acknowledge Mohammed Jalloh and Serigne M. Gueye for their support in the collection of Senegalese samples and Charnita Zeigler-Johnson, Elaine Spangler, and Bruce Malkowicz for their involvement in the collection of Philadelphia samples. References 1. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, et al. (1998) Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 63: 1839–1851. 2. Salas A, Carracedo A, Richards M, Macaulay V (2005) Charting the ancestry of African Americans. Am J Hum Genet 77: 676–680. 3. Salas A, Richards M, Lareu MV, Scozzari R, Coppa A, et al. (2004) The African diaspora: mitochondrial DNA and the Atlantic slave trade. Am J Hum Genet 74: 454–465. 4. Goncalves VF, Prosdocimi F, Santos LS, Ortega JM, Pena SD (2007) Sex-biased gene flow in African Americans but not in American Caucasians. Genet Mol Res 6: 156–161. 5. Lind JM, Hutcheson-Dilks HB, Williams SM, Moore JH, Essex M, et al. (2007) Elevated male European and female African contributions to the genomes of African American individuals. Hum Genet 120: 713–722. 6. Goncalves VF, Carvalho CM, Bortolini MC, Bydlowski SP, Pena SD (2008) The phylogeography of African Brazilians. Hum Hered 65: 23–32. 7. Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, et al. (2009) Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas. PLoS ONE 4: e7842. 8. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat Genet 36: 388–393. 9. Barnholtz-Sloan JS, McEvoy B, Shriver MD, Rebbeck TR (2008) Ancestry estimation and correction for population stratification in molecular epidemio- logic association studies. Cancer Epidemiol Biomarkers Prev 17: 471–477. 10. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512–517. 11. Kohler K, Bickeboller H (2006) Case-control association tests correcting for population stratification. Ann Hum Genet 70: 98–115. 12. Wang Y, Localio R, Rebbeck TR (2004) Evaluating bias due to population stratification in case-control association studies of admixed populations. Genet Epidemiol 27: 14–20. 13. Chakraborty R, Kamboh MI, Nwankwo M, Ferrell RE (1992) Caucasian genes in American blacks: new data. Am J Hum Genet 50: 145–155. 14. Miljkovic-Gacic I, Ferrell RE, Patrick AL, Kammerer CM, Bunker CH (2005) Estimates of African, European and Native American ancestry in Afro- Caribbean men on the island of Tobago. Hum Hered 60: 129–133. 15. Reiner AP, Carlson CS, Ziv E, Iribarren C, Jaquish CE, et al. (2007) Genetic ancestry, population sub-structure, and cardiovascular disease-related traits among African-American participants in the CARDIA Study. Hum Genet 121: 565–575. 16. Tian C, Hinds DA, Shigeta R, Kittles R, Ballinger DG, et al. (2006) A genomewide single-nucleotide-polymorphism panel with high ancestry informa- tion for African American admixture mapping. Am J Hum Genet 79: 640–649. 17. Lao O, van Duijn K, Kersbergen P, de Knijff P, Kayser M (2006) Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry. Am J Hum Genet 78: 680–690. 18. Benn-Torres J, Bonilla C, Robbins CM, Waterman L, Moses TY, et al. (2008) Admixture and population stratification in African Caribbean populations. Ann Hum Genet 72: 90–98. 19. Bonilla C, Bertoni B, Gonzalez S, Cardoso H, Brum-Zorrilla N, et al. (2004) Substantial Native American female contribution to the population of Tacuarembo, Uruguay, reveals past episodes of sex-biased gene flow. Am J Hum Biol 16: 289–297. 20. Martinez-Cruzado JC, Toro-Labrador G, Viera-Vera J, Rivera-Vega MY, Startek J, et al. (2005) Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis. Am J Phys Anthropol 128: 131–155. 21. McLean DC, Jr., Spruill I, Argyropoulos G, Page GP, Shriver MD, et al. (2005) Mitochondrial DNA (mtDNA) haplotypes reveal maternal population genetic affinities of Sea Island Gullah-speaking African Americans. Am J Phys Anthropol 127: 427–438. 22. Ribeiro-dos-Santos AK, Carvalho BM, Feio-dos-Santos AC, dos Santos SE (2007) Nucleotide variability of HV-I in Afro-descendents populations of the Brazilian Amazon Region. Forensic Sci Int 167: 77–80. 23. Salas A, Acosta A, Alvarez-Iglesias V, Cerezo M, Phillips C, et al. (2008) The mtDNA ancestry of admixed Colombian populations. Am J Hum Biol 20: 584–591. 24. Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, et al. (2002) The making of the African mtDNA landscape. Am J Hum Genet 71: 1082–1111. Within-Africa Ancestry Author Contributions Conceived and designed the experiments: KS TR. Performed the experiments: KS. Analyzed the data: KS MCD AAP. Contributed reagents/materials/analysis tools: AHW TR. Wrote the paper: KS MCD JBS TR. Designed the AIMs panel. 