Fig 1.
Interior links were generated by SyMap between homeologous regions (only blocks larger than 2 Mbp are shown). Circle A) Larson et al. (2016) [62] female genetic map markers plotted against the corresponding chromosomal positions. Centromeres from Larson et al. (2016) are shown in blue below the genetic map. Circle B) The percent identity between homeologous regions in 1 Mbp intervals and weighted by alignment length (scale: 75–100%). Percent identities above 90% are highlighted with orange. Circle C) The fraction of repetitive sequences in 1 Mbp windows ranging from zero to one (fractions above 0.65 are shown in orange). Circle D) Log-transformed counts of variants with LD (r2 ≥ 0.5) to other markers ≥ 100 kbp away in 1 Mbp windows. Window counts between 100–999 are green, while those with counts greater than 999 are orange.
Fig 2.
Clustering sockeye and kokanee individuals (population stratification).
This figure shows the clustering of individuals based on: A) DAPC and B) maximum likelihood analysis (phylogenetic tree). Both analyses began with the same 124,663 variants already filtered for common factors (e.g. maf 0.05) and was specifically filtered for linkage disequilibrium (LD), to reduce the effects of a single genomic location in high LD overwhelming all other signals. A) DAPC analysis clustering with the optimal group number [3] and optimal number of PCAs chosen [6]. The axes represent the first two linear discriminants (LD1 and LD2). The gray, coral (red/orange), and teal (blue) colours correspond to the different clusters. B) An unrooted maximum-likelihood phylogenetic tree, with bootstrap values (based on 1,000 bootstraps) shown as green dots with the larger dots representing greater bootstrap values (min: 0.1 max: 100). Only 7,357 variants remained after default SNPhylo filters. Colours are consistent with the DAPC analysis (DAPC group names shown for comparison). Please note in the Klukshu and Hansen groups, one individual from the other group was found in the grouping and likely represents a switched sample (see S1 Table). Also, there is one Takla kokanee in the Hansen grouping. Sockeye are represented by (S) and kokanee are represented by (K).
Fig 3.
Population stratification relative to location.
This figure shows the map of the sample sites and the admixture and DAPC clustering analyses. A) The sample site locations with the DAPC assignments overlaid. Specific locations from group 2 are shown with lines. Red lines represent kokanee samples. Only group 2 and 3 body of water names (with drainage in parentheses) are displayed for clarity. The insert shows greater detail of Skeena, Bella Coola, Fraser, and Columbia River bodies of water and is linked by lines to Fig 3B. B) An admixture analysis with k = 3. The colours are consistent with the DAPC analysis and DAPC groups are shown. From the DAPC group 2, there appears to be differentiation between proximal sockeye and kokanee samples based on the admixture ancestry values (in the Fraser River drainage). There also appears to be a latitudinal cline of the gray admixture ancestry values for some sites of DAPC groups 2 and 3.
Fig 4.
Genomic regions associated with eigenvalues from DAPC groups 2 and 3.
A) A Manhattan plot of an eigenGWA using the LD1 values from the DAPC analysis after accounting for the genomic inflation factor. Only the individuals from groups 2 and 3 were included in this analysis to specifically find genomic regions underlying clustering differences in DAPC 2 and 3. The horizontal blue line represents the Bonferroni correction at the 0.05 alpha level (variants interrogated = 450,868) and the red line at the 0.01 alpha level (0.01 was chosen as the level of significance for this study). Only peaks with at least 5 significant variants within 100 kbp of each other were considered. B) A screenshot from IGV showing genetic markers in LD (r2 > = 0.3) with the variant with the lowest p-value from the eigenGWA (distance ~200 kb). The dark blue colour represents homozygous reference variants (HomRef), the green colour represents homozygous alternative variants (HomVar), and the light blue colour represents heterozygous variants (Het). Near the bottom of Fig 4B shows the location of the immunoglobulin heavy chain genes and the variant with the lowest p-value are shown. Below that are examples of the haplotypes seen in the data (see Fig 4B legend: dark blue, homozygous for the reference allele; green, homozygous with the alternative allele; light blue, heterozygous). These example data are shown to illustrate that this region is often homozygous for all the alleles in this block.
Table 1.
Summary of significant eigenGWAS underlying population structure.
Table 2.
Significant eigenGWAS underlying Fraser River kokanee and sockeye ecotypes.
Table 3.
Genomic locations of ecotype associations.
Fig 5.
Sockeye salmon and kokanee sex chromosomes.
A) A GWA between all known male and female sockeye salmon and kokanee salmon with the DAPC LD1 values as covariates. The two peaks (Chr. 9a and 9b) did not reach significance. B) A GWA between all individuals scored for the presence or absence of the sex-determining gene (red line indicates significance threshold). C) A depiction of the proposed X1 (9b), X2 (9a), and Y chromosomes. D) IGV was used to visualize variants on chromosome 9a with only minimal filtering for known females (no upper Columbia River kokanee), males (no upper Columbia River kokanee), Freshwater Fisheries Society of British Columbia female kokanee, and Freshwater Fisheries Society of British Columbia male kokanee. E) On the left, LD plot of chromosome 9a from 4.6 Mbp to the end of the chromosome (~2 Mbp) with a minimum LD threshold of r2 = 0.5 for both plots. On the right, LD plot of chromosome 9b from 3.5 Mbp to 11.5 Mbp.