Date

Fall 2026

Document Type

Master's Thesis (Open Access)

Degree Name

Master of Science (M.S.)

Department

Moss Landing Marine Laboratories

Abstract

Understanding how genetic structure is distributed across space and influenced by the environment informs basic questions in evolutionary biology and applications for fisheries management. This can be particularly relevant for marine fishes where high dispersal potential, both of drifting larvae and swimming adults, can obscure biologically meaningful subdivision. Canary rockfish (Sebastes pinniger) are commercially important Pacific groundfish that were historically overfished and later rebuilt, yet their population genetic structure remains poorly resolved, across both latitudinal and depth gradients. In this study, reduced-representation genomic (RADseq) data from 171 individuals and 12,726 single nucleotide polymorphisms (SNPs) were used to evaluate coastwide structure and depth-associated differentiation in canary rockfish sampled from 14 ports spanning over 1800 km from Washington to Southern California, along the U.S. West Coast. Across the coastwide dataset, genetic differentiation among sampling ports was weak, and no evidence of isolation by distance was detected over this extensive geographic scale. Broad-scale analyses also suggested that spatial and environmental gradients leave only minor genomic signatures across the species' range. These results support high connectivity across the sampled coastwide distribution. A separate genome-wide clustering pattern unrelated to geography or depth was detected by principal component analysis, suggesting that additional genomic processes, such as structural rearrangements, may contribute to genetic variation in this species. Among the four ports evaluated for fine-scale depth structure, only Neah Bay, Washington showed repeated evidence of separation between shallow and deep individuals across complementary analyses. Outlier analyses provided limited but suggestive support for the Neah Bay signal, identifying a small set of loci putatively associated with depthrelated differentiation. Overall, these results suggest that canary rockfish populations function as a broadly connected genetic system at coastwide scales while exhibiting localized depth-associated differentiation under particular ecological conditions. Future research should apply more comprehensive genomic approaches to clarify the basis of both the coastwide clustering pattern and localized depth-associated differentiation detected at Neah Bay.

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