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consistent among countries and populations including Argentina (Dipierri et al., 1998), Ecuador (González-Andrade et al., 2007), Mexico (Green et al., 2000), Cuba (Mendizabal et al., 2008), Brazil (Marrero et al., 2007), Uruguay (Sans et al., 2002), Colombia (Carvajal-Carmona et al., 2003), and Costa Rica (Carvajal-Carmona et al., 2003).

The rich diversity of variation in ancestry among Hispanic/Latino populations, coupled with consistent differences among populations in the incidence of chronic heritable diseases, suggests that Hispanic/Latino populations may be very well suited for admixture mapping (Smith et al., 2001; González Burchard et al., 2005). For example, differences in relative European ancestry proportions correlate with higher susceptibility in Puerto Ricans to asthma as compared with Mexicans (Salari et al., 2005). Data have also shown an increased risk of breast cancer in Latinas with greater European ancestry (Fejerman et al., 2008) and an interplay between African ancestry and cardiovascular disease and hypertension in Puerto Ricans from Boston (Lai et al., 2009). Hispanic/Latinos are also likely to play an increasingly important role in multi- and transethnic genetic studies of complex disease. Genome-wide scans have identified candidate markers for onset of type 2 diabetes in Mexican-Americans from Texas (Hayes et al., 2007) as well as a region on chromosome 5 associated with asthma in Puerto Ricans (Choudhry et al., 2008).

Quantifying the relative contributions of ancestry, environment (including socioeconomic status), and ancestry by environment interaction to disease outcome in diverse Hispanic/Latino populations will also be critical to applying a genomic perspective to the practice of medicine in the United States and in Latin America. For example, whereas European ancestry was associated with increased asthma susceptibility in Puerto Ricans (Salari et al., 2005), it was also shown that the effect was moderated by socioeconomic status (Choudhry et al., 2006). This suggests that quantifying fine-scale patterns of genomic diversity among diverse U.S. and non-U.S. Hispanic/Latinos may be critical to the efficient and effective design of medical and population genomic studies. A fine-scale population genomics perspective may also provide a powerful means for understanding the roles of ancestry, genetics, and environmental covariates on disease onset and severity (González Burchard et al., 2005).

Here, we introduce a larger, high-density SNP and haplotype dataset to investigate historical population genetics questions—such as variation in sex-biased ancestry and genome-wide admixture proportions within and among Latino populations—as well as provide a genomic resource for the study of population substructure within putative European, African, and Native American source populations. Our dataset includes three Latino populations that are underrepresented in whole-genome analyses, namely, Dominicans, Colombians, and Ecuadorians, as well as Mexicans

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