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Pipeline publication

[…] ndent dataset of Mexican individuals analyzed by Moreno-Estrada, Gignoux et al. (in preparation) projected onto ASPCA space using the same reference panel of European populations. A bivariate test was performed to measure the relative deviation from the Iberian cluster of the distribution given by the Caribbean versus the Mexican dataset. To determine whether insular versus mainland Caribbean populations disperse over significantly different ranges in ASPC2, a Wilcoxon rank test was performed between (COL+HON) versus (CUB, PUR, DOM). Haitians were excluded due to low sample size (N = 2 haplotypes). Boxplot is available in . Population differentiation estimates between clusters inferred with ADMIXTURE were visualized and compared across runs where both the Latino-specific and southern European components were detected. Values are available in and . To provide independent evidence on the sub-continental ancestry of European haplotypes, we considered segments that are identical by descent (IBD) between unrelated Latino individuals and a representative subset of European populations. We used our high-density dataset to extract a subset of 203 POPRES European individuals and the founders of the 65 complete admixed trios. We first performed a genome-wide pairwise IBS estimation using PLINK to ensure that the dataset contains no samples with more than 10% IBS with any other sample. Then we used fastIBD to phase the data and estimate segments shared IBD longer than 2 Mb to eliminate false positive IBD matches and assuming that ancestry will be shared among pairwise IBD hits of segments this long. All 2 Mb or greater segments shared IBD between pairs of individuals were summed, and histograms were created for pairwise matches within each group (i.e., POPRES Europeans, Iberians, and Caribbean Latinos). To inform about the proportion of shared DNA between pairs of populations we calculated a summed pairwise IBD statistic, which is the sum of lengths of all segments inferred to be shared IBD between a given European population and each Latino population, normalized by sample size., Giv […]

Pipeline specifications

Software tools ADMIXTURE, PLINK, BEAGLE