Fig. 2: A combination of genome-wide allelic variation and major effect loci underpins parallel ecomorph differentiation in the Alpine whitefish radiation.
From: Genomic architecture of adaptive radiation and hybridization in Alpine whitefish
a CSS scan (calculated between 12 ‘Balchen’ individuals and 12 ‘Albeli’ individuals, with each ecomorph group comprising four distantly related species) highlights genome-wide parallel allele-frequency shifts between ‘Balchen’ and ‘Albeli’ ecomorphs across the four lakes. Outlier CSS windows are shown in black. b PC1 calculated using linkage filtered SNPs from across the 1659 CSS outlier windows for all whitefish individuals separates whitefish within lakes and lake systems (rows separated by dashed lines). Widespread and less-widespread ecomorphs within the same lake are separated along the same axis. c Whitefish standard length plotted against CSS PC1 for all lakes together (black line; R2 = 0.498, P = 8.06 × 10−15) and for each lake separately. Significant lake-system-specific regressions are coloured by lake system and range in R2 from to 0.322 in Lake Lucerne (P = 0.01405) to 0.6925 in the lake Walen/Zurich system (P = 1.84 × 10−5). d Gill-raker count plotted against CSS PC1 for all lakes together including (black line; R2 = 0.3921, P = 4.1 × 10−11) or excluding (grey line; R2 = 0.5107, P = 7.63 × 10−15) the outlier species C. profundus, and for each lake system separately. Significant lake-system-specific regressions are coloured by lake and range in R2 from 0.3871 in the Lake Thun–Brienz system (including the outlier C. profundus; P = 1.11 × 10−4; when excluding C. profundus R2 = 0.6051, P = 4.22 × 10−7) to 0.8113 in lake Lucerne (P = 3.47 × 10−7). See Supplementary Table 2 for all details regarding lake-specific statistics. e Allele frequencies for the SNP significantly associated with gill-raker count variation where all 91 Alpine whitefish are grouped by ecomorph (black symbols) compared to ecomorph-averaged gill-raker counts (red symbols); commissioned fish illustrations by Verena Kälin. f GWAS results for the gill-raker count and g sex for all 9,120,498 polymorphic SNPs within the Alpine whitefish radiation across the 90 individuals with corresponding phenotypes.
