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

Abstract

Parentage-based tagging (PBT) is a non-lethal, genetic tagging method that has been successfully applied in hatchery supplemented populations to manage hatchery broodstock 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 (O. 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 non-overlapping 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.

Largemouth Bass Hatchery Contributions Quantified via Parentage‐Based Tagging

“…mykiss are sampled annually in the Snake River basin to tag approximately 20 million smolts (Hargrove et al. 2021a). In the current study, genotyping of 184 broodstock resulted in genetically “tagging” 150,346 offspring, which may reduce the per‐offspring cost of batch marking.…”

“…Additionally, Hargrove et al. (2021a) estimated false positive rates of 0.09% when comparing 4,356 wild steelhead against 46,296 potential hatchery parents. Together, these points illustrate the importance of statistical characteristics of PBT marker panels and their relevance in ensuring that parent–offspring assignments are accurate.…”

“…2008), and the ability to unambiguously assign a sample of unknown origin to hatchery and SY of origin (Hargrove et al. 2021a). To date, PBT has been used to generate information on stock‐specific patterns of migration and abundance (Hess et al.…”

Grandparent Inference from Genetic Data: The Potential for Parentage‐Based Tagging Programs to Identify Offspring of Hatchery Strays

“…In these situations, having data available to reduce the number of comparisons can be critical for making an analysis feasible. For example, if natural‐origin steelhead are sampled at Lower Granite Dam on the Snake River (Hargrove et al 2021), then all steelhead hatcheries adjacent to and upstream of the dam must be considered (~5,000 total steelhead spawned annually). With no data other than the year and hatchery at which fish were spawned, the number of potential pairs of grandparents would be approximately 5.5 × 10 6 each year, while considering phenotypic (or genetic) sex would reduce this to 1.4 × 10 6 (Idaho Department of Fish and Game, unpublished).…”

Grandparent inference from genetic data: The potential for parentage-based tagging programs to identify offspring of hatchery strays

“…In these situations, having data available to reduce the number of comparisons can be critical for making an analysis feasible. For example, if natural-origin steelhead are sampled at Lower Granite Dam on the Snake River (Hargrove et al 2021), then all steelhead hatcheries adjacent to and upstream of the dam must be considered (approximately 5,000 total steelhead spawned annually). With no data other than the year and hatchery at which fish were spawned, the number of potential pairs of grandparents would be approximately 5.5 • 10 6 each year, while considering phenotypic (or genetic) sex would reduce this to 1.4 • 10 6 (IDFG, unpublished).…”