this research. IRB approval for this study has been provided by the Committee on Studies Involving Human Beings of the University of Pennsylvania (Protocol #3614-2) and by the Commission Ethique et Evaluation at the Hopital General de Grand Yoff in Dakar (FWA 00002772). The primary set of AIMs consisted of 149 SNPs that were selected from Tian et al. [16] to address the European admixture by maximizing Fishers Information Coefficients (FIC) based on three admixture scenarios [56] (i.e., 10%/90%, 50%/50%, and 90%/10% European/African contribution). We also typed two additional AIMs sets based on the published sets from Lao et al. [17] (9 SNPs) and Reiner et al. [15] (17 SNPs). The Lao additional panel allowed us to further explore Native American-SE Asian ancestry. The individual level ancestry was estimated using STRUCTURE [57], [58] with 10,000 burn-in cycles and 50,000 replicates under the admixture model for 3 populations (see LnP(D) for K = 1–5 in Table S8 in File S3) and including control ‘‘parental’’ individuals of known African, European (selected individuals with ,2% admixture from the Senegalese and European American pool) and Asian ancestry (Native American and Asian populations are related more closely and for K = 3, we use Asian ancestry as a surrogate for Native American ancestry). To calculate Native American-SE Asian ancestry, we have included individuals of known Asian (n = 33) or admixed ancestry (n = 10, mainly European-Asian) as additional Within-Africa Ancestry controls. We obtained the group ancestry simply by averaging the individual ancestry estimates for each group. MDS plots Multidimensional scaling (MDS) plots were constructed using SPSS with input data in the form of an Arlequin-generated matrix of Slatkin’s linearized FST distances [59], incorporating the phylogenetic relationship among the 429 mtDNA haplotypes. For each MDS plot, we report the stress and RSQ statistics, which summarize the goodness of fit of multidimensional data in 2 dimensions. Additionally, AMOVA was reported for the parental populations (indicated in each MDS figure) showing the percentage of variation captured by defining the language/ geography/ethnicity groups. For Figure S7 in File S3, the coordinates for MDS plot capturing Senegalese and US African Americans with ,5% of European ancestry based on 175 AIMs were calculated using PLINK and plotted using Excel. Admixture estimates The group level admixture based on uniparental markers was estimated using ADMIX 2.0 [60], which incorporates both molecular divergence and haplotype frequencies. Both mtDNA and NRY were treated as a single locus. After 50,000/100,000 (mtDNA/NRY) bootstrap simulations, the data were reported as a percent contribution from a particular parental population along with an estimate of the sampling error (SD). Additional information about the groups that were chosen as parental populations in ADMIX-based admixture coefficient calculations is listed in Text S1 in File S3. For continental admixture, we used complete profiles of admixed populations. For within-Africa admixture, we considered only the African-derived haplogroups (L, U6, U5b1b). For the admixed populations considered here, only 3 regions were shown to contribute: W/WC non-Bantu/non- Pygmy, Bantu of SW/WC, and SE Africa. These regions were further subdivided based on geography (SW/WC Bantu, Figure 2) or, in the case of W/WC, based on geography (Figure S2 in File S3), language (Figure S3 in File S3), and ethnicity (Figure S4 and Figure S5 in File S3). Supporting Information File S1 mtDNA sequence information. Found at: doi:10.1371/journal.pone.0014495.s001 (2.90 XLS) File S2 NRY marker information. Found at: doi:10.1371/journal.pone.0014495.s002 (0.11 XLS) File S3 This file contains Tables S1–S8, Figures S1–S7, Text S1, and References S1. Found at: doi:10.1371/journal.pone.0014495.s003 (2.96 MB PDF) File S4 AIMs. Found at: doi:10.1371/journal.pone.0014495.s004 (0.04 XLS) File S5 W/WC ethnic groups with language affiliations. Found at: doi:10.1371/journal.pone.0014495.s005 (0.92 XLS) MB MB MB MB Acknowledgments We would like to thank Andre´ E.X. Brown, David Thybert, and Alexandra Brown for their critical reading of the manuscript. Also, we would like to PLoS ONE | www.plosone.org 8 January 2011 | Volume 6 | Issue 1 | e14495