The 2020 Columbia River System Biological Opinion calls for Action Agencies to fund conservation and safety-net hatcheries to “to rebuild and enhance the naturally reproducing ESA-listed fish in their native habitats using locally adapted broodstock, while maintaining genetic and ecological integrity and supporting harvest”.  Only 4 hatchery programs are specified in the BiOp, including the steelhead program at the USFWS Winthrop National Fish Hatchery (WNFH), which supports recovery of the ESA-threatened Upper Columbia River Steelhead population.  Reasonable and Prudent Alternative (RPA) 63.2 of the previous FCRPS Biological Opinion called for determining the effects of implemented hatchery reforms on salmon and steelhead populations. There is currently a specified gap in coverage for Upper Columbia River steelhead (RM&E workgroup June 2009 predecisional draft document and subsequent workgroups). Project 1993-056-00 evaluates major hatchery reforms identified by the RM&E workgroup for the US Fish and Wildlife Service’s, Winthrop National Fish Hatchery. The required transition to local broodstock requires hatchery reform actions that i) can accommodate a later return and spawn timing, ii) induce proper smoltification, iii) promote high survival, and iv) maintain natural levels of fitness in the hatchery stock. The research activities of the Methow Steelhead project are included in the HGMP covering the steelhead program for the USFWS WNFH.  In summary, this hatchery research project shares the common legislative and management objectives across federal entities including BPA, NOAA, USFWS, and the Bureau of Reclamation to recover ESA-listed species and promote sustainable fisheries.
Steelhead in Pacific Northwest hatcheries are typically reared for release as 1-year-old smolts, rather than the 2- and 3-year-old smolt life history patterns found in nature. High growth rates associated with accelerated hatchery rearing to a 1-year-old smolt life history may contribute to maladaptive behavioral traits and reduced post-release survival, and may constitute a primary mechanism leading to reduced fitness in hatchery fish. The current proposal offers a unique opportunity to evaluate genetic, physiological, and life history impacts of rearing 1- vs 2-year-old steelhead smolts and a hybrid rearing model where age-at-release is determined by the natural growth rates of fish. The study is cost effective in that it will be conducted using groups of integrated steelhead already being reared in Washington tributaries of the upper Columbia River as part of ESA recovery efforts. The study aims to provide husbandry solutions that will help increase fitness, and alleviate maladaptive traits of hatchery-reared steelhead. It will develop hatchery reform actions and best management practices for artificial production programs to make a net positive contribution to recovery of listed populations.  

Nearly all steelhead intervention programs within the Basin will require non-conventional rearing methods in order to minimize the fitness loss described by Araki et al. (2008and 2009) while achieving high smoltification and survival rates. The methods developed and tested under this proposal will be transferable in real time to other intervention programs wrestling with the same issues (e.g., Touchet, Tucannon, East Fork Salmon River). The RME workgroup indicated under RPA 64.2 that additional analysis may be needed to determine if supplementation programs are having a negative impact on recovery.  The reduced reproductive success of hatchery steelhead, especially females, has a negative impact on recovery.  Project 1993-056-00 determined that females released as age-2 smolts have equivalent reproductive success as those released as age-1 smolts.  An additional negative impact affecting females from the age-2 smolt program might be reduced fecundity stemming from a reduction in ocean residence duration which is correlated with smaller adult size.  Because fecundity is positively correlated with size, the ISRP recommended during the RM&E research review that the project examine whether females from the age-2 programs have reduced fecundity.  Primary negative ecological and genetic effects of hatchery steelhead programs stem from high residualism rates. Project 1993-056-00 focuses on how hatchery reform actions affect residualism rates and develops rearing regimes to reduce production of residual phenotypes in steelhead hatcheries.  Hatchery-induced residualism caused by early male maturity would make it nearly impossible to implement hatchery reform alternatives because controlling the proportionate natural influence (PNI) and other important parameters included in HSRG models cannot be controlled if residuals are maturing and interbreeding with natural-origin fish.

