Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

PCA, phylogenetics and admixture evaluation

PLINK v.1.90⁷² was used to supply a genomic PCA of all 91 Alpine whitefish genomes with the intention of understanding how every of the people, species, and lakes had been differentiated from each other. All eight outgroup people had been faraway from the complete dataset of leaving solely Alpine whitefish from the 5 lake techniques. Loci had been then filtered primarily based on linkage disequilibrium utilizing PLINK v.1.90 (ref. 72; 50 kb home windows with a step dimension of 10 bp and filtering for an R² > 0.1). This resulted in 1,133,255 loci which had been processed by PLINK to calculate eigenvector distances between people. PCAs had been plotted utilizing R⁷⁵.

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