Proposal RMECAT-2003-063-00 - Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington

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Proposal History

Archive	Date	Time	Type	From	To	By
Download	7/30/2010	2:40 PM	Status	Draft	ISRP - Pending First Review	<System>
	10/15/2010	5:57 PM	Status	ISRP - Pending First Review	ISRP - Pending Response	<System>
Download	11/15/2010	5:50 PM	Status	ISRP - Pending Response	ISRP - Pending Final Review	<System>
	1/19/2011	2:47 PM	Status	ISRP - Pending Final Review	Pending Council Recommendation	<System>
	7/8/2011	1:31 PM	Status	Pending Council Recommendation	Pending BPA Response	<System>

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Basics

Proposal Number:		RMECAT-2003-063-00
Proposal Status:		Pending BPA Response
Proposal Version:		Proposal Version 1
Review:		RME / AP Category Review
Portfolio:		RM&E Cat. Review - Artificial Production
Type:		Existing Project: 2003-063-00
Primary Contact:		Patricia Crandell (Inactive)
Created:		6/7/2010 by (Not yet saved)
Proponent Organizations:		US Fish and Wildlife Service (USFWS)

Project Title:		Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington

Proposal Short Description:		Our goal is to determine the natural reproductive success and mean relative fitness of hatchery-origin and natural-origin steelhead and assess the demographic effects of hatchery fish supplementation in Abernathy Creek relative to two control streams. This work is important because the ability of hatchery-origin steelhead to reproduce successfully and contribute genetically to the recovery of naturally spawning populations while minimizing genetic and ecological risks is unknown.

Proposal Executive Summary:		This project will evaluate relative reproductive success between hatchery-origin (HOR) and natural-origin (NOR) steelhead trout, simultaneously investigating methods of operating a conservation hatchery and the effectiveness of artificial production of an integrated NOR/HOR broodstock on recovery. This directly addresses 2008 NOAA Fisheries FCRPS Biological Opinion (NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon)) reasonable and prudent alternatives (RPAs) 63.1, 64.1, and 64.2. This work is important because hatchery programs for steelhead may pose genetic or ecological risks to natural populations. Also, the ability of HOR adults to reproduce successfully and contribute genetically, via supplementation, to the recovery of naturally spawning steelhead populations is still a major uncertainty in the Pacific Northwest. This question has been debated intensively throughout the Columbia River Basin for over 10 years but remains unresolved. Indeed, a major symposium on this topic was conducted in 2000 to specifically address these uncertainties and identify future research and co-manager needs (IMST 2000). We propose to continue the project conducted at US Fish and Wildlife Service’s (FWS’s) Abernathy Fish Technology Center (AFTC) that was first approved for funding in 2004. AFTC developed an integrated steelhead broodstock starting with pre-smolt NOR juveniles collected from a stream from which the native broodstock was desired and then rearing the broodstock to sexual maturity in a hatchery. This is a technique such as might be employed by a conservation hatchery charged with supplementing a small steelhead population. AFTC minimally impacted the natural spawning population because juvenile (age 0+parr)-to-adult survivals are typically very small (<1%) under natural conditions, increased genetic effective population size because juveniles can theoretically represent the offspring of all adults that spawn successfully within a stream or watershed, and reduced the risk of genetically “swamping” the natural spawning population (Ryman and Laikre 1991; Ryman et al. 1995) as occurs when HOR fish represent a relatively small number of trapped adults. In order to minimize genetic differences between NOR and HOR steelhead, we will continue to utilize captured NOR steelhead to maintain an integrated NOR/HOR broodstock. To achieve our goal of evaluating relative reproductive success, all NOR and HOR upstream-migrating adults will continue to be genotyped and samples of their naturally-produced offspring will be identified via parentage analyses. We have started to compare the reproductive success and demographic changes (to both juvenile steelhead production and adult returns) occurring within Abernathy Creek to two control streams (i.e. Germany and Mill creeks) to determine whether supplementation was successful and are attempting to understanding why (e.g. behavioral, physiological differences between hatchery and wild fish) supplementation has succeeded or failed. This work has been and will continue to be conducted by the AFTC staff. A major motivation for the captive-rearing work described in this proposal resulted from NOAA-Fisheries 1999 Biological Opinion on Artificial Propagation in the Columbia River Basin and the 2008 NOAA-Fisheries FCRPS Biological Opinion (NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon)). In these biological opinions (BOs), NMFS concluded that non-native hatchery stocks of steelhead jeopardize the continued existence of Endangered Species Act (ESA)-listed, naturally spawning populations in the Columbia River Basin. As a consequence of the 1999 BO, NOAA-Fisheries recommended that federal and state agencies phase out non-native broodstocks of steelhead and replace them with native broodstocks. However, NOAA-Fisheries provided no guidance regarding how to achieve that RPA. The most recent (2008)FCRPS BO recommended that hatchery effectiveness and reform (HSRG 2004, 2009) efforts be monitored, specifically suggesting that hatchery programs preserve genetic resources, monitor and evaluate migration characteristics and fish performance in order to determine the effects of hatchery programs on the viability and recovery of salmon and steelhead populations. Although these recommendations are intuitively logical, the development of native broodstocks of hatchery steelhead may pose unacceptable biological risks to naturally spawning populations, particularly those that are already listed as threatened or endangered under the ESA. The traditional method of initiating new hatchery broodstocks of anadromous salmonid fishes is by trapping adults during their upstream, spawning migration. However, removing NOR adults from ESA listed populations may not be biologically acceptable because such activities may further depress those populations via “broodstock mining”. In addition, trapping a large proportion of adult steelhead may be logistically unfeasible in many subbasins because high water in the spring when steelhead move upstream to spawn will often destroy temporary weirs. As a result, alternative methods for developing native broodstocks are highly desired. Much of the uncertainty associated with the impact of artificial production on recovery of NOR steelhead is due to the absence of detailed studies on a small, experimental scale with control populations. Virtually all evaluations to date have either been at large watershed levels (i.e. on a production scale; see Araki et al. 2007) and/or have failed to incorporate comparisons between appropriate control and supplemented populations (IMST 2000). Our work on Abernathy Creek steelhead differs significantly from that of the Araki et al. (2007) Hood River project but is a complementary study. For example, the original broodstock for the AFTC project was initiated with juvenile steelhead that were captively reared to maturity, in contrast to the Hood River project which was initiated with returning adult steelhead. Therefore, the AFTC project provides an assessment of an alternative method of establishing a native broodstock when large numbers of native adults are unavailable. Both projects had a large number of juvenile fish that could not be assigned parents, possibly the result of spawning with resident rainbow and residual hatchery steelhead. Through analysis of PIT tag information and supplementary studies (otolith microchemistry and fatty acid comparisons of resident and anadromous juveniles), we are working assess the impact of resident rainbows and their genetic contribution and ecological effects on wild fish, something that is beyond the scope of a large project like the Hood River study. Additionally, while our results to date are predominantly based on parentage assignment for juvenile outmigrating smolts, continuation of this work until the majority of our released progeny return as adults will provide the opportunity to compare the relative reproductive success of HOR and NOR parents from spawning to the smolt stage with relative reproductive success from spawning to adult return. Determining the relative reproductive success of individual HOR and NOR adults, coupled with monitoring demographic changes in population abundance (i.e. juvenile production and adult returns) with appropriate natural population controls, is critical to (a) determining whether artificial production would be a useful tool for recovery and (b) understanding why supplementation succeeded or failed. Performing such assessments in the Columbia River below Bonneville Dam offers the added advantage of maximizing adult return rates and, thus, the statistical power and efficiency of detecting true differences between HOR and NOR fish. The work outlined in this proposal will be carried out by AFTC staff employed within the applied Conservation Genetics, Ecological Physiology, and Fish Culture programs. The field data collection will be conducted on Abernathy, Germany, and Mill Creeks and laboratory and data analyses will be conducted at AFTC. The effectiveness of the particular artificial production program as a tool for recovery will be assessed by monitoring demographic changes (i.e. juvenile production and adult returns) within the populations as well as through refined genetic, physiological, and modeling techniques as outlined in the methods section.

