Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

The identical linkage-pruned dataset of 1,133,255 SNPs that was used to supply the complete genomic PCA was used to calculate admixture proportions. The.mattress file from PLINK ensuing from the PCA was analysed utilizing admixture v.1.3.0⁸⁰ to estimate admixture for values of Okay between 2 and 14, specifying 20 cross-validations (–cv=20). Because the CV error elevated with the vary of Okay that we examined (Supplementary Fig. 2, we chosen the Okay which helped to resolve the lake techniques and deep clade splits finest, Okay = 7, and plotted admixture barplots in R (extra admixture plots for Okay = 2-Okay = 10 might be present in Supplementary Fig. 3).

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