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libria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.

The term “Hispanic/Latinos” refers to the ethnically diverse inhabitants of Latin America and to people of Latin American descent throughout the world. Present-day Hispanic/Latino populations exhibit complex population structure, with significant genetic contributions from Native American and European populations (primarily involving local indigenous populations and migrants from the Iberian peninsula and Southern Europe) as well as West Africans brought to the Americas through the trans-Atlantic slave trade (Sans, 2000; S. Wang et al., 2008). These complex historical events have affected patterns of genetic and genomic variation within and among present-day Hispanic/Latino populations in a heterogeneous fashion, resulting in rich and varied ancestry within and among populations as well as marked differences in the contribution of European, Native American, and African ancestry to autosomal, X chromosome, and uniparentally inherited genomes.

Many key demographic variables differed among colonial Latin American populations, including the population size of the local pre-Columbian Native American population, the extent and rate at which European settlers displaced native populations, whether or not slavery was introduced in a given region, and, if so, the size and timing of introduction of the African slave populations. There were also strong differences in ancestry among social classes in colonial (and postcolonial) populations with European ancestry often correlating with higher social standing. As a consequence, present-day Hispanic/Latino populations exhibit very large variation in ancestry proportions (as estimated from genetic data) not only across geographic regions (Sans, 2000; S. Wang et al., 2008), but also within countries themselves (Seldin et al., 2007; Silva-Zolezzi et al., 2009). In addition, the process of admixture was apparently sex-biased and preferentially occurred between European males and Amerindian and/or African females; this process has been shown to be remarkably

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