Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

We took a phylogenetic strategy to know the relationships between every of the Alpine whitefish species we sampled. First, the complete VCF file was thinned to incorporate solely SNPs which had been 500 bp aside utilizing VCFtools (ref. 70;–skinny 500). The thinned SNP dataset containing 2,039,744 SNPs was then filtered utilizing bcftools (a part of SAMtools v.1.8⁷⁶; bcftools view -i ‘COUNT(GT = “RR”) > 0 & COUNT(GT = “AA”) > 0’) to go away solely SNPs that had been current no less than as soon as in our dataset as homozygous for the reference allele, and homozygous for the choice allele, as required by RAxML. This lowered the dataset to 1,692,559 SNPs (particularly compiled for RAxML and never utilized in another evaluation). This filtered VCF file was then transformed to a PHYLIP file utilizing vcf2phylip v.2⁷⁷ earlier than RAxML v.8.2.12⁷⁸ was run with the ASC_GTRGAMMA substitution mannequin (-m ASC_GTRGAMMA–asc-corr=lewis, -k -f a) with 100 bootstraps and specifying the C. albula samples as outgroups to supply the utmost chance tree. The phylogenetic tree, excluding the lengthy node to C. albula, was then plotted utilizing Figtree v.1.4.4⁷⁹.

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