Purpose:		Artificial Production
Emphasis:		RM and E
Species Benefit:		Anadromous: 100.0% Resident: 0.0% Wildlife: 0.0%
Supports 2009 NPCC Program:		No
Subbasin Plan:
Fish Accords:		None
Biological Opinions:		FCRPS 2008 (RPA 63.1, RPA 64.2, RPA 64.1)

Contacts

Contacts:

Project Significance & Problem Statement

Project Significance to Regional Programs:

Systemwide concerns exist about the ecological and genetic effects that may occur when non-native fish interact biologically with NOR fish (Hindar et al. 1991, Waples 1991, Campton 1995).  Not only do non-native stocks pose genetic and ecological risks to naturally spawning populations of NOR fish, but HOR salmonids developed from non-native stocks stray as returning adults at a much higher rate than do NOR fish, potentially affecting several populations (Quinn 1993).  Biologists and managers throughout the region recognize the need to (a) maintain the genetic resources associated with naturally spawning populations of NOR fish and (b) restore or recover NOR populations wherever possible.  As a result, the FWS and the NOAA-Fisheries have recommended a general policy that discourages the use of HOR fish developed from non-native fish and encourages development of broodstocks from NOR fish in order to minimize potential negative effects resulting from genetic or ecological interactions between HOR and NOR fish, and use integrated NOR/HOR broodstocks developed initially from NOR fish to assist with recovery of NOR populations.

The artificial production work described herein initiated from NOAA-Fisheries 1999 Biological Opinion on Artificial Propagation in the Columbia River Basin.  In that biological opinion (BO), NOAA-Fisheries concluded that non-native HOR stocks of steelhead jeopardize the continued existence of ESA-listed, naturally spawning populations of NOR steelhead in the Columbia River Basin.  As a consequence, NOAA-Fisheries recommended that federal and state agencies replace non-native broodstocks with those developed using NOR fish.  As a result, alternative methods for developing NOR  broodstocks are highly desired.  This project also responds directly to the 2008 NOAA Fisheries FCRPS Biological Opinion (NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon)), RPAs (63.1, 64.1, and 64.2) by starting an artificial production program with local-origin, NOR steelhead and continuing propagation of a NOR/HOR integrated broodstock. 

