Abstract
The vermilion rockfish complex, which consists of the cryptic sister species vermilion and sunset rockfish, is one of the most valuable recreational fisheries on the U.S. West Coast. These species are currently managed as a single complex, and because of uncertainty surrounding the relative contribution of each species within existing data sources, the stock status of each species is not fully known. A reliable and cost-effective method is needed to disentangle these species that will allow for the development of abundance indices, life history profiles, and catch histories that may potentially support species-specific stock assessments. Using restriction-site associated DNA sequence (RADseq) markers we generated 10,003 polymorphic loci to characterize the vermilion rockfish complex. PCA and Bayesian clustering approaches based on these loci clearly distinguished between sunset and vermilion rockfishes and identified hybrid individuals. These loci included 203 highly differentiated (FST ≥ 0.99) single nucleotide polymorphisms, which we consider candidates in the planned development of a diagnostic assay capable of distinguishing between these cryptic species. In addition to clearly delineating to species, subsets of the interspecific markers allowed for insight into intraspecific differentiation in both species. Population genetic analyses for sunset rockfish identified two weakly divergent genetic groups with similar levels of genetic diversity. Vermilion rockfish, however, were characterized by three distinct genetic groups with much stronger signals of differentiation and significantly different genetic diversities. Collectively, these data will contribute to well-informed, species-specific management strategies to protect this valuable species complex.
Highlights
The genus Sebastes (Scorpaeniformes:Sebastidae) is a rapidly evolving lineage of marine fishes that includes many commercially and recreationally important species
We used the restriction-site associated DNA sequence (RADseq) protocol of Ali et al (2016) to construct libraries with the following specific details: (1) genomic DNA from each sample was digested with the restriction enzyme SbfI; (2) libraries were sheared to 300–500 bp using a Qsonica sonicator (Newton, CT); and, (3) 100 bp paired-end sequencing was conducted in 3 lanes using a HiSeq 4000 (Illumina, Inc., San Diego, CA) at the University of Oregon Genomics and Cell Characterization Core Facility (GC3F, Eugene, Oregon)
Stacks filtering parameters on the entire interspecific dataset resulted in 35,910 total RADseq markers, including monomorphic loci
Summary
The genus Sebastes (Scorpaeniformes:Sebastidae) is a rapidly evolving lineage of marine fishes that includes many commercially and recreationally important species. In the North Pacific, the genus has been characterized as an adaptive radiation with rapid diversification into heterogeneous ecological niches and habitats that often occur along a depth gradient (Heras and Aguilar 2019; Hyde and Vetter 2007; Ingram 2011; Johns and Avise 1998; Love et al 2002) In such rapidly diverging lineages, the true extent of species diversity can be underestimated as some closely related taxa may be difficult to differentiate morphologically. In the rougheye rockfish species complex, S. aleutianus and S. melanostictus exhibit significantly different reproductive parameters (Conrath 2017) These parameters are vital for accurate stock assessment models and the estimation of stock biomass. In cases such as this, treating distinct taxa as a single complex may present significant risk to one or both species and place them at risk of overfishing (Burford et al 2011; Frable et al 2015; Hyde and Vetter 2009)
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