Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation‐driving adaptations, particularly along a depth gradient. A reduced‐representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black‐and‐yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation‐with‐gene‐flow evolutionary model followed by post‐speciation selective sweeps within each species. Limited whole‐genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.

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More than half of Earth is covered by ocean, yet little is known about the deep sea (> 200 meters), particularly the water column. From 200 to 1,000 meters below the ocean surface is the mesopelagic zone, where a variety of organisms thrive. Within this zone, there is a portion of the water column where mesopelagic organisms are highly abundant due to light differences and predator avoidance, causing the region to be acoustically dense; this is known as the deep scattering layer (DSL). We hypothesized