Maximum Likelihood Estimation of the Proportion of Hatchery‐Origin Fish on Spawning Grounds Using Coded Wire Tagging and Parentage‐Based Tagging

Abstract

For salmon populations in the Columbia River and Snake River basins, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimates of the proportion of hatchery‐origin adults in spawning areas (p) are needed to assess population status and the genetic and demographic interactions of hatchery‐ and natural‐origin fish. Some hatchery fish receive visible marks, coded wire tags (CWTs), parentage‐based tags (PBTs), or all three. This allows one to identify whether fish recovered after release are of hatchery origin. Parentage‐based tagging involves genotyping hatchery broodstock and uses parentage assignments as “tags” that identify the origin and brood year of their progeny. We derived a maximum likelihood estimator of p and applied it to the 2012 and 2013 carcass survey data for spring–summer Chinook Salmon Oncorhynchus tshawytscha in the South Fork Salmon River, Idaho. Maximum likelihood estimation was also applied to CWT data and, for investigating the importance of expected tag recoveries on precision, to simulated PBT data for fall Chinook Salmon spawning in the Hanford Reach of the Columbia River. Precision of p from maximum likelihood estimation increased with the expected number of tag recoveries in a carcass survey, whether CWTs or PBTs. In the South Fork Salmon River application, there were 340% more PBT recoveries than CWT recoveries, leading to greater precision in release‐specific values of p from maximum likelihood estimation. The maximum likelihood estimation procedure provides fisheries managers a method to design a tagging and sampling program aimed at estimating p, a valuable measure of the potential for interaction of wild‐ and hatchery‐origin fish on the spawning grounds. To design a program for estimating p, we recommend selecting a target level of precision and then choosing a tagging fraction and sampling rate that delivers that precision in the most cost‐effective way. Received August 21, 2015; accepted January 19, 2016 Published online April 27, 2016

Parentage‐Based Tagging: Reviewing the Implementation of a New Tool for an Old Problem

“…In addition, PBT is being used to identify stock composition of hatchery Chinook Salmon in sport fisheries in Idaho (Sullivan et al 2015(Sullivan et al , 2016; identifying unclipped hatchery-origin fish in steelhead fisheries (Byrne et al 2014a(Byrne et al , 2014b(Byrne et al , 2016; identifying hatchery-origin kelts (Matala et al 2016); characterizing run timing of hatchery stocks (Hess et al 2016b); and estimating proportion of hatchery-origin spawners on spawning grounds (Hinrichsen et al 2016;Young et al 2017). In addition, PBT is being used to identify stock composition of hatchery Chinook Salmon in sport fisheries in Idaho (Sullivan et al 2015(Sullivan et al , 2016; identifying unclipped hatchery-origin fish in steelhead fisheries (Byrne et al 2014a(Byrne et al , 2014b(Byrne et al , 2016; identifying hatchery-origin kelts (Matala et al 2016); characterizing run timing of hatchery stocks (Hess et al 2016b); and estimating proportion of hatchery-origin spawners on spawning grounds (Hinrichsen et al 2016;Young et al 2017).…”

“…The studies mentioned here represent only a portion of the recent publications making use of PBT. In addition, PBT is being used to identify stock composition of hatchery Chinook Salmon in sport fisheries in Idaho (Sullivan et al 2015(Sullivan et al , 2016; identifying unclipped hatchery-origin fish in steelhead fisheries (Byrne et al 2014a(Byrne et al , 2014b(Byrne et al , 2016; identifying hatchery-origin kelts (Matala et al 2016); characterizing run timing of hatchery stocks (Hess et al 2016b); and estimating proportion of hatchery-origin spawners on spawning grounds (Hinrichsen et al 2016;Young et al 2017). Ongoing studies also make use of PBT to evaluate origin and reproductive success of stray steelhead (Smith et al 2016) and to manage endangered Sockeye Salmon (Peterson et al 2014).…”

Population and individual identification of coho salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

“…However, the increasing cost of applying CWTs has restricted the application to only a small proportion of fish released from hatcheries, with many hatcheries in Canada releasing juvenile coho salmon with no CWTs applied. The resulting small sample size of recovered CWTs greatly reduces confidence in estimates of stock contributions to mixed-stock fisheries because the precision of these estimates is directly related to the number of CWTs recovered (Reisenbichler and Hartmann 1980;Hinrichsen et al 2016). …”

Fisheries Volume 43 Number 7 July 2018

“…For example, Hess et al ( 2016 ) used a Columbia River basin GSI baseline for steelhead (FishGen Dataset identifi cation number [ID] 20150220) and a Snake River steelhead PBT baseline (FishGen Dataset ID 20150221) in conjunction, to estimate the stock-specifi c abundance and run timing of wild and hatchery steelhead returning to the Columbia River basin during three consecutive migration years (2012)(2013)(2014). In addition, Hinrichsen et al ( 2016 ) used a Snake River Chinook PBT hatchery baseline (FishGen Dataset ID 20160248) to effectively estimate the proportion of hatchery-origin fi sh on spawning grounds in the South Fork Salmon River.…”