Select Page

Maximum Likelihood Estimation of the Proportion of Hatchery-origin Fish on Spawning Grounds Using Coded-wire and Parentage-based Tagging

Jul 25, 2016


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.


Richard Hinrichsen, Craig Steele, Michael Ackerman, Matthew Campbell, Shawn Narum, Maureen Hess, William Young, Barbara Shields, and Brian Maschhoff


Hinrichsen, R.A., C.A. Steele, M.W. Ackerman, M.R. Campbell, S.R. Narum, M.A. Hess, W.P. Young, B.A. Shields, and B.L. Maschhoff. 2016. Maximum likelihood estimation of the proportion of hatchery-origin fish on spawning grounds using coded-wire and parentage-based tagging.  Transactions of the American Fisheries Society 145(3):671-686. Online at



Report No.


Media Type

Journal Article