Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex

The Neosho Bass (Micropterus velox), a former subspecies of the keystone top‐predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single‐nucleotide polymorphisms (SNPs) obtained through ddRAD‐seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories. Using over 50,000 SNPs obtained from ddRAD‐seq, we detected genomic divergence between the globally popular and ecologicaly important Smallmouth Bass (Micropterus dolomieu) and Neosho Bass (M. velox) where their native distributions come together in the Central Interior Highlands ecoregion, USA. We also show strong signatures of genetic differentiation among stream populations due to neutral drift within both subspecies, and we detected adaptive divergence within the Boston Mountains ecoregion of the Neosho native range. Despite differentiation, Neosho Bass stream populations exhibit variable demographic h