Divergent population structure in five common rockfish species of puget sound, WA suggests the need for species-specific management

Quantifying connectivity between endangered or threatened marine populations is critical information for scientifically sound management. Of the 86 species managed by the Pacific Fishery Management Council (PFMC) on the West Coast of the United States, over 75% are rockfishes, and of those species, 27 were once deemed ‘at risk’. Although most stocks have been successfully rebuilt along the Washington Coast, Puget Sound stocks have yet to recover despite fisheries closures. The connectivity of Puget Sound stocks to coastal populations is relatively unknown, despite the potential of recruitment subsidies from the coast and considerable interest in reopening many fisheries for recreational use. The importance of accurate connectivity estimates was demonstrated by recent research on two of three Endangered Species Act (ESA) listed species in Puget Sound, which showed that one species was not sufficiently distinct to warrant listing as a separate Puget Sound distinct population segment (DPS)..., Sampling Procedure 
We used 279 samples from five species of rockfish (Black (S. melanops), Yellowtail (S. flavidus), Redstripe (S. proriger), Greenstriped (S. elongatus), and Puget Sound (S. emphaeus), Figure 1) that were collected in 1999-2021 in previous surveys of WDFW, NOAA-NMFS, and the Department of Fisheries and Oceans (DFO Canada). Individual fin clips were preserved in 95% ethanol or dried on filter paper. Samples were collected from multiple locations (see Figure 3), grouped into four different regions: 1) southern Puget Sound (Puget Sound proper, south of Admiralty Inlet, SPS), 2) British Columbia (Canadian Salish Sea north of the US/Canada border, BC), 3) northern Puget Sound (US Salish Sea north of Admiralty Inlet, NPS and east of the Victoria Sill) and 4) the US west coast (US Pacific Coast west of Victoria Sill, WC). Due to differences in the abundance and distribution of species across this geographic range, we have no Puget Sound Rockfish from WC and one Greenstriped R..., , # Divergent Population Structure In Five Common Rockfish Species Of Puget Sound, WA Suggests The Need For Species-Specific Management

[https://doi.org/10.5061/dryad.866t1g1xj](https://doi.org/10.5061/dryad.866t1g1xj)

**Description of the data and file structure**

This repository contains the raw fastq files (gzipped) and end product files (in VCF format) for a study on the population structure of five Rockfish species common in Puget Sound, WA using RADseq. We found species-specific patterns of genetic differentiation, attributable to both extrinsic and intrinsic factors. Specifically, Black and Puget Sound Rockfishes showed no genetic differentiation; Yellowtail and Greenstriped Rockfish were structured according to known geographic barriers; and Redstripe Rockfish revealed evidence for temporal genetic differentiation, suggesting irregular recruitment influences population structure.

## Description of the data and file structure

Here are a few notes about the zipping structure:

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