Genetic Make Up and Structure of Colombian Populations by Means of Uniparental and Biparental DNA Markers Winston Rojas, 1 * Marı´a Victoria Parra, 1 Omer Campo, 1 Marı´a Antonieta Caro, 1 Juan Guillermo Lopera, 1 William Arias, 1 Constanza Duque, 1 Andre ´ s Naranjo, 1 Jharley Garcı ´a, 1 Candelaria Vergara, 1,2 Jaime Lopera, 1 Erick Hernandez, 1 Ana Valencia, 1 Yuri Caicedo, 1 Mauricio Cuartas, 1 Javier Gutie ´ rrez, 1 Sergio Lo ´ pez, 1 Andre ´ s Ruiz-Linares, 3 and Gabriel Bedoya 1 1 Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellı´n, Colombia 2 Institute for Immunological Research, University of Cartagena, Cartagena, Colombia 3 Department of Genetics, Evolution and Environment, University College, London, UK KEY WORDS Colombia; mestizo; genetic markers; admixture ABSTRACT Colombia is a country with great geo- graphic heterogeneity and marked regional differences in pre-Columbian native population density and in the extent of past African and European immigration. As a result, Colombia has one of the most diverse populations in Latin America. Here we evaluated ancestry in over 1,700 individ- uals from 24 Colombian populations using biparental (autosomal and X-Chromosome), maternal (mtDNA), and paternal (Y-chromosome) markers. Autosomal ancestry varies markedly both within and between regions, confirm- ing the great genetic diversity of the Colombian population. The X-chromosome, mtDNA, and Y-chromosome data indi- cate that there is a pattern across regions indicative of admixture involving predominantly Native American women and European and African men. Am J Phys Anthro- pol 143:13–20, 2010. V V C 2010 Wiley-Liss, Inc. Colombia has one of the most diverse populations in Latin America. Of a total population of 50 million, 86% recently self-reported as of mixed ancestry, 10.5% as African-Colombian, and 3.4% as Native American (DANE, 2006). The population of mixed ancestry concen- trates mainly in urban areas, particularly on the Andes. African-Colombians live predominantly on the Caribbean and Pacific coasts and islands. Native American popula- tions concentrate mainly in the East (on the vast Ori- noco and Amazon river basins) and in rural areas of the SouthWest and North of the country. Genetic studies can provide refined descriptions of pat- terns of admixture in human populations. These studies can provide insights into the biological history of these populations. They are also important for the identifica- tion of trait-associated genes through ‘‘admixture map- ping’’ (Smith et al., 2001; Collins-Schramm et al., 2002; Patterson et al., 2004; Smith and O’Brien, 2005; Seldin, 2007) and because of the need for correcting for popula- tion stratification in association studies (Pritchard and Rosenberg, 1999; Hoggart et al., 2003). Admixture analy- ses use so called ‘‘ancestry informative markers’’ (AIMs; i.e.. autosomal and X-chromosome markers showing large allele frequency differences in the parental popula- tions) (Chakraborty et al., 1992; Dean et al., 1994; Parra et al., 1998; Tang et al., 2005), as well as Y-chromosome and mtDNA variants defining paternal and maternal lineages with well established geographic distributions (e.g., American, European, or African). In recent years, admixture studies have documented the considerable heterogeneity of the population of Latin America, albeit with great variation in the number and type of genetic markers used across studies (Dipierri et al, 1998; Carvajal-Carmona et al., 2000; Sans, 2000; Collins- Schramm et al., 2002; Rodas et al., 2003; Bertoni et al., 2005; Bolnick et al., 2006; Mao et al., 2007; Price et al., 2007; Seldin et al., 2007; Wang et al., 2008). We have pre- viously reported detailed analyses of admixture in the province of Antioquia in North-West Colombia. Here we aim to perform a broader description of admixture across Colombia through the analysis of autosomal, X-chromo- some, mtDNA, and Y-chromosome markers in 24 popula- tion samples from regions with different settlement histories. This represents one of the largest surveys of admixture carried out so far in a Latin American country. MATERIALS AND METHODS Population samples A total of 24 population samples were examined across Colombia (Fig. 1 and Table 1). These comprise 15 urban centers (from the Andes and the sea coasts), 8 Native WR and MVP participated equally in this work. Grant sponsor: Colombian Institute for the Development of Science and Technology, COLCIENCIAS; Grant number: 111540520279; Grant sponsor: Programa de Sostenibilidad CODI 2009–2010 Universidad de Antioquia. Additional Supporting Information may be found in the online version of this article. *Correspondence to: Winston Rojas, Laboratorio de Gene ´tica Molecular, Instituto de Biologia, Universidad de Antioquia, Medellı´n, Colombia. E-mail: winstonrojas@yahoo.com Received 13 August 2009; accepted 10 December 2009 DOI 10.1002/ajpa.21270 Published online 8 June 2010 in Wiley InterScience (www.interscience.wiley.com). V V C 2010 WILEY-LISS, INC. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 143:13–20 (2010)