The project responds to the ISAB Supplementation Report (2003) that recommends more and better monitoring of supplementation programs. This project’s primary goal is to allow monitoring of artificial production by evaluating the relative reproductive success between HOR and NOR steelhead spawning naturally in Abernathy Creek. The project also allows the evaluation of methods of operation for a conservation hatchery and the effectiveness of artificial production on recovery directly addressing RPA 63.1, 64.1, and 64.2. These evaluations will be applicable systemwide.

Problem Statement:

Background: Many artificial production programs for steelhead pose risks to natural populations because those programs release or outplant fish from non-native stocks. The goal of many steelhead programs has been to simply provide “fishing opportunities” with little consideration given to conservation concerns. For example, the Washington Department of Fish and Wildlife has widely propagated and outplanted one stock of winter-run steelhead (Chambers Creek stock) and one stock of summer-run steelhead (Skamania stock) throughout western Washington. Systemwide concerns exist about the ecological and genetic effects that may occur when non-native fish interact biologically with NOR fish (Hindar et al. 1991, Waples 1991, Campton 1995). Not only do non-native stocks pose genetic and ecological risks to naturally spawning populations of NOR fish, but HOR salmonids developed from non-native stocks stray as returning adults at a much higher rate than do NOR fish, potentially affecting several populations (Quinn 1993). Biologists and managers throughout the region recognize the need to (a) maintain the genetic resources associated with naturally spawning populations of NOR fish and (b) restore or recover NOR populations wherever possible. As a result, the FWS and the NOAA-Fisheries have recommended a general policy that discourages the use of HOR fish developed from non-native fish and encourages development of broodstocks from NOR fish in order to minimize potential negative effects resulting from genetic or ecological interactions between HOR and NOR fish, and use integrated NOR/HOR broodstocks developed initially from NOR fish to assist with recovery of NOR populations

A major motivation for the artificial production work described in this proposal resulted from NOAA-Fisheries 1999 Biological Opinion on Artificial Propagation in the Columbia River Basin and the 2008 NOAA Fisheries FCRPS Biological Opinion (NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon)) RPAs 63.1, 64.1, and 64.2. In these BOs, NMFS concluded that non-native hatchery stocks of steelhead jeopardize the continued existence of ESA-listed, naturally spawning populations in the Columbia River Basin. As a consequence, NMNOAA-Fisheries recommended that federal and state agencies phase out non-native HOR broodstocks of steelhead and replace them with NOR broodstocks. More specifically, the latest 2008 NOAA-Fisheries FCRPS remand recommended that hatchery effectiveness and reform efforts are monitored, suggesting that hatchery programs preserve genetic resources, monitor and evaluate migration characteristics and fish performance in order to determine hatchery programs effects on the viability and recovery of salmon and steelhead populations.

Although these recommendations are intuitively logical, the development of native broodstocks of hatchery steelhead may pose unacceptable biological risks to naturally spawning populations, particularly those that are already listed as threatened or endangered under the ESA. The traditional method of initiating new hatchery broodstocks of anadromous salmonid fishes is by trapping adults during their upstream, spawning migration. However, removing NOR adults from ESA listed populations may not be biologically acceptable because such activities may further depress those populations via “broodstock mining”. In addition, trapping a large proportion of adult steelhead may be logistically unfeasible in many subbasins because high water in the spring when steelhead move upstream to spawn will often destroy temporary weirs. As a result, alternative methods for developing native broodstocks are highly desired.

One alternative for developing native broodstocks, particularly when the collection of adults is logistically unfeasible or biologically unacceptable, is the captive rearing to sexual maturity of natural-origin juveniles. In this approach, pre-smolt juveniles are collected from the streams or watershed for which a native broodstock is desired, and then those juveniles are raised to sexual maturity in a hatchery. Those hatchery-reared adults of natural origin then become the broodstock source for gametes and initial progeny releases. Such a captive rearing program offers many potential, genetic advantages over traditional adult-trapping programs for developing native broodstocks. For example, large numbers of juveniles can be collected from the wild with only minimal impacts to naturally spawning populations because juvenile (age 0+parr)-to-adult survivals are typically very small (<1%) under natural conditions. Secondly, the genetic base of the broodstock (i.e. genetic effective population size) can be substantially larger for juveniles than adults because juveniles can theoretically represent the offspring of all adults that spawned successfully within a stream or watershed, as opposed to trapping only a small portion of returning adults for broodstock. Thirdly, collecting juveniles for broodstock can substantially reduce the risk of genetically “swamping” naturally spawning populations with hatchery-origin fish (i.e. via a “Ryman-Laikre effect”) as occurs when hatchery-released fish represent the progeny of a relatively small number of trapped adults (Ryman and Laikre 1991; Ryman et al. 1995). Nevertheless, the ability of hatchery-origin adults to reproduce successfully and contribute genetically, via supplementation, to the recovery of naturally spawning populations is a major uncertainty confronting salmon co-managers in the Pacific Northwest. This question has been debated intensively throughout the Columbia River Basin for over 10 years but remains unresolved. Indeed, a major symposium was conducted in June, 2000 to specifically address these uncertainties and identify future research and co-manager needs (IMST 2000).

