Supplemental Material for Bassham et al., 2018

RAD consensus sequences for each locus with its aligned genomic position are available in FASTA format for populations (File_S01) and for population groups (File_S06). SNP and haplotype calls are available in VCF format for populations (SNP: File_S02; haplotype: File_S03) and for population groups (SNP: File_S07; haplotype: File_S08). Values of divergence (F<sub>ST</sub> or F<sub>ST</sub>ʹ and Φ<sub>ST</sub>) at each locus are available for populations (SNP: File_S05; haplotype: File_S04), and for population clusters (SNP: File_S10; haplotype: File_S09). Figure S1 contains genetic groupings and a reference map of studied populations. Figure S2 depicts continuous genetic divergence across the genome for marine versus each freshwater genetic group. Figure S3 shows the full HMM analysis across all linkage groups. Figure S4 contains gene and haplotype diversity measures. Figure S5 shows Cases along the genome in independent populations. Figure S6 depicts alternative freshwater haplotypes across LGI. Figure S7 contains per-chromosome allele frequency spectra. Figure S8 contains boxplots of alternative freshwater allele frequencies. Figure S9 contains per-marine fish counts of alternative freshwater alleles. Figure S10 is a comparison of genomic divergence patterns between this and an independent published analysis. Figure S11 shows LD patterns in freshwater fish. Figure S12 shows an aerial photograph of collection sites on Montague Island. Table S1 lists genome-wide genetic divergence values for freshwater versus marine comparisons. Table S2 reports fractions of the diverged genome that overlap among populations. Table S3 quantifies categories of divergent loci (Cases) in different populations. Table S4 contains the mean, median, and SD of the frequencies of alternative freshwater alleles in marine populations. Table S5 contains the fraction of alternative freshwater alleles found on each chromosome for each marine fish. Tables S6-S8 report sequencing statistics. Table S9 contains a key for which data set was used in each figure/table.