Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history

Hybridization can provide evolutionary benefits (e.g., population resilience to climate change) through the introduction of adaptive alleles and increase of genetic diversity. Nevertheless, management strategies may be designed based only on the parental species within a hybrid zone, without considering the hybrids. This can lead to ineffective spatial management of species, which can directly harm population diversity and negatively impact food webs. Three species of rockfish (Brown Rockfish (Sebastes caurinus), Copper Rockfish (S. auriculatus), and Quillback Rockfish (S. maliger)) are known to hybridize within Puget Sound, Washington, but genetic data from these species are used to infer population structure in the entire genus, including in species that do not hybridize. The goal of this project was to estimate the hybridization rates within the region and determine the effect of hybridization on geographic patterns of genetic structure. We sequenced 290 Brown, Copper, and Quillback ..., Sampling procedure
We used 290 individuals from three species of rockfish (Brown, Copper, and Quillback) that were previously collected by the Washington Department of Fish and Wildlife (WDFW), the National Marine Fisheries Service’s Northwest Fisheries Science Center (NWFSC), and the Department of Fisheries and Oceans (DFO Canada) from 1999-2021 (Fig. 1, Table 1). Tissue was clipped from individual fins and either preserved in 95% ethanol or dried. Individuals were collected from four regions: 1) British Columbia (Canadian Salish Sea north of US/Canada border, BC), 2) northern Puget Sound (US Salish Sea north of Admiralty Inlet, south of the US/Canada border and east of the Victoria sill, NPS), 3) southern Puget Sound (Puget Sound proper, south of Admiralty Inlet, SPS), and 4) the US West Coast (US Pacific Coast west of Victoria sill, WC) (Fig. 1). We also re-sampled 62 individuals from a study on rockfish hybridization that were identified as ‘pure’ parental species, including 26 Brow..., , # Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history

[https://doi.org/10.5061/dryad.j0zpc86mv](https://doi.org/10.5061/dryad.j0zpc86mv)

This repository contains the raw fastq files (gzipped tarballs) and end product files (in VCF format) for a study on the inter- and intraspecific population structure between three species of rockfish common in Puget Sound, WA, using RADseq. We show that (i) hybridization within Puget Sound was asymmetrical, ancient, widespread, and relatively low level, (ii) hybridization affected population structure in Copper and Brown rockfish, but not in Quillback Rockfish and (iii) after taking hybridization into account, there were two populations in Quillback, one in Copper, and three populations in Brown Rockfish.

## Description of the data and file structure

This repository contains:

* All final VCF files for the inter- and intraspecific analyses
* All VCF files were filtered for both high ...,