The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.

[1]  G. Suarez-Kurtz Pharmacogenomics and the genetic diversity of the Brazilian population. , 2009, Cadernos de Saúde Pública.

[2]  Peter M Vallone,et al.  Evaluating Self-declared Ancestry of U.S. Americans with Autosomal, Y-chromosomal and Mitochondrial DNA , 2010, Human mutation.

[3]  B. Browning,et al.  Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. , 2007, American journal of human genetics.

[4]  John Novembre,et al.  The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. , 2008, American journal of human genetics.

[5]  A. J. Cooper,et al.  SELECTION, GENE MIGRATION AND POLYMORPHIC STABILITY IN A U. S. WHITE AND NEGRO POPULATION. , 1963, American journal of human genetics.

[6]  Á. Carracedo,et al.  Shipwrecks and founder effects: divergent demographic histories reflected in Caribbean mtDNA. , 2005, American journal of physical anthropology.

[7]  Mark Shriver,et al.  A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications , 2008, Human mutation.

[8]  J. Burma The Measurement of Negro "Passing" , 1946, American Journal of Sociology.

[9]  G. Fredrickson,et al.  Brown History@@@New People: Miscegenation and Mulattoes in the United States. , 1980 .

[10]  H. Ostrer,et al.  Genome-wide patterns of population structure and admixture among Hispanic/Latino populations , 2010, Proceedings of the National Academy of Sciences.

[11]  M. Bamshad,et al.  Race, genetics and medicine: does the color of a leopard's spots matter? , 2007, Current opinion in pediatrics.

[12]  R. Ward,et al.  Admixture Studies and the Detection of Selection , 1973, Science.

[13]  C. Hirschman,et al.  The Changing Racial and Ethnic Composition of the US Population: Emerging American Identities. , 2009, Population and development review.

[14]  T. E. Reed,et al.  Caucasian genes in American Negroes. , 1969, Science.

[15]  D. Comas,et al.  Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba , 2008, BMC Evolutionary Biology.

[16]  R. Chakraborty,et al.  Caucasian genes in American blacks: new data. , 1992, American journal of human genetics.

[17]  D. Allison,et al.  Estimating African American admixture proportions by use of population-specific alleles. , 1998, American journal of human genetics.

[18]  Christopher R. Gignoux,et al.  History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico , 2011, PloS one.

[19]  N. Freimer,et al.  Genetic demography of Antioquia (Colombia) and the Central Valley of Costa Rica , 2003, Human Genetics.

[20]  D. Shriner Overview of Admixture Mapping , 2013, Current protocols in human genetics.

[21]  W. Pollitzer,et al.  ANALYSIS OF A TRI-RACIAL ISOLATE 1 , 2016 .

[22]  Julia H. Coates Trail of Tears , 2014 .

[23]  Swapan Mallick,et al.  Ancient Admixture in Human History , 2012, Genetics.

[24]  H. Muller The American Journal of Human Genetics Vol . 2 No . 2 June 1950 Our Load of Mutations 1 , 2006 .

[25]  J. Dipierri,et al.  Paternal directional mating in two Amerindian subpopulations located at different altitudes in northwestern Argentina. , 1998, Human biology.

[26]  Rong Chen,et al.  Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. , 2012, American journal of human genetics.

[27]  Nicholas Eriksson,et al.  Web-Based Genome-Wide Association Study Identifies Two Novel Loci and a Substantial Genetic Component for Parkinson's Disease , 2011, PLoS genetics.

[28]  Cory Y. McLean,et al.  Reducing Pervasive False-Positive Identical-by-Descent Segments Detected by Large-Scale Pedigree Analysis , 2013, Molecular biology and evolution.

[29]  B. Glass On the unlikelihood of significant admixture of genes from the North American Indians in the present composition of the Negroes of the United States. , 1955, American journal of human genetics.

[30]  W. Pollitzer,et al.  Physical anthropology of the Negroes of Charleston, S. C. , 1970, Human biology.

[31]  G. Hodges,et al.  From Africa to America : African American history from the Colonial era to the early Republic,1526-1790 , 1998 .

[32]  E. Parra Admixture in North America , 2007 .

[33]  Eduardo Barrientos,et al.  Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico , 2009, Proceedings of the National Academy of Sciences.

[34]  Chuong B. Do,et al.  Genome-Wide Analysis Points to Roles for Extracellular Matrix Remodeling, the Visual Cycle, and Neuronal Development in Myopia , 2012, PLoS genetics.

[35]  Nicholas Eriksson,et al.  Novel Associations for Hypothyroidism Include Known Autoimmune Risk Loci , 2011, PloS one.

[36]  Scott M. Williams,et al.  A high-density admixture map for disease gene discovery in african americans. , 2004, American journal of human genetics.

[37]  D. F. Roberts The dynamics of racial intermixture in the American Negro-some anthropological considerations. , 1955, American journal of human genetics.

[38]  G. Miller,et al.  Genetic admixture, self-reported ethnicity, self-estimated admixture, and skin pigmentation among Hispanics and Native Americans. , 2009, American journal of physical anthropology.

[39]  Jake K. Byrnes,et al.  Reconstructing the Population Genetic History of the Caribbean , 2013, PLoS genetics.

