Rockfishes in the genus Sebastes are highly speciose with over 100 recognized species, most of which inhabit the Northeast Pacific Ocean. Adult rockfishes are highly diverse in both ecological niche and morphology. In contrast, many sympatric rockfish species are morphologically indistinguishable as juveniles. In such cases, genetic species identification provides a valuable alternative to traditional visual methods. Here we evaluate the performance of a genetic species identification tool, originally developed for rockfishes of the central California coast, in accurately identifying the species of a cohort of larval rockfish from Baja California, Mexico. We extracted DNA from 166 larval specimens collected during mid-water trawl surveys, and used high-throughput DNA sequencing to genotype 96 nuclear microhaplotype loci. Then we implemented multiple species assignment tests and compared the results to corroborate identifications for each sample. Our findings indicate largely high confidence assignments with strong concordance across assignment methods. These results demonstrate this tool’s effectiveness in identifying larval rockfish outside of the region in which it was originally calibrated. When integrated with traditional visual identification methods, this genetic approach could strengthen research surveys and stock assessments in Baja California marine ecosystems. Ultimately, more accurate species identification can support better-informed management decisions and contribute to the sustainability of both commercial and recreational fisheries in the region.

Rockfishes, Sebastes spp., are an unusually speciose clade of fish. They are mostly found along the North Pacific Coast and include over 100 species. Occupying a wide variety of depth ranges, rockfishes are highly diverse in both their morphology and ecological niches. This level of diversity is not seen in most fish genera. We hypothesize that a primary driver of this diversification is adaptation to different depths. For visual predators, sufficient ambient illumination is critical for locating prey. As depth increases, illumination decreases and the spectrum of underwater light becomes increasingly narrowed. Rhodopsin, Rh1, is a depth-associated gene that is responsible for vision and color perception in low light environments. We propose that Rh1 can be demonstrated to show convergent evolution and signatures of selection if compared across many rockfish species across varying depths. This could indicate an environmental pressure for diversification. Our past work has shown a greater level of Rh1 selection in deep water habitats. We seek to provide a better representation of deep water rockfish through our selection of species of interest. We extracted, amplified, sequenced, and edited the Rh1 genes from multiple rockfish species for whom the gene has never been sequenced. We uploaded these novel sequences to the National Center for Biological Information (NCBI) to make these sequences available to the public. These sequences were tested for selection against those of other species. This project seeks to gain a stronger understanding of Rh1 selection in narrow, low light environments among rockfishes.