Reasonable and Prudent Alternative (RPA) 63.2 of the FCRPS Biological Opinion calls 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). This project provides for implementation and evaluation of major hatchery reforms identified by the RM&E workgroup for the US Fish and Wildlife Service’s, Winthrop National Fish Hatchery (WNFH). 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. Simply, transition to local broodstock cannot be successful without effective implementation of the hatchery reforms described in this proposal, which is part and parcel to the USFWS HGMP for WNFH.

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. 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. The design fills gaps identified in the FCRPS BiOp Reasonable and Prudent Alternatives 39, 63.2, 64.2. 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. Negative effects from ecological interactions constitute one of the primary concerns with hatchery programs. This project will include a focus on the effects of hatchery reform actions on residualism, which can exacerbate competition and predation effects on natural-origin fish survival. It will also develop 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, reproductive success, and gamete quality studies of S1 and 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 S2 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.  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 sorts juvenile steelhead produced from natural-origin broodstock according to their growth rate within 9 weeks after ponding to hatchery tanks.  The fast growing fish will be raised as yearling (S1) smolts using warmer water temperatures and larger rations, while the slow growing fish will be 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 BY18 S2 production group 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 2022 we will complete the hatchery scale experiment data collection at WNFH for the final brood years of production for the split age-2 smolts, and control age-2 and control age-1 smolts. We will complete the quantitative genetic analyses of the broodyear 2017 and 2018 fish from the split rearing laboratory study.  We will analyze the data from e the 3-broodyear experiment initiated in FY 2019 at the Manchester Research Station, and initiate a mechanistic study to determine how metabolic phenotype influences age-at-smoltification.  In FY22, we will analyze the RADseq and whole genome sequence data collected from steelhead in our BY20 laboratory experiment to measure heritability of growth and smoltfication traits and use a genome wide association study to identify loci associated with growth and seawater adaptation.