Much of the uncertainty associated with supplementation is due to the absence of detailed studies on a small, experimental scale with adequate control populations. Virtually all evaluations to date have either been at large watershed levels (i.e. on a production scale; see Araki et al 2007) or have failed to incorporate appropriate control populations that supplemented populations could be directly compared (IMST 2000). Although our work on Abernathy Creek steelhead is most similar to Araki et al. (2007) the AFTC study differs significantly yet still provides a complementary study in an additional watershed for comparison to their results. For example, the original broodstock for the AFTC project was initiated with juvenile local steelhead that were captively reared to maturity, in contrast to the Hood River project which was initiated with returning adult steelhead. Therefore, the AFTC project provides an assessment of an alternative method of establishing a native broodstock for supplementation hatcheries. Both the Hood River and AFTC had a large number of juvenile fish that could not be assigned parents, possibly the result of spawning with resident rainbow and residual hatchery steelhead. Through our PIT tagging work we are able to assess residuals and their respective genetic contribution and ecological effects on wild fish, something that is beyond the scope of the Hood River study. Additionally, while our results to date are predominantly based on parentage assignment for juvenile outmigrating smolts, continuation of this work until the majority of our released progeny return as adults will provide the opportunity to compare the relative reproductive success of hatchery and natural orgin parents from spawning to the smolt stage with relative reproductive success from spawning to adult returns. Finally, through the addition of potential parents straying from nearby Mill and Germany Creeks to our parentage analyses, we can assess the contribution of strays in our system. Determining the relative reproductive success of individual hatchery- and natural-origin adults, coupled with monitoring demographic changes in population abundance with appropriate natural population controls, are critical to (a) determining whether supplementation is successful and (b) understanding how and/or why supplementation succeeded or failed. Performing such assessments in the lower Columbia River below Bonneville Dam offers the added advantage of maximizing adult return rates and, thus, the statistical power and efficiency of detecting true differences between hatchery-origin and natural-origin fish.

History: BPA Project No. 2003-063-00, Contract Number No. 016522 (FY04 to 06), and 36369 (FY07 to 09) has been underway since 2004. Earlier versions of our proposal were submitted for BPA funding in FY2001 under the Innovative category (Project No. 22031) and subsequently under the Lower Columbia/Estuary Provincial Review (Project No. 30003) and again under the Mainstem/Systemwide Provincial Review (Project No. 35027). Previous versions of our proposal received positive reviews, both from the Independent Scientific Review Panel (ISRP) and the Columbia River Fish & Wildlife Authority (CBFWA). Although this work was first approved for funding by the Bonneville Power Administration in fiscal year (FY) 2004 AFTC initiated this work in 1999 in response to the 1999 NMFS Biological Opinion on Artificial Propagation in the Columbia River. The project continued from FY07 to FY09 under contract number (36369).

Location: The FWS’s AFTC and Abernathy Creek offer a unique opportunity to investigate new hatchery methodologies designed to assist with recovery of naturally spawning populations via natural population supplementation. The AFTC is located at stream km 5.4 on Abernathy Creek, a tributary to the lower Columbia River (Figure 1), approximately 16 km west of Longview, Washington. AFTC is a research hatchery and science center that investigates new propagation strategies and technologies used for the recovery of anadromous fishes in the Columbia River Basin. AFTC is equipped with all the components necessary for a self-sufficient salmon/steelhead hatchery including an electric weir and holding pond for trapping and enumerating upstream-migrating adults. Abernathy Creek is a small, 3^rd order stream with a drainage area of approximately 110 km² that is particularly amenable to intensive, scientific study of salmonid fishes. One of the major advantages of Abernathy Creek as a “treatment” stream is the proximity of two neighboring streams, Germany and Mill Creeks that can serve as natural population controls for assessing demographic responses in Abernathy Creek. All three streams are approximately the same drainage area (91-110 km²) and enter the Columbia River within 4.8 to 6.4 km of each other; Germany Creek enters the Columbia River approximately two miles upstream and Mill Creek enters the Columbia River approximately one mile downstream, from the mouth of Abernathy Creek. Lastly, Abernathy Creek and the two adjacent streams are located approximately 160km downstream from Bonneville Dam in a rural area of Cowlitz County. The opportunity of the AFTC to test new culture and recovery strategies in a natural stream without the constraints imposed by dams, mitigation responsibilities, and urban impacts is unique among artificial propagation facilities in the Pacific Northwest.

Work of Key Personnel:

Kenneth G. Ostrand (Co-Principal Investigator)

K.G. Ostrand (Ph.D., Texas Tech University) will serve as lead biologist and serve as technical contact and responsible for filing quarterly and annual reports. Dr. Ostrand has worked in the field of fish ecology for 15 years and been the principal investigator on 20 state and federally funded research grants and contracts. He has authored more than 40 peer reviewed publications. He is currently the head of the Ecological Physiology program at AFTC and his current research projects included the effect of stress on physiology, development and reproduction of fishes, the environmental and physiological control of smolting and osmoregulatory processes, understanding the behavioral and physiological differences between hatchery and wild fishes, and the effectiveness of new and current hatchery practices.

