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Pipeline publication

[…] and allelic richness was estimated by rarefaction (N = 30) using the software HPRARE []., To identify likely genetic clusters and possible origins for each cluster, we used a Bayesian clustering method implemented by the software STRUCTURE v. 2.3.4 []. STRUCTURE identifies K genetic clusters and estimates what proportion of each individual’s ancestry is attributable to each cluster, with no a priori location information about the individuals. Twenty independent runs were conducted at K = 1–15 for the full set of CA and North American reference populations and at K = 1–12 for the subset of just CA populations. We ran each for 600,000 generations with 100,000 discarded as burn-in, assuming an admixture model and correlated allele frequencies. The optimal number of K clusters was chosen using the guidelines from Prichard et al. [] and the Delta K method [, ]. The results were visualized using the program DISTRUCT v.1.1 []., To further explore population structure, discriminant analyses of principle components (DAPC), Principle Component Analyses (PCA), and plots illustrating FST values were created using the Adegenet package v. 2.0.2. [], available on R software v. 3.2.4 and RStudio v.0.99.893 []. DAPC optimizes variation between clusters while minimizing variation within them. Data are transformed using a PCA and then clusters are identified using discriminant analysis. We assessed genetic differentiation among population pairs by calculating FST values with GenoDive v. 2.0b27 []. We also ran isolation by distance (IBD) analyses for all populations and for all CA populations using Genodive v. 2.0b27., While the SNP chip has 50,000 probes, only 27,674 passed the initial stringent testing requiring unambiguous genotyping, biallelic and polymorphic markers, and Mendelian inheritance []. Further filtering was done using PLINK v.1.9 to exclude alleles showing up in <1% of samples as these could be genotyping errors, as well as loci not conforming to Hardy-Weinberg expectations (threshold of 0.00001), and those that genotyped in <98% of the samples [, ]. These filtering parameters are standard for SNP chip data [–]. The dataset contained 15,698 […]

Pipeline specifications

Software tools ADMIXTURE, DISTRUCT, adegenet, Genodive