With the completion of the reproductive behavior and success studies of age-1 (S1) and age-2 (S2) adult steelhead returning to the Methow River in FY 17, the project has two biological objectives: 1) Improve survival and reduce fitness loss in Columbia River steelhead smolts by minimizing unnatural selection on body size and other smolt characteristics, and 2) Identify behavioral and physiological traits under selection through laboratory-scale research to develop hatchery rearing methods to reduce selection.  Objective 1 has been greatly informed by the complementary results of our hatchery and laboratory scale research done under Objective 2.  At the WNFH, we have demonstrated that the age-2 rearing methodologies for steelhead produce smolts with equal or greater survival and faster rates of outmigration than a yearling smolt program.  This has enabled the use of natural origin broodstock at WNFH to reduce genetic impacts of hatchery steelhead on natural origin steelhead.  However, some problems remain, including higher rates of precocious male maturation at WNFH when using S2 rearing than when using S1 rearing, and a significant portion of S1 fish that grow too slowly to smolt upon release.  Our laboratory scale research has provided evidence for selection on rapid early growth under a S1 rearing regime, and that the selection may contribute to fitness loss of hatchery reared fish.  Our current laboratory scale experiments are testing alternative rearing regimes designed to minimize selection for rapid growth, and investigating other traits under selection associated with rapid early growth.
Project 1993-056-00 has come to the point where we can offer adaptive management solutions at the hatchery scale that increase the proportion of smolts produced by reducing the number of steelhead that residualize as parr due to insufficient growth and as precociously mature males.  Beginning with broodyear 2018, Objective 1 implemented an experiment at WNFH that compares a new rearing regime for steelhead to the standard S2 rearing regime.  The new rearing method sorted juvenile steelhead produced from natural-origin broodstock according to their growth rate within 9 weeks after ponding to hatchery tanks.  The fast growing fish are raised as yearling (S1) smolts using warmer water temperatures and larger rations, while the slow growing fish are raised using the tested S2 protocols established at WNFH. We will assess the proportion of smolts and precocious males produced under the split rearing regime and estimate their survival and travel rate during outmigration. Results will be compared to the S2 production groups at WNFH.  In parallel, mechanistic laboratory-based research under Objective 2 will be conducted at the Manchester Research Station using hatchery steelhead produced from the local natural broodstock at WNFH.  In FY 2019 the laboratory experiment tested for family effects on seawater survival under the new sorting regime and estimated heritability of growth and survival traits. We also started a new three broodyear experiment in FY 2019 to determine how the relationship between broodstock spawn timing and the thermal regime juveniles experience in the hatchery rearing environment affects the proportion of fish that will successfully smolt at age-1 or age-2.  The data generated from this experiment will populate an empirical model to provide a tool for hatchery professionals interested in the split rearing strategy to improve performance of smolts produced using natural-origin broodstock.  Hatchery personnel could input the spawn timing of the broodstock and the juvenile rearing temperature into the model to determine the percentages of smolts to be allocated between age-1 and age-2 rearing.

In FY 2021 we will replicate the hatchery scale experiment conducted at WNFH with an additional brood year of production under the new rearing protocol and add an unsorted S1 rearing group as an additional control treatment.  Upon approval to reoccupy Montlake laboratory facilities according to COVID protocols, we will complete the quantitative genetic analyses of the broodyear 2017 and 2018 fish from the split rearing laboratory study.  We will continue the 3-broodyear experiment initiated in FY 2019 at the Manchester Research Station, and test static respirometry equipment procured during the last funding cycle to generate preliminary data to design an experiment investigating physiological traits under selection in hatcheries.  In FY21, we will begin genetic analysis of samples collected from steelhead in our BY20 laboratory experiment using RAD sequencing to measure heritability of growth and smoltfication traits and use a genome wide association study to identify loci associated with growth and seawater adaptation.  We will also analyze fecundity data of returning females produced from age-1 and age-2 hatchery smolts to determine if smolt age has any negative effects on fecundity that would potentially affect recovery when hatchery produced fish spawn naturally.