Denise K. Hawkins (Co-Principal Investigator)

D.K. Hawkins (Ph.D. Fisheries, University of Washington) is the Regional Geneticistfor FWS Region 1, and head of the Applied Program in Conservation Genetics at the AFTC. Previous work involved an analysis of hybridization between coastal cutthroat trout and steelhead which included both field and lab components. Additionally, she has experience supervising, designing, and conducting genetic studies of assignment of stock of origin for mixed stock fisheries, brood stock selection for recovery and supplementation of listed Chinook, population structure, and parentage analysis for comparison of reproductive success. Dr. Hawkins will be primarily responsible for the molecular genetic work and pedigree reconstructions associated with this project.

Patricia A. Crandell (Co-Principal Investigator)

P.A. Crandell (Ph.D. Genetics, University of California, Davis) is the Deputy Director the AFTC. The AFTC is the largest of the Service’s seven applied fishery research centers. Dr. Crandell’s previous research includes quantitative genetic analyses of growth and maturation traits in rainbow trout and Pacific salmon. She has also worked professionally as a statistician for the National Marine Fisheries Service in Juneau, Alaska. P.A. Crandell has served as Principal Investigator or co-P.I. on 6 contracts or grants. She has authored or co-authored approximately 11 peer-reviewed publications. She has worked professionally in the general areas of quantitative analysis and fishery genetics for approximately 17 years. Dr. Crandell will be responsible for all administration of the project and will assist in the quantitative genetic analyses of adult life history traits derived from the pedigree reconstructions obtained via DNA genotypic identifications. She will also provide statistical consulting and advice to the other investigators on this project.

Objectives

Objectives:

Maintain a conservation hatchery broodstock of steelhead using protocols to minimize effects of artificial rearing on an integrated broodstock (OBJ-1)

Develop and follow protocols appropriate for rearing a native-origin (NOR)/hatchery-origin (HOR) integrated broodstock (Ford 2002) in a conservation hatchery with the aim of using artificial production to contribute to recovery of a small steelhead population. Rearing protocols will be designed to minimize effects of hatchery domestication. Family numbers will be equalized and, as much as possible, HOR smolts will be reared to be phenotypically similar to NOR smolts upon release. Artificially produced (HOR) smolts will be released each spring during the period when most NOR smolts emmigrate. In order to minimize negative impacts on NOR steelhead smolts, no more than 20,000 HOR steelhead smolts will be released each year. HOR steelhead will be externally marked in order to be able to segregate them from NOR. The effect of the artifically produced conservation hatchery broodstock will be determined in part by estimating relative reproductive success.

Use selectively-neutral, DNA markers to determine the amount of genetic change associated with captive rearing of NOR steelhead. (OBJ-2)

This objective provides an opportunity to gauge the efforts initiated in the hatchery protocols to minimize the genetic hazards associated with a hatchery supplementation program, and to identify temporal changes or trends in genetic variability that may occur within and among the HOR and NOR components of the steelhead population in Abernathy Creek. Indices of genetic diversity will be compared between samples of steelhead collected from the raceways just prior to release and samples of out-migrating steelhead collected from the screw trap in Abernathy Creek.

Estimate total annual smolt emigration and behavior of steelhead in Abernathy, Germany, and Mill Creeks (OBJ-3)

We hypothesize that integrated hatchery programs that reduce genetic risk, will result in HOR that are phenotypically and behaviorally similar to NOR fish, thereby increasing the potential for substantial negative ecological effects on wild populations. Therefore our objective is to evaluate if hatchery programs that minimize this divergence negatively affect NOR conspecifics and other species. We hypothesize that the number of salmonid smolts will increase as a result of supplemental stocking which in turn may negatively affect NOR conspecifics and other species if significant overlaps and delays in emigration behavior occur.

Assess physiological status of HOR and NOR steelhead smolts (OBJ-4)

Although HOR steelhead produced at AFTC are genetically similar to NOR steelhead within Abernathy Creek, different rearing conditions may influence juvenile physiology resulting in differences in parr-smolt transformation, phenotypes, and behavior. Since the release of HOR steelhead are generally used to mitigate for the deleterious effects of habitat loss and over-fishing, production strategies for steelhead need to ensure that juveniles are morphologically, behaviorally, and physiologically prepared for downstream migration, thereby maximizing survival and minimizing residualism. The goal of this objective is to determine if the smolt physiology of HOR juveniles differs from NOR conspecifics and relate these differences to specific hatchery practices. Ultimately, this information should lend insight into which factors affect survival to adulthood of HOR and NOR fish, and the subsequent reproductive fitness of returning HOR and NOR adults.

