Abstract
Unlike most anadromous fishes that have evolved strict homing behaviour, P acific lamprey ( E ntosphenus tridentatus ) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within‐region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site–associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism ( SNP ) loci for 518 individuals collected across a broad geographical area including B ritish C olumbia, W ashington, O regon and C alifornia. A subset of putatively neutral markers ( N = 4068) identified a significant amount of variation among three broad populations: northern B ritish C olumbia, C olumbia R iver/southern coast and ‘dwarf’ adults ( F CT = 0.02, P ≪ 0.001). Additionally, 162 SNP s were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNP s were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNP s were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNP s aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow.