Genome-wide affiliation mapping
To establish the genetic foundation of gill-raker variation throughout the Alpine whitefish radiation, we used a combined mannequin strategy applied in EMMAX v.2012021084 (as in ref. 14). First, EMMAX was used to supply a Balding-Nichols kinship matrix between all 90 Alpine whitefish samples for which we had gill-raker counts utilizing ‘emmax-kin’ utilizing solely the 9,120,498 SNPs that had been polymorphic inside the Alpine whitefish radiation. We then used EMMAX to calculate the affiliation of every SNP marker with gill-raker depend. Two significance thresholds had been decided. A strict Bonferroni multiple-testing P-value threshold was calculated utilizing the whole variety of SNPs examined: −log10(0.05/9120498) = 8.26, along with an LD-considerate threshold of −log10(0.05/4536915) = 7.96, which was calculated by eradicating linked markers (R2 > 0.95) in 50 kb sliding home windows throughout the genome utilizing PLINK72. One SNP on WFS23 had an affiliation above the LD-considerate threshold and the allele frequencies inside every of the six ecomorph teams was calculated for this SNP utilizing vcftools –freq on every subset of ecomorphs individually (Fig. 2e; along with every ecomorph inside every lake individually; Supplementary Fig. 9). The gene that overlapped with this SNP was recognized with BEDTools71 and the complete protein sequence from the gene that overlapped with the SNP (maker-PGA_scaffold22__199_contigs__length_52020451-snap-gene-302.9) was BLASTed utilizing Ensembl TBLASTN towards the Atlantic Salmon, Rainbow Trout, Brown Trout and Coho Salmon genomes, hitting with excessive confidence towards the ectodysplasin-A receptor (edar) gene (E-value 1e-20; ID% 97.62 in Brown Trout fSalTru1.1; ENSSTUG00000036900 and E-value 7e-20; ID% 100 in Atlantic Salmon ICSASG_v2; ENSSSAG00000053655). The variance in gill-raker depend throughout our samples defined by essentially the most considerably related SNP was calculated utilizing the equation: PVE = ((2*(beta2)*MAF*(1-MAF))/(2*(beta2)*MAF*(1-MAF) + (se_beta2)*2*N*MAF*(1-MAF))) the place N = the pattern dimension (90), se_beta = the usual error of impact dimension of the SNP, beta = SNP impact dimension, and MAF = SNP minor allele frequency (from the Supplementary Info S1 related to ref. 85).
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