There is growing interest in the application of admixture mapping to the identification of genes influencing complex traits (including disease) in populations tracing their ancestry to genetically differentiated populations[1]–[5]. This approach is potentially more powerful and economical than high-density whole genome association studies and should also allow the identification of trait-related genetic variants that are fixed in one of the parental populations. Considerable progress has been made in the application of admixture mapping in African-Americans[6]–[11]. Similarly, it is hoped that admixture mapping may be a powerful approach for gene identification in populations from Latin America[12], and first generation marker maps for use in these populations have recently been developed[13]–[15]. Ideally, the application of admixture mapping should build on knowledge regarding the genetic makeup of the admixed population, as well as of the specific ancestral populations that contributed to the admixture. Unfortunately, although it is broadly known that the history of Latin America entailed an extensive admixture of Native Americans, Europeans and Africans, few details are known about this process or about its genetic correlates[16]–[19]. Early demographic history data is scant
