To discover whether or not ‘Balchen’ and ‘Albeli’ species of whitefish present a parallel genetic foundation of evolution in numerous lakes, no matter lake construction, we used the cluster separation rating (CSS; launched in ref. 42 and the therein reported formulation corrected in ref. 43), a measure of genomic differentiation between people assigned to 2 teams. Right here we assigned people from the 4 ‘Balchen’ species to at least one group and people from the 4 ‘Albeli’ species to a different. When calculated in home windows of the genome, the CSS rating quantifies the genetic distance between these ecomorph teams relative to the general genetic variance on this explicit window42. We calculated CSS in 50 kb home windows utilizing a customized R script (https://github.com/marqueda/PopGenCode/blob/master/CSSm.R) the place the 24 whitefish people had been break up into two teams in accordance with ecomorph (i.e., ‘Balchen’ or ‘Albeli’). A stratified permutation check which reshuffles the task of people to every of the ecomorph teams inside every lake to check the statistical significance of the CSS rating for every window, while sustaining inhabitants construction, was then carried out 100,000 occasions utilizing a customized R script (https://github.com/marqueda/PopGenCode/blob/master/CSSm_permutation.R). Home windows with fewer than 24 SNPs had been eliminated (in accordance with ref. 43) and outlier home windows had been recognized primarily based on a false discovery price adjusted P-value cut-off of P < 0.01, utilizing ‘fdr.degree = 0.01’ within the R package deal ‘qvalue’ (ref. 82; equally to ref. 43). The median CSS rating throughout all 34,102 home windows with ≥24 SNPs was 0.0083 and the median CSS rating throughout all 1659 outlier home windows was 0.0973. A PCA was then produced for all 91 Alpine whitefish (excluding our outgroup samples) utilizing PLINK v.1.90 beginning with solely the 690,101 SNPs that fell inside these 1659 CSS outlier home windows. Filtering for linkage disequilibrium was carried out as above, leading to 56,127 SNPs that had been then used to find out the genomic variation between whitefish species inside these genomic areas. Correlations between PC1, which separated out species, and traits (gill-raker depend and normal size) had been carried out utilizing the linear mannequin operate (lm) in R.
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