This EMMAX affiliation mapping was repeated utilizing intercourse as a binary trait for 90 Alpine whitefish people. Essentially the most substantial related peak was noticed on WFS04. As above, genes that overlapped with these SNPs had been recognized with BEDTools71 and the protein sequence from the one gene that overlapped with this peak of SNPs on WFS04, maker-PGA_scaffold3__454_contigs__length_92224161-snap-gene-551.2, was BLASTed utilizing Ensembl TBLASTN towards the Atlantic Salmon, Rainbow Trout, Brown Trout and Coho Salmon genomes, nevertheless, no annotated genes had been hit with excessive confidence utilizing this strategy.
F-branch statistics
To calculate extra allele-sharing throughout the dataset, and check whether or not species of the less-widespread ecomorphs with distinctive trait combos (i.e., combos of traits that distinction with the course of correlation amongst combos of traits seen within the widespread ecomorphs) have advanced because of gene move between lake techniques, we used the f-branch statistic fb(C) as calculated by the package deal Dsuite v.0.386 as in ref. 87. First, a simplified model of the complete RAxML phylogenetic tree was ready. To utilize the a number of samples per species in our dataset and get sturdy estimates of extra allele-sharing each inside and between lake techniques, collapsed nodes within the phylogenetic tree utilizing the R package deal ‘ape’88 the place doable. People which appeared like potential F1 hybrids as indicated by near 50/50 splitting within the admixture evaluation or had been positioned discordantly in our genome-wide PCA and phylogeny (together with the C. alpinus 0129 and C. zuerichensis 099) and people which didn’t sit in the identical clade as different people of the identical species in the identical lake system had been stored separated in order to not skew species-wide estimates of extra allele-sharing from single, doubtlessly latest introgression occasions, and thus not included in node collapsing. Nodes had been then collapsed, and the people inside that clade assigned as a single tree tip, if all people inside the clade belonged to the identical species or species of the identical ecomorph from a single lake or, the place doable, single lake system (excluding potential F1 people). All outgroup people within the tree had been collapsed right into a single outgroup tip. Dsuite86 was then run specifying Dtrios, DtriosCombine, and at last f-branch, every time specifying the collapsed tree. Dsuite was used to first calculate f4 admixture ratios f(A,B;C,O) throughout the dataset the place combos of taxa match the mandatory relationship ((A, B), C) in our phylogenetic tree, with the 8 non-Alpine whitefish set because the outgroup. The f-branch statistic fb(C) was then calculated from these f4 statistics utilizing the phylogenetic tree to establish extra allele-sharing between any taxa into another taxon or node within the phylogeny. fb(C) is especially highly effective for complicated techniques such because the Alpine whitefish radiation since, in contrast to Patterson’s D, it supplies branch-specific estimates of extra allele-sharing, that means that particular situations of gene move don’t skew extra allele-sharing estimates throughout a number of nodes or branches, offering a phylogenetically-guided and sturdy estimate of extra allele-sharing87. F-branch statistics plotted in Fig. 3 are offered in Supplementary Knowledge 4 together with a model of the determine highlighting within-lake introgression in Supplementary Fig. 10. Important situations of extra allele-sharing had been recognized by calculating a stringent Bonferroni multiple-testing significance threshold, which concerned dividing the p-value threshold of P < 0.01 by the variety of cells within the f-branch matrix for which fb(C) may very well be calculated (1910) and changing this to a Z-score utilizing R. All cells with Z-scores greater than this threshold i.e., Z > 4.41 represented important extra allele-sharing between taxa within the tree and had been indicated as such.
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