Parentage-based tagging (PBT), an innovative and large-scale application of genetic parentage assignments, is transforming how fisheries managers determine the age and origin of sampled fish. PBT is an efficient alternative for mass tagging and has been widely implemented in the Pacific Northwest. While still an emerging technology, PBT is being used to provide information to managers in state, federal, and tribal agencies on the harvest, research, and conservation of Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss in this region. We review the development of PBT in the Pacific Northwest focusing on the technical and logistical challenges for implementing a regional PBT program. We also showcase recent results and review management efforts that made use of PBT-derived data.
Genetic Markers for Conservation Monitoring of Burbot Populations
Abstract The transboundary (Idaho, USA; and British Columbia, Canada) population of Burbot Lota lota native to the Kootenai River basin once provided a popular sport and commercial ﬁshery and has been culturally signiﬁcant to the Kootenai Tribe of Idaho for millennia. However, the population has experienced signiﬁcant declines over the last 30 years, due primarily to habitat loss and alteration caused by water storage and diversion. By the late 1990s, the population was considered functionally extinct, with estimates of fewer than 50 Burbot in the wild and little to no recruitment, prompting an ongoing international recovery effort. As part of these recovery efforts, managers have been actively developing a hatchery supplementation program to rebuild the population and support future tribal subsistence harvest and recreational ﬁsheries. Although supplementation breeding programs have the potential to rapidly rebuild depleted natural populations, careful genetic management is critical. To monitor genetic diversity and potential inbreeding in the broodstock and to provide parentage-based tagging of supplementation offspring, we developed a set (N = 96) of highly variable single-nucleotide polymorphism (SNP) genetic markers. The subset of 96 SNP markers was developed from a larger suite of 6,517 SNPs that were discovered by using restriction site-associated DNA sequencing. This cost-efﬁcient technology allows for the rapid discovery of thousands of SNP markers in species that have not been extensively studied previously or for which there are little existing DNA sequence data. We demonstrated high accuracy (>99%) of our SNP set for parentage and individual identiﬁcation through simulated and empirical tests. The SNP marker set provides a powerful new tool for managing broodstock and for monitoring and genetically tagging Burbot to track the growth, survival, and movement of released individuals.
It's all in the genes -- Including the tracking device
Parentage-based tagging (PBT) is an emerging genetic-based fish tagging method that involves genotyping hatchery broodstock. PBT is a passive non-invasive approach to stock identification because the parents, not the offspring, are genetically sampled at spawning, thereby "tagging" the offspring. This method provides the same information as traditional physical tags but also allows for collection of more detailed information that previously was impossible or impractical to gather using traditional tagging methods.
According to the article published today in the Canadian Journal of Fisheries and Aquatic Sciences: "This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of fisheries-based research and management questions."
Genetically tagging hatchery-reared fish using PBT is extremely efficient because genotyping hundreds of broodstock parents results in millions of tagged offspring. When fully implemented, PBT can "tag" 100% of hatchery-origin fish.
"The role of genetic methods in fisheries management has reached a milestone," says Craig Steele, a researcher at the Idaho Department of Fish and Game's Fish Genetics Laboratory in Eagle, Idaho, and lead author of the study. "The main application of this technology is to provide information on the origin and age of hatchery fish. But it can also provide additional information relevant to conservation and management efforts including assessments of genetic diversity, relative reproductive success, and the heritability of different physical or behavioral traits."
Since 2008, a regional sampling effort by collaborating state, tribal, and federal agencies has resulted in the implementation of this genetic tagging approach in hatchery-origin steelhead and spring-summer Chinook in the Snake River Basin. The Idaho Department of Fish and Game (IDFG) and the Columbia River Inter-Tribal Fish Commission (CRITFC) verified the accuracy of this new approach and presented the results of their collaborative study in the Canadian Journal of Fisheries and Aquatic Sciences.
The IDFG is committed to adopting PBT as a tool for fisheries management. Collaborative efforts with CRITFC are now underway to expand genetic sampling outside the Snake River Basin and throughout the Columbia River Basin. Adopting this genetic approach for large-scale fisheries management positions the region among the first to use this cutting-edge technology.
Yes, you can fish for trout on the Boise River right near downtown!
Fish population surveys on the Boise River below Lucky Peak Reservoir though downtown Boise. Surveys are performed every 3 years to monitor trends in the fish community using electrofishing gear. Fish are momentarily stunned, then weighed, measured and released unharmed