Genetic methods for informing conservation and management of salmonids in the Pacific Northwest, USA

The management of Pacific salmonids Oncorhynchus sp. is complex, requiring a balance between conserving imperilled natural-origin stocks and mitigation for hydrosystem operations, including supporting fisheries, using hatchery-origin stocks. To achieve these objectives, various types of data are used such as genetic information. Given the wide geographic distribution of salmonids and the numerous institutions involved in their management, the genetic methods employed often vary by region. Additionally, the ways in which these methods inform management are frequently documented only in agency reports, making access difficult. Here, we provide a case study of how genetic stock identification and parentage-based tagging are used to address diverse management goals in the Columbia River basin with a particular focus on the Snake River basin where a genetic monitoring programme has operated for over 15 years. Additionally, we describe how advancements in sequencing technologies have been leveraged to reduce genotyping costs, generate additional data and address emerging management and conservation challenges.