Phylogenetically Diverse Introgression Drives Subtle Population Structure in Pacific Rockfishes

Genomic methods have shown that admixture and introgression are common across animal taxa. Pacific rockfishes, genus Sebastes, are a group of commercially important species that primarily inhabit inshore, shelf and slope habitats along the North American west coast. Among these, Copper and Quillback Rockfishes are closely related species known to hybridize, particularly within the Salish Sea in North America's Pacific Northwest. Here, we investigate genetic population structure and introgression patterns in Copper and Quillback Rockfish from Alaska to California. Using whole-genome resequencing across a broad geographic range, we seek to (1) compare population structure between these species, and (2) assess how introgression affects population structure patterns. Our analyses reveal that Copper exhibits much higher levels of population differentiation compared to Quillback, especially separating Salish Sea samples from all other populations. In contrast, Quillback populations appear to be nearly panmictic, with lower overall differentiation. Surprisingly, we detected signatures of introgression from seven other rockfish species in Copper and 10 species in Quillback. This introgression was highly regional, suggesting hybridization depended on geographic or environmental context. Yelloweye Rockfish introgression in the Salish Sea drives the strongest signal of regional population structure in Quillback. These findings provide novel insights into the range-wide genetic structure of these species and highlight that hybridization in Sebastes is phylogenetically broader than previously appreciated.