Parentage-based tagging improves escapement estimates for ESA-listed adult Chinook salmon and steelhead in the Snake River basin

• Published in: Canadian journal of fisheries and aquatic sciences Vol. 78; no. 4; pp. 349 - 360
• Main Authors: Hargrove, John S, Camacho, Carlos A, Schrader, William C, Powell, John H, Delomas, Thomas A, Hess, Jon E, Narum, Shawn R, Campbell, Matthew R
• Format: Journal Article
• Language: English
• Published: 1840 Woodward Drive, Suite 1, Ottawa, ON K2C 0P7 NRC Research Press 01.04.2021; Canadian Science Publishing NRC Research Press
• Subjects: Abundance; adults; Analysis; Animal behavior; Animal marking; Biological sampling; Breeding stock; Case studies; Censuses; Chinook salmon; Confidence intervals; Endangered & extinct species; Endangered species; Endangered Species Act of 1973; Escapement; Estimates; Fins; Fish; Fish hatcheries; Fishery management; Freshwater; Genetic aspects; Genetics; Genotypes; hatcheries; Marking; Methods; Monitoring; Natural populations; Oncorhynchus mykiss; Oncorhynchus tshawytscha; Physiological aspects; Populations; Rare species; Restocking; River basins; River fisheries; Salmon; Salmoniformes; Snake River; Spawning migrations; Sport fishing; Steelhead (Fish); Tagging; Threatened species; Trap nets; watersheds; United States; USA, Idaho, Snake River; Snake River
• ISSN: 0706-652X; 1205-7533; 1205-7533
• DOI: 10.1139/cjfas-2020-0152

Parentage-based tagging (PBT) is a nonlethal, genetic tagging method that has been successfully applied in hatchery-supplemented populations to manage hatchery brood stock and monitor hatchery harvest and straying rates. We show that PBT can also improve the accuracy of escapement estimates by significantly reducing the number of hatchery-origin fish falsely classified as natural-origin. Unlike conventional abundance estimates, which use physical marks and tags to distinguish hatchery individuals from their wild counterparts, PBT identifies origin independent of physical form. We applied PBT to populations of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss), which are classified as Threatened under the Endangered Species Act and subject to extensive hatchery supplementation efforts. For spawn years 2014–2018, 16 511 adipose-intact Chinook salmon and 21 953 adipose-intact steelhead were sampled, and PBT identified 19.6% of returning Chinook salmon and 8.3% of steelhead were of hatchery-origin, despite having no physical or mechanical marks. The 90% confidence intervals for escapement estimates of natural-origin Chinook salmon and steelhead made with and without corrections using PBT were nonoverlapping for nine of ten comparisons, indicating that failing to account for unmarked, untagged hatchery-origin fish would result in a significant overestimation of natural abundance.