FIGURE 8.4 Linkage disequilibrium, genotype r² estimated by PLINK, by population as a function of physical distance (Mb). (Left) Native American, European, and African populations. (Right) Hispanic/Latino populations. Scale is the same.

10 individuals, choosing subsets of 10 individuals, and averaging more than 100 random subsets of the data. Patterns of decay of LD were consistent with previously published results (Jakobsson et al., 2008), with Native American populations showing the highest levels of LD and African populations the lowest (Fig. 8.4A). Interestingly, the Hispanic/Latino populations demonstrated rates of decay of LD that correlated strongly with the amount of Native American, European, and African ancestry (Fig. 8.4B). Specifically, the populations with the most Native American ancestry, Mexican and Ecuadorian, exhibited higher levels of linkage disequilibrium among SNP markers, whereas the populations with the highest proportions of African ancestry, the Dominican and Puerto Rican samples, had the lowest levels of LD.

To reconstruct local genomic ancestry at a fine scale, we used the ancestry deconvolution algorithm LAMP (Sankararaman et al., 2008), allowing for a three-way admixture and focused on the four Hispanic/Latino populations genotyped on the Illumina 610-Quad platform—Dominicans, Colombians, Puerto Ricans, and Ecuadorians (Materials and Methods). Because this same SNP panel had also been genotyped across the HGDP samples (1,043 individuals from 53 populations), the merged dataset containing more than 500,000 markers provided a unique resource for investigating the extent of subcontinental ancestry among diverse Hispanic/Latino populations. We found that individual average ances