Nucleotide sites and SNPs identified on each linkage group.

1 Linkage group of the stickleback genome (Ensembl), where “Other” includes all unassembled scaffolds. 2 Total length (bp) of each linkage group. 3 The total number of nucleotide sites for which sequence information was generated in at least one individual, after trimming restriction enzyme recognition sequence. 4 The remaining columns give the number of single-nucleotide polymorphisms identified within each population. Oceanic populations are RS (Rabbit Slough) and RB (Resurrection Bay); freshwater populations are BP (Bear Paw Lake), BL (Boot Lake), and ML (Mud Lake); OC is both oceanic populations (RS + RB); FW is all freshwater populations (BP + BL + ML); ALL is all 5 populations combined.