25. Silva WA, Bortolini MC, Schneider MP, Marrero A, Elion J, et al. (2006) MtDNA haplogroup analysis of black Brazilian and sub-Saharan populations: implications for the Atlantic slave trade. Hum Biol 78: 29–41. 26. Alves-Silva J, da Silva Santos M, Guimaraes PE, Ferreira AC, Bandelt HJ, et al. (2000) The ancestry of Brazilian mtDNA lineages. Am J Hum Genet 67: 444–461. 27. Abe-Sandes K, Silva WA, Jr., Zago MA (2004) Heterogeneity of the Y chromosome in Afro-Brazilian populations. Hum Biol 76: 77–86. 28. Hammer MF, Chamberlain VF, Kearney VF, Stover D, Zhang G, et al. (2006) Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases. Forensic Sci Int 164: 45–55. 29. Silva DA, Carvalho E, Costa G, Tavares L, Amorim A, et al. (2006) Y- chromosome genetic variation in Rio de Janeiro population. Am J Hum Biol 18: 829–837. 30. Batista dos Santos SE, Rodrigues JD, Ribeiro-dos-Santos AK, Zago MA (1999) Differential contribution of indigenous men and women to the formation of an urban population in the Amazon region as revealed by mtDNA and Y-DNA. Am J Phys Anthropol 109: 175–180. 31. Benn Torres J, Kittles RA, Stone AC (2007) Mitochondrial and Y chromosome diversity in the English-speaking Caribbean. Ann Hum Genet 71: 782–790. 32. Carvajal-Carmona LG, Soto ID, Pineda N, Ortiz-Barrientos D, Duque C, et al. (2000) Strong Amerind/white sex bias and a possible Sephardic contribution among the founders of a population in northwest Colombia. Am J Hum Genet 67: 1287–1295. 33. Guerreiro V, Bisso-Machado R, Marrero A, Hunemeier T, Salzano FM, et al. (2009) Genetic signatures of parental contribution in black and white populations in Brazil. Genetics and Molecular Biology 32: 1–11. 34. Mendizabal I, Sandoval K, Berniell-Lee G, Calafell F, Salas A, et al. (2008) Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. BMC Evol Biol 8: 213. 35. Sans M, Weimer TA, Franco MH, Salzano FM, Bentancor N, et al. (2002) Unequal contributions of male and female gene pools from parental populations in the African descendants of the city of Melo, Uruguay. Am J Phys Anthropol 118: 33–44. 36. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, et al. (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18: 830–838. 37. Underhill PA, Kivisild T (2007) Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41: 539–564. 38. Watson E, Forster P, Richards M, Bandelt HJ (1997) Mitochondrial footprints of human expansions in Africa. Am J Hum Genet 61: 691–704. 39. Corach D, Lao O, Bobillo C, van Der Gaag K, Zuniga S, et al. (2010) Inferring continental ancestry of argentineans from Autosomal, Y-chromosomal and mitochondrial DNA. Ann Hum Genet 74: 65–76. 40. Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, et al. (2010) Genome- wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci U S A 107: 786–791. 41. Parra EJ, Kittles RA, Argyropoulos G, Pfaff CL, Hiester K, et al. (2001) Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. Am J Phys Anthropol 114: 18–29. 42. Zakharia F, Basu A, Absher D, Assimes T, Go A, et al. (2009) Characterizing the admixed African ancestry of African Americans. Genome Biology 10: R141. 43. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11: 2571–2581. 44. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, et al. (2009) The Genetic Structure and History of Africans and African Americans. Science 324: 1035–1044. 45. Rawley JA (2005) Transatlantic slave trade. Lincoln, NE: University of Nebraska Press. 46. Collins-Schramm HE, Kittles RA, Operario DJ, Weber JL, Criswell LA, et al. (2002) Markers that discriminate between European and African ancestry show limited variation within Africa. Hum Genet 111: 566–569. 47. Yaeger R, Avila-Bront A, Abdul K, Nolan PC, Grann VR, et al. (2008) Comparing genetic ancestry and self-described race in african americans born in the United States and in Africa. Cancer Epidemiol Biomarkers Prev 17: 1329–1338. 48. Halder I, Shriver M, Thomas M, Fernandez JR, Frudakis T (2008) A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. Hum Mutat 29: 648–658. 49. Campbell MC, Tishkoff SA (2008) African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 9: 403–433. PLoS ONE | www.plosone.org 9 January 2011 | Volume 6 | Issue 1 | e14495