Estimation of conservation unit and population contribution to Chinook salmon mixed-stock fisheries in British Columbia, Canada, using direct DNA sequencing for single nucleotide polymorphisms

Terry D Beacham,Carrie Gummer,Colin Wallace,Eric B Rondeau,Kim Jonsen,Ben J.G Sutherland

doi:10.1139/cjfas-2020-0462

Terry D Beacham, Carrie Gummer + Show 4 more

Open Access

https://doi.org/10.1139/cjfas-2020-0462

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Abstract

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline comprised of some 125 198 individuals from 369 populations ranging from Russia to California was employed for genetic stock identification (GSI). GSI analysis based on variation at up to 547 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 68 conservation units (CUs) in British Columbia, 23 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian Chinook salmon.

Highlights

In Canada, the Policy for Conservation of Wild Pacific Salmon (WSP) was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making (Fisheries and Oceans Canada (DFO) 2005)
An overall accuracy of 93.8% was observed across 92 conservation units (CUs) or geographic regions for all 369 populations evaluated, fulfilling the initial requirement of accurate estimation of stock composition by reporting group
The ability to provide reliable estimates of stock composition by CU was facilitated by the switch from a microsatellite baseline (Beacham et al 2006a, 2006b) to a single nucleotide polymorphisms (SNPs) baseline with the SNPs genotyped via direct DNA sequencing of amplicons

Summary

Introduction

In Canada, the Policy for Conservation of Wild Pacific Salmon (WSP) was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making (Fisheries and Oceans Canada (DFO) 2005). Under the WSP, wild salmon populations are identified and maintained in conservation units (CUs) that are determined based on genetic traits, biogeographic distribution, life-history characteristics, and local knowledge where available. For Chinook salmon (Oncorhynchus tshawytscha), 84 CUs have been defined for Canadian populations. Under the WSP, the objective is to manage fisheries and hatchery production to ensure that wild populations are safeguarded and harvest benefits are sustainable. Price et al (2014, 2017) suggested that any suitable assessment technique must provide resolution for all individual. CUs to meet the conservation requirements of Canada’s WSP. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. The question becomes how can fishery management regimes adapt to meet the requirement of evaluating fishery impacts on increasingly smaller assessment units

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