Control passage of HOR and NOR for evaluation of relative reproductive success; retain some steelhead for conservation hatchery broodstock (OBJ-5)

Use the electric barrier weir at AFTC to control passage of all salmonids returning to Abernathy Creek. Controlling passage will allow us to monitor the migration of all salmonids, collect fin clips for genetic analyses from all steelhead passed upstream, and evaluate the impact of artificial steelhead production on other species in the creek. It will also give us the ability to release only known (genotyped) NOR and HOR above AFTC allowing us to evaluate relative reproductive success and determine possible impacts of artificial production on recovery of a small steelhead population. NOR and HOR steelhead will be retained at AFTC and crossed following a specified protocol in order to continue to maintain a genetically integrated conservation hatchery broodstock.

Develop conservation hatchery broodstock of steelhead that is genetically integrated (OBJ-6)

Using returning adult NOR and HOR steelhead, we will continue development of a hatchery broodstock that is genetically integrated with the natural spawning population in Abernathy Creek. A minimum of one-third of spawners will be NOR steelhead in order to maintain an integrated broodstock. If few NOR are captured, few fish will be spawned. This will help us to realistically assess the effect of a conservation hatchery on a small NOR steelhead population, and the effect of a small NOR steelhead population on an integrated broodstock. Adult steelhead retained for broodstock will be spawned in 2x2 factorial crosses and family sizes will be equalized in order to maximize the effective population size under artificial production. Each NOR adult will be paired, as much as possible, with two HOR adults to produce HORxHOR and HORxNOR crosses. Fin clips will be collected from all broodstock for genetic analyses.

Determine the relative, natural reproductive success of hatchery-origin (HOR) and natural-origin (NOR) steelhead in Abernathy Creek above AFTC (OBJ-7)

For a supplementation program to be successful in contributing to the recovery of a small population in decline, the HOR component of a population released to spawn naturally must produce offspring. Comparing relative reproductive success (RRS) between HOR and NOR components of a population is one way to assess fitness differences. We will determine the parentage of NOR juveniles collected from above the FWS AFTC weir and compare the number of juveniles with HOR parentage to the number of juveniles with NOR parentage.

Manage and administer project and communicate work and results to BPA and the scientific community (OBJ-8)

This is a large project involving many varied researchers. The project will require substantial administrative and supervisory oversight in order to meet deadlines. A summary report, periodic progress reports, and a statement of work will be produced each year. Research that evaluates genetic, behavioral, and ecological interactions between NOR and HOR salmonids is of great interest to the scientific community. This project has, and will continue to be of interest to the fisheries community. Information from this project will continue to be presented in many professional forums and published in many peer-reviewed scientific journals.

Validate steelhead redd count surveys (OBJ-9)

Project History

Financials

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Summary of Budgets

To view all expenditures for all fiscal years, click "Project Exp. by FY"

To see more detailed project budget information, please visit the "Project Budget" page

Expense	SOY Budget	Working Budget	Expenditures *
FY2019	$146,549	$146,549	$199,560

BiOp FCRPS 2008 (non-Accord)		$146,549	$199,560

FY2020	$146,549	$146,549	$107,239

BiOp FCRPS 2008 (non-Accord)		$146,549	$107,239

FY2021	$0	$0	$67,297

BiOp FCRPS 2008 (non-Accord)		$0	$67,297

FY2022		$0	$0


FY2023		$0	$0


FY2024		$0	$0


FY2025		$0	$0


* Expenditures data includes accruals and are based on data through 31-Mar-2025

Actual Project Cost Share

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Current Fiscal Year — 2025

Cost Share Partner	Total Proposed Contribution	Total Confirmed Contribution
There are no project cost share contributions to show.

Previous Fiscal Years

Fiscal Year	Total Contributions	% of Budget
2021	$0	0%
2020	$5,000	3%
2019	$5,000	3%
2018	$132,500	31%
2017	$132,500	18%
2016	$132,500	18%
2015	$132,500	18%
2014	$132,500	18%
2013	$137,000	19%
2012	$137,000	19%
2011	$205,000	29%
2010	$205,000	30%
2009	$205,000	30%
2008	$160,793	25%

Explanation of Recent Financial Performance:

This project has carefully managed to meet performance goals and produce deliverables while working within a tight budget. The differences that appear in the financial performance table between the working budget, contracted amount, and expenditures appear to be due to the fact that our performance year was not a fiscal year and because data was not consistently loaded in the table. For example, our project year began in January and ended in December in 2004, 2005, 2006, 2007, 2008, 2009, and 2010. The working budget includes an entire year's (12 months) funding. The working budget totals do not match the expenditures totals because that column includes only purchases made within the fiscal year. Thus, the expenditures totals include purchases made during the last 9 months of a fiscal year or 12 months of purchases that include the last 3 months of one project year plus 9 months of the next project year. 

It is also not possible to compare the contracted amount column to the working budget or the expenditures columns since the information in the contracted amount column is inconsistent. Amounts are missing (2004, 2005, 2006, 2007), are for PIT tags only (2008, 2009), or are the same as the working budget (2010). 

It is not possible to compare total proposed contributions to confirmed contributions since the proposed amount is not available.

