Rapid phenotypic stock identification of Chinook Salmon in recreational fishery management

Rapid phenotypic stock identification in mixed-stock fisheries can provide a useful alternative to more time-intensive methods (e.g., coded wire tags, genetics) in assessing harvest and informing management decisions. We leveraged local ecological knowledge, existing stock identification methods, and understanding of life history differences to develop rapid stock identification tools for fall-run Chinook Salmon Oncorhynchus tshawytscha encountered in the Buoy 10 recreational fishery at the mouth of the Columbia River. Specifically, we sought to differentiate between the fishery’s two dominant genetic lineages: lower river tules and upriver brights. We sampled recreationally landed Chinook Salmon in 2017, 2018, and 2019, assigned sampled individuals to functional reporting groups using a single-nucleotide-polymorphism-based genetic baseline, and collected measurements on phenotypic traits. Using traits including pigmentation patterns (e.g., spotting), fin morphology, characteristics indicative of sexual maturity, and muscle lipid content, random forest classification models provided consistently high classification success across and within genetic groups (i.e., up to 90%). Classification success remained consistent over time within fishery seasons and between years but showed meaningful bias between sexes. Based on observed classification success, we developed and evaluated a categorical visual identification guide capable of facilitating more rapid trait observations and on-site stock identification. The resulting classification key, built using classification trees and visual guide observations from 2019, achieved slightly lower classification success across and within genetic groups and had variable success among samplers. Compared with the existing use of coded wire tags in harvest assessment, phenotypic stock identification methods can provide more rapid and more numerous assignments, albeit with a greater degree of individual assignment error. Applied as a complement to standard methods like coded wire tags, the use of rapid phenotypic stock identification methods offers the potential for increased overall precision and timeliness in harvest assessments.