[40]  K. Shianna,et al.  Long-range LD can confound genome scans in admixed populations. , 2008, American journal of human genetics.

[41]  Chuong B. Do,et al.  Genetic variants associated with breast size also influence breast cancer risk , 2012, BMC Medical Genetics.

[42]  J. Belmont,et al.  Argentine population genetic structure: large variance in Amerindian contribution. , 2007, American journal of physical anthropology.

[43]  M. Stein,et al.  Measurement of admixture proportions and description of admixture structure in different U.S. populations , 2009, Human mutation.

[44]  Chao Qian,et al.  Population , 1940, State Rankings 2020: A Statistical View of America.

[45]  F. J. Davis,et al.  Who Is Black? One Nation's Definition , 1991 .

[46]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[47]  R. Kittles,et al.  Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina. , 2001, American journal of physical anthropology.

[48]  R. Rotberg,et al.  Two Societies, Both Unfree@@@White Supremacy: A Comparative Study in American and South African History. , 1981 .

[49]  B. Martínez-Jarreta,et al.  Sex-Specific Genetic Admixture of Mestizos, Amerindian Kichwas, and Afro-Ecuadorans from Ecuador , 2007, Human biology.

[50]  J. Hesser,et al.  Loci differentially affected by selection in two American black populations. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[52]  Stephen L. Hauser,et al.  Genome-wide patterns of population structure and admixture in West Africans and African Americans , 2009, Proceedings of the National Academy of Sciences.

[53]  A. Knight,et al.  mtDNA affinities of the peoples of North-Central Mexico. , 2000, American journal of human genetics.

[54]  F. Salzano,et al.  Unequal contributions of male and female gene pools from parental populations in the African descendants of the city of Melo, Uruguay. , 2002, American journal of physical anthropology.

[55]  Scott M. Williams,et al.  Elevated male European and female African contributions to the genomes of African American individuals , 2006, Human Genetics.

[56]  A. Hama DNA USA: A Genetic Portrait of America , 2013 .

[57]  W. Pollitzer,et al.  The Relationship of the Gullah-Speaking People of Coastal South Carolina and Georgia to Their African Ancestors , 1993 .

[58]  Chuong B. Do,et al.  A genetic variant near olfactory receptor genes influences cilantro preference , 2012, Flavour.

[59]  Nicholas Eriksson,et al.  Efficient Replication of over 180 Genetic Associations with Self-Reported Medical Data , 2011, PloS one.

[60]  Ranajit Chakraborty,et al.  Gene admixture in human populations: Models and predictions , 1986 .

[61]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[62]  Chuong B. Do,et al.  A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci , 2013, Nature Genetics.

[63]  C. Bustamante,et al.  RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. , 2013, American journal of human genetics.

[64]  Christian Gieger,et al.  Correlation between Genetic and Geographic Structure in Europe , 2008, Current Biology.

[65]  S. Gravel Population Genetics Models of Local Ancestry , 2012, Genetics.

[66]  Pui-Yan Kwok,et al.  Population structure, admixture, and aging-related phenotypes in African American adults: the Cardiovascular Health Study. , 2005, American journal of human genetics.

[67]  Itsik Pe'er,et al.  Cryptic Distant Relatives Are Common in Both Isolated and Cosmopolitan Genetic Samples , 2012, PloS one.

[68]  D. F. Roberts,et al.  The dynamics of racial intermixture. , 1962, American journal of human genetics.

[69]  Brian T. Naughton,et al.  Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits , 2010, PLoS genetics.

[70]  N. Lemann The Promised Land: The Great Black Migration and How It Changed America , 1991 .

[71]  Scott M. Williams,et al.  The Genetic Structure and History of Africans and African Americans , 2009, Science.

[72]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[73]  Amit R. Indap,et al.  Genes mirror geography within Europe , 2008, Nature.

[74]  N. Freimer,et al.  Geographic Patterns of Genome Admixture in Latin American Mestizos , 2008, PLoS genetics.

[75]  F. Salzano,et al.  Pre- and Post-Columbian Gene and Cultural Continuity: The Case of the Gaucho from Southern Brazil , 2007, Human Heredity.

[76]  Menéndez Alarcón,et al.  New People: Miscegenation and Mulattoes in the United States , 1998 .

[77]  D. Absher,et al.  Characterizing the admixed African ancestry of African Americans , 2009, Genome Biology.

[78]  Sarah Webster Fabio What Is Black? , 1968, College Composition & Communication.

[79]  B. Glass,et al.  The dynamics of racial intermixture; an analysis based on the American Negro. , 1953, American journal of human genetics.

[80]  Roberts Df The dynamics of racial intermixture in the American Negro-some anthropological considerations. , 1955 .

[81]  M. Sans,et al.  Admixture studies in Latin America: from the 20th to the 21st century. , 2000, Human biology.

[82]  Christopher R. Gignoux,et al.  The genetics of Mexico recapitulates Native American substructure and affects biomedical traits , 2014, Science.

[83]  Chuong B. Do,et al.  Ancestry Composition: A Novel, Efficient Pipeline for Ancestry Deconvolution , 2014, bioRxiv.

[84]  W. Pollitzer,et al.  The Negroes of Charleston: a study of hemoglobin types, serology, and morphology. , 1958, Journal of the South Carolina Medical Association.