Explanation of Financial History:

This project was funded by calendar year.  It is a technically complex project and has had up to 8 Ph.D. researchers from AFTC assisting with analyses and providing technical assistance. Because of promotions and the level of personnel involved, the working budget has not fully covered costs since 2005. However, FWS and AFTC consider this work to be significant enough to subsidize and have provided funds for travel and for increased costs for items such as utilities, fish feed, genetics assays, remote PIT tag detection supplies, ancillary studies etc. The Washington Office of the FWS, Fisheries, also funded a professional level fish biologist in FY06 and FY07 to assist with this project. The FY12 to FY16 budgets accurately reflect the costs of items identified in the original budget and proposal and include the normal increases that have not been reflected in our budgets over the years.  

In CY2004 we met project goals with by spending 53% of our working budget on salaries and benefits (lumped as salary) and 21% on supplies, utilities, and tagging (lumped as miscellaneous). NOAA-Fisheries was funded to perform snorkel work. In CY2005 we added approximately 1/2 FTE for a geneticist and performed the snorkel work by adding 1/3 FTE for a fish biologist. Salary costs increased to 61% and our miscellaneous costs were about 18%. CY2006 was similar with a small increase in our working budget; salary and miscellaneous costs were at 62% and 17%, respectively. In CY2007, genetic analyses were becoming more complex, so we added another 1/2 FTE for a geneticist and increased the number of genetic analyses, doubling our laboratory purchases (from $27K to $45K). Our salary and miscellaneous costs remained at 62% and 17%, respectively. We got a small increase in our working budget. In CY2008 and CY2009, based on recommendations from the ISRP concerning our low assignment rate for parentage analysis, we contracted laboratory work (otolith microchemistry with University of Alaska) to increase our understanding of resident and residualized O. mykiss in the creek. We worked with the AFTC Nutrition program in CY2008 to investigate whether fatty acid analysis might be useful to identify juveniles as progeny of resident or anadromous O. mykiss. We utilized salary money for the contract and laboratory supplies. Our salary and miscellaneous costs in CY2008 were 57% and 19%, respectively. In CY2009, with completion of fatty acid analysis, salary and miscellaneous costs were 62% and 14%, respectively.

Reporting & Contracted Deliverables Performance

Annual Progress Reports
Expected (since FY2004):	16
Completed:	15
On time:	15

Status Reports
Completed:	63
On time:	41
Avg Days Early:	1

								Count of Contract Deliverables
Earliest Contract	Subsequent Contracts	Title	Contractor	Earliest Start	Latest End	Latest Status	Accepted Reports	Complete	Green	Yellow	Red	Total	% Green and Complete	Canceled
16522	25708, 36369, 40846, 45565, 51233, 55849, 59842, 64022, 67795, 71238, 74723, 78003, 81000, 84082	2003-063-00 EXP USFWS REPRO SUCCESS ABERNATHY CREEK	US Fish and Wildlife Service (USFWS)	02/01/2004	12/31/2020	Complete	63	361	0	0	2	363	99.45%	1
BPA-5562		PIT Tags - Repro Success Abernathy Cr	Bonneville Power Administration	10/01/2006	09/30/2007	Active	0	0	0	0	0	0		0
BPA-3722		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2007	09/30/2008	Active	0	0	0	0	0	0		0
BPA-4209		PIT Tags - Repro Success Abernathy Cr	Bonneville Power Administration	10/01/2008	09/30/2009	Active	0	0	0	0	0	0		0
BPA-4868		PIT Tags - Repro Success Abernathy Cr	Bonneville Power Administration	10/01/2009	09/30/2010	Active	0	0	0	0	0	0		0
BPA-5723		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2010	09/30/2011	Active	0	0	0	0	0	0		0
BPA-6391		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2011	09/30/2012	Active	0	0	0	0	0	0		0
BPA-6951		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2012	09/30/2013	Active	0	0	0	0	0	0		0
BPA-7738		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2013	09/30/2014	Active	0	0	0	0	0	0		0
BPA-8419		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2014	09/30/2015	Active	0	0	0	0	0	0		0
BPA-8948		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2015	09/30/2016	Active	0	0	0	0	0	0		0
BPA-9533		PIT Tags - Repro Success Abernathy Creek	Bonneville Power Administration	10/01/2016	09/30/2017	Active	0	0	0	0	0	0		0
Project Totals							63	361	0	0	2	363	99.45%	1

Selected Contracted Deliverables in CBFish (2004 to present)

The contracted deliverables listed below have been selected by the proponent as demonstrative of this project's major accomplishments.

