Siegle, M. R. | bioRxiv Science

bioRxiv2025

Phylogenetically diverse introgression drives subtle population structure in Pacific rockfishes

Genomic methods have shown that admixture and introgression is common across animal taxa. Pacific rockfishes, genus Sebastes, are 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 (abbreviated to Copper and Quillback) are closely related species known to hybridize, particularly within the Salish Sea in North Americas Pacific Northwest. Here, we investigate genetic population structure and introgression patterns in Copper and Quillback from Alaska to California. Using whole-genome resequencing (WGS) 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 exhibit 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 13 other rockfish species in Copper and 16 species in Quillback. This introgression was highly regional suggesting hybridization depended on geographic context and congener ranges. Yelloweye Rockfish introgression 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.

evolutionary biology↗

bioRxiv2025

Prevalence of the parasitic copepod, Sarcotaces sp., infection in British Columbia rockfishes (Sebastes sp.) and implications for rockfish life-history

Marine fishes often suffer detrimental effects of parasitism, which can affect multiple life-history traits, such as maturity, growth, fecundity, and mortality. Rockfishes (genus Sebastes), in the northeast Pacific Ocean, are commonly parasitized by copepods in the genus Sarcotaces. These copepods form large cysts within the body cavity, or in the musculature of individuals. There is a lack of baseline data on the prevalence of Sarcotaces sp. infection and the effect of infection on rockfish health and life-history. Here, we present data on Sarcotaces sp. infection in 23 rockfish species (including two thornyhead species, genus Sebastolobus) that includes over 37,000 individual records collected on Fisheries and Oceans Canadas (Pacific Region) groundfish research surveys. Sarcotaces sp. were found in all geographic areas covered by the surveys (the coastal waters of British Columbia), and at all depths fish were encountered. Infection rates in the various species ranged from 0% to 10%, and were highest for Pacific Ocean Perch (POP), Silvergray, Rougheye/Blackspotted Complex (REBS), Yellowmouth, and Yelloweye rockfishes. We found that Sarcotaces sp. infection shifted the length-at-maturity ogive, with infected individuals maturing at larger sizes--particularly for males, who exhibited a 22.3 mm increase (95% CrI [credible interval]: 5.5, 39.8) in length-at-maturity across species. For most species, this effect was greater in males than in females, and the effect was most pronounced in POP, Silvergray, and REBS rockfish. Moreover, we found that immature males were 2.5 times more likely to be infected than mature males (95% CrI: 1.3, 4.7) and immature females were 1.7 times more likely to be infected than mature females (95% CrI: 0.9, 3.0). While speculative, this is consistent with Sarcotaces sp. infection acting as a co-morbidity, possibly affecting fish health and the probability of perishing before reaching maturity. Body condition was largely unrelated to infection status; however, a slight increase ({approx} 5%) in condition was associated with infection in REBS, Yelloweye, and Yellowmouth rockfishes. To our knowledge, this is the first large-scale report on Sarcotaces sp. infection within rockfishes and on rockfish life-history traits. Future work is needed to elucidate how infection influences other life-history traits and, importantly, whether these changes affect key stock assessment parameters and, ultimately, catch advice provided to fisheries managers.

ecology↗