Color code of each population refers to the spawning season that a given pool was sampled.
Seasonal sea water temperature profiles across the North Atlantic and the Baltic Sea. Herring sampling locations are overlaid on top of the temperature data. Climatic data layers at a 0.25° spatial …
(a) PCA based on 169,934 genetically undifferentiated markers. (b) PCA based on 794 markers that are likely under natural selection. Color of each population represents spawning season, as coded in F…
(a) Neighbor-joining tree of 53 Atlantic herring populations based on allele frequency of genome-wide SNPs. (b) Geographical distribution of populations in relation to phylogenetic clustering. Color …
We selected 22,195 undifferentiated markers and 794 markers that are likely under natural selection based on the cutoffs (SD <0.02 and SD >0.2).
(a) Genetic differentiation between superpools of Baltic and Atlantic herring in spring- spawners (above) and in autumn-spawners (below) and (b) a zoomed-in profile for Chr12. (c) Genetic …
Results for individual chromosomes. SNPs with raw p>10−30 in both spring and autumn-spawners are colored in grey. SNPs with raw raw p<10−30 in both spring and autumn-spawners are colored in red …
Raw p-values are presented here and adjusted p-values are given in Supplementary files 4 an5, respectively.
Results for individual chromosomes. SNPs with raw p>10−30 in both spring and autumn-spawners are colored in grey. SNPs with raw p<10−30 in both spring and autumn-spawners are colored in red while …
For each contrast used, the same three sub-panels are shown. i: a QQ-plot of observed vs. expected –log10(P)-values, where the red line is a line with slope one and the black line represents a …
(a) Putative structural variants on Chr6, 12, 17 and 23 are indicated with red stars. (b to e) are zoomed-in profiles on the corresponding chromosomes. Strong genetic differentiation is observed in …
Average nucleotide diversity was estimated for S and N haplotypes in each tree.
(a) A QQ-plot of observed vs. expected –log10(P)-values, where the red line is a line with slope one and the black line represents a linear regression using the first (i.e. least significant) 90% of …
(a) Genome-wide screen. (b) Genetic differentiation on Chr2 and a zoom-in profile of the AHR2B2 locus. Red dots refer to the four missense mutations.
There are four isoforms of AHR in herring organized as two gene pairs: AHR1B2-AHR2B2 on chromosome two and AHR1B1-AHR2B1 on chromosome 21. These have been named based on sequence similarity to the Ah…
The color side-bar indicates the frequency of the reference allele, and the top bar highlights (in purple) the one non-synonymous SNP in the set: chr19_6359267. This polymorphism causes a missense …
(a) A QQ-plot of observed vs. expected –log10(P)-values, where the red line is a line with slope one and the black line represents a linear regression using the first (i.e. least significant) 90% of …
(a) Chromosome 6. The orientation of an informative read is indicated with arrows above the Chr6 reference panel. The breakpoints are indicated with dotted blue lines. The region just outside the …
Specimen information of 53 pooled samples.
Specimen information of 55 individual sequencing samples.
Definition of how superpools were formed by pooling population samples of major groups of herring.
Sample names correspond to those given in Supplementary file 1.
List of SNPs showing strong genetic differentiation between superpools of Atlantic and Baltic herring.
The criteria for inclusion was raw p<10−30 for both comparisons (among spring-spawners and among autumn-spawners) or raw p<10−50 for a single comparison. These are the SNPs colored in red or black in Figure 3—figure supplement 1. Raw p-values are given in columns E and G and corrected p-values in columns F and H.
List of loci showing strong genetic differentiation between superpools of spring and autumn-spawning herring.
The criteria for inclusion was raw p<10−30 for both comparisons (among Atlantic populations and among Baltic populations) or raw p<10−50 for a single comparison. These are the SNPs colored in red or black in Figure 3—figure supplement 3. Raw p-values are given in columns E and G and corrected p-values in columns F and H.
Genes within inverted regions and 200 kb flanking inversion breakpoints on chromosome 6 and 17 in Atlantic herring.
Reference allele frequencies for the 794 markers used in the PCA shown in Figure 2b.