Selective sweeps should display localized, elevated and linked FST values between populations (Sabeti et al., 2006 ). SNP-wise Weir and Cockerham’s FST values were calculated by vcftools (v0.1.13; Danecek et al., 2011 ). In addition, the FST outlier test implemented in bayescan was conducted (Foll & Gaggiotti, 2008 ) using default settings. Finally, a haplotype based test, hapflk (Fariello, Boitard, Naya, SanCristobal, & Servin, 2013 ), was also used. First, we calculated the Reynolds distance matrix using the thinned data set. No outgroups were defined, 20 local haplotype clusters (K = 20) were specified and the hapflk statistic computed using 20 EM iterations (nfit = 20). Statistical significance was determined though the script “scaling_chi2_hapflk.py”. To adjust for multiple testing, we set the false discovery rate (FDR) level to 5% using qvalue / r (Storey, Bass, Dabney, & Robinson, 2019 ). Samples from the western and southern locations were grouped into their respective groups (South, N = 34 and West, N = 24) in all three tests.
3.step 1 Genotyping
The entire genome resequencing studies made a maximum of step 3,048 mil reads. Everything 0.8% of those checks out was indeed continued which means discarded. Of the kept reads regarding combined analysis put (step 3,024,360,818 checks out), % mapped with the genome, and you will % were precisely matched. The new suggest breadth regarding visibility for every single private is ?9.sixteen. As a whole, 13.dos mil succession versions was basically imagined, at which, 5.55 million got a good metric >40. Immediately after using min/maximum depth and restriction forgotten filter systems, dos.69 million versions was basically leftover, at which 2.25 billion SNPs was biallelic. I efficiently inferred the newest ancestral county of 1,210,723 SNPs.