Figures S1 - S6 and Tables S1 - S5 from Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon.

Figure S1. Genome assembly diagram. Counts of annotated genes in red for each assembled chromosome in grey (scale in megabases Mb). Figure S2. Chinook salmon and rainbow trout comparative map. Alignment of Chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (Oncorhynchus mykiss) chromosome sequences demonstrates conservation of large collinear syntenic blocks between the two species. Collinear blocks with an average identity ≥ 96% (black lines), 94-96% (blue), or 90-94% (red). Figure S3. Duplicated regions in the Chinook salmon genome. The interior links represent the duplicated collinear blocks larger than 1Mb in the Chinook salmon genome. 37.4% of the identified duplicated regions can be assigned to a state of delayed rediploidization (similarity 90-95%) and 4.9% to a state of retained residual tetrasomy (similarity ≥ 95%). Figure S4. Manhattan plots of genomic divergence among lineages. a) interior ocean-type vs. coastal, collections 4,5,6,7 vs. 9,10,11,12. b) interior ocean-type vs. interior stream type, collections 1a,2,3, vs. 5,6,7,8. c) interior stream-type vs. coastal, collections 1a,2,3 vs. 9,10,11,12. Local score (Fariello et al. 2017) shown on upper half (alternating chromosome color black and gray), sliding window FST on lower half (alternating chromosome color red and blue). Critical value for significance shown by red line (Bonferroni corrected α = 0.05). Number of annotated genes in significant peaks shown, with details in Dryad. Figure S5. Manhattan plots of genomic divergence within lineages. a) within interior ocean-type, collections 4,5,6,7. b) within interior stream type, collections 1a,2,3. c) within coastal, collections 9,10,11,12. Local score (Fariello et al. 2017) shown on upper half (alternating chromosome color black and gray), sliding window FST on lower half (alternating chromosome color red and blue). Critical value for significance shown by red line (Bonferroni corrected α = 0.05). Number of annotated genes in significant peaks shown, with details in Dryad. Figure S6. Picture of Chinook salmon mating on spawning grounds. Photo credit Mary Edwards. Table S1. Populations for whole genome resequencing. Phenotypes, sample sizes (n), and sequencing statistics. Collection ID corresponds to map locations on Figure 1. Table S2. Genotype frequencies of maturation associated alleles for Chinook salmon populations across the North American range. Diagnostic SNP from GREB1L (Ots28 position 11,033,626). Summary of populations analyzed, including an assigned population number, the population name, genetic lineage, migratory run time, the number of individual samples collected from each population (n), and the geographic region (AK = Alaska, USA; BC = British Columbia, Canada; CA = California, USA; ID = Idaho, USA; OR = Oregon, USA; WA = Washington, USA), coordinates of the sampling location, and genotype frequency of a SNP from GREB1L region. Table S3. Genome summary statistics. Includes contigs, scaffolds, and scaffold gaps. Table S4. Chromosome assembly statistics. Includes total assembly (All), each of 34 chromosomes, and unplaced scaffolds. Table S5. Significant candidate genes for premature vs. mature collection pairs within each lineage. LS=local score result that corresponds to significant peaks in Figure 3b-d.

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