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Genetic Parentage Analysis to Evaluate Reproductive Success of Spring Chinook Salmon (Oncorhynchus tshawytscha) in Newsome Creek, Idaho: 2013 Annual Report

Aug 10, 2014


The Clearwater River Subbasin historically supported large spawning populations of Chinook Salmon (Oncorhynchus tshawytscha) that represented a significant cultural, economic and subsistence resource for the Nez Perce Tribe. Extirpation of spring Chinook Salmon throughout the subbasin occurred following construction of the Lewiston Dam in 1927. However, spring Chinook Salmon were reintroduced in Clearwater River tributaries beginning in 1971 via release of hatchery-reared juveniles originating from multiple out-of-basin stocks, including Carson Hatchery, and Rapid River Hatchery (see HGMP 2011). Following initiation of reintroduction efforts, brood stock have been comprised of hatchery and natural origin returns captured in-basin. Returning adult hatchery fish reared as juveniles in the Nez Perce Tribal Hatchery (NPTH) are coded wire tagged (CWT) and are designated as “supplementation”. Natural-origin or “naturalized” fish are not tagged and have no physical markings. Although naturalized, the current local populations in the Clearwater River are not considered wild because they were re-established from non-endemic stocks, and thus are not listed under the ESA.

Parentage analysis provides a means to directly and accurately evaluate natural productivity on the basis of several metrics including relative reproductive success (RRS) between different categories of fish (i.e. hatchery vs. natural origin). This report summarizes results of overall Chinook Salmon productivity in Newsome Creek. The results herein specifically focus on RRS among naturalized fish and NPTH origin fish (e.g., those with a CWT); and to a lesser degree any strays (ad-clipped) originating from other releases in the subbasin. The primary long-term objective is to quantify the net demographic benefit of supplementation as a component of the natural spawning population. The overarching question is whether or not naturalized fish demonstrate a reproductive success rate that differs significantly from natural spawning hatchery-origin fish. If so, this may suggest an adaptive advantage among the naturalized population. In this and subsequent reports the potential effects of hatchery rearing on natural reproduction is evaluated at two stages: 1 – proportions of naturally produced juvenile and adult progeny between hatchery and natural origin parents (F1), 2 – reproductive success following adult-to-adult returns (F2) between the two population components. Additionally, these analyses aid in determining weir efficiency, and verification of both gender ID and origin ID for fish sampled at the weir and/or during spawning surveys.


Andrew Matala, Shawn Narum, Justin Bretz, Thomas Backman, and Peter Galbreath


Matala, A.P., S.R. Narum, J. Bretz, T.W.H. Backman, and P. Galbreath. 2014. Genetic parentage analysis to evaluate reproductive success of spring Chinook Salmon (Oncorhynchus tshawytscha) in Newsome Creek, Idaho: 2013 Annual Report. Submitted to: Department of Fisheries, Nez Perce Tribe, Orofino Field Office, 3404 Highway 12 Orofino, ID 83544. Columbia River Inter-Tribal Fish Commission Technical Report 14-08. Portland, OR. 27p.



Report No.


Media Type

Inter-Agency Report