Contract	WE Ref	Contracted Deliverable Title	Due	Completed
25708	B: 176	Rear 20,000 BY05 steelhead and release into Abernathy Creek	7/17/2006	7/17/2006
25708	E: 157	Collect samples from and determine Na+, K+-ATPase for 225 BY05 steelhead, 60 BY06 steelhead	9/1/2006	9/1/2006
25708	F: 157	Monitor salmonid migration from Germany, Abernathy and Mill Creeks	9/1/2006	9/1/2006
25708	L: 157	Evaluate ecological impact of HOR on NOR steelhead	9/1/2006	9/1/2006
25708	M: 157	Multi-locus DNA genotypes will be determined for HOR and NOR steelhead smolts	9/1/2006	9/1/2006
25708	N: 162	Determine genetic change	9/1/2006	9/1/2006
25708	G: 162	Estimate salmonid migration from Germany, Abernathy and Mill Creeks	9/1/2006	9/1/2006
25708	AF: 162	Construct genetic pedigrees of HOR and NOR steelhead	9/30/2006	9/30/2006
25708	AE: 162	Determine genetic change	10/12/2006	10/12/2006
25708	R: 161	Present results at scientific meetings	11/1/2006	11/1/2006
25708	S: 183	Submit and publish papers for publication	12/29/2006	12/29/2006
25708	J: 157	Monitor PIT tagged fish with in-stream detectors; transfer data to PTAGIS	12/29/2006	12/29/2006
25708	P: 157	Establish genetic database to conduct parentage analysis	12/29/2006	12/29/2006
25708	Q: 162	Construct genetic pedigrees of HOR and NOR steelhead	12/29/2006	12/29/2006
25708	K: 162	Determine the impacts of HOR steelhead on NOR steelhead at the individual and population level	12/29/2006	12/29/2006
25708	X: 157	Collect samples from and determine Na+, K+-ATPase for 225 BY06 steelhead	5/31/2007	5/31/2007
25708	AD: 157	Establish genetic database to conduct parentage analysis	5/31/2007	5/31/2007
25708	Z: 162	Estimate salmonid migration from Germany, Abernathy and Mill Creeks	6/5/2007	6/5/2007
25708	AI: 157	Evaluate ecological impact of HOR on NOR steelhead	8/31/2007	8/31/2007
25708	AT: 157	Monitor salmonid migration from Germany, Abernathy and Mill Creeks	9/30/2007	9/30/2007
25708	AP: 162	Determine genetic change	10/1/2007	10/1/2007
25708	AK: 161	Present results at scientific meetings	10/29/2007	10/29/2007
25708	AG: 183	Submit and publish papers for publication	10/29/2007	10/29/2007
25708	AS: 157	Collect samples from and determine Na+, K+-ATPase for 225 BY07 steelhead, 60 BY07 steelhead	10/29/2007	10/29/2007
25708	AJ: 157	Multi-locus DNA genotypes will be determined for HOR and NOR steelhead smolts	11/29/2007	11/29/2007
25708	BA: 161	Present results at scientific meetings	12/31/2007	12/31/2007
25708	AQ: 183	Submit and publish papers for publication	12/31/2007	12/31/2007
25708	AV: 157	Monitor PIT tagged fish with in-stream detectors; transfer data to PTAGIS	12/31/2007	12/31/2007
25708	AW: 157	Evaluate ecological impact of HOR on NOR steelhead	12/31/2007	12/31/2007
25708	AX: 157	Multi-locus DNA genotypes will be determined for HOR and NOR steelhead smolts	12/31/2007	12/31/2007
25708	AZ: 157	Establish genetic database to conduct parentage analysis	12/31/2007	12/31/2007
25708	AM: 162	Determine the impacts of HOR steelhead on NOR steelhead at the individual and population level	12/31/2007	12/31/2007
25708	AO: 162	Construct genetic pedigrees of HOR and NOR steelhead	12/31/2007	12/31/2007
36369	B: 176	Rear 20,000 steelhead and release into Abernathy Creek	5/15/2008	5/15/2008
36369	F: 157	Count out-migrating smolts of each species; collect samples, fish, and data	6/30/2008	6/30/2008
36369	G: 162	Estimate outmigration for salmonids in Abernathy, Germany, and Mill Creeks using standard m	7/31/2008	7/31/2008
36369	R: 157	Collect tissues, conduct analysis; distinguish resident & anadromous steelhead	9/29/2008	9/29/2008
36369	M: 157	Investigate ecological impact of residualized HOR on NOR steelhead	9/29/2008	9/29/2008
36369	C: 157	Multi-locus DNA genotypes will be determined for 150 HOR & NOR steelhead	9/29/2008	9/29/2008
36369	D: 162	Genetic change will be estimated	9/29/2008	9/29/2008
36369	S: 161	Present information from project formally at meetings	12/30/2008	12/30/2008
36369	T: 183	Communicate results to scientific community via peer reviewed publications	12/30/2008	12/30/2008
36369	P: 157	Determine multilocus, microsatellite DNA genotypes for returning steelhead	12/30/2008	12/30/2008
36369	J: 157	Monitor physiological status of steelhead at AFTC and emigrating steelhead and	12/30/2008	12/30/2008
36369	L: 162	Determine population estimates of NOR/HOR steelhead in Abernathy Creek	12/30/2008	12/30/2008
36369	Q: 162	Produce genetic pedigrees to determine success of the NOR/HOR steelhead	12/30/2008	12/30/2008
36369	O: 176	Produce/rear 100 full-sib families from 140 HOR and 60 NOR steelhead	12/30/2008	12/30/2008
40846	C: 176	Rear 20,000 steelhead and release into Abernathy Creek	5/14/2009	5/14/2009
40846	H: 162	Estimate outmigration for salmonids in Abernathy, Germany, and Mill Creeks using standard methods	7/31/2009	7/31/2009
40846	N: 157	Investigate ecological impact of residualized HOR