Fig. 1
Distribution of population genetic parameters and repetitive elements calculated in nonoverlapping 5 kb windows in a comparison of Atlantic and Pacific herring. (A) Estimates of genetic differentiation (FST), intraspecies nucleotide diversities in Atlantic (πAtlantic) and Pacific herring (πPacific) and interspecies nucleotide diversity between Atlantic and Pacific herring (dxy) across chromosome 6 are displayed in the first to fourth tracks, respectively. Corresponding plots for all chromosomes are shown in Supplementary Fig. S1. Each dot represents a 5 kb window. Windows in the lower 5th percentile of the genome-wide distribution of FST and the top 5th percentile of the genome-wide distributions of πAtlantic and πPacific are highlighted in red. The bottom track represents the cumulative proportion of repeats across the chromosome. (B) The box plots show the distributions of genetic differentiation (FST) and nucleotide diversities (π and dxy) in the high-diversity regions (red) in comparison with the genomic background (black); the mean values are represented with yellow dots inside the boxes. All comparisons are statistically significant (P < 0.001). (C) The bar chart summarizes the proportion of coverage by different repeat superclasses within the high-diversity regions and background sequences. ***=P < 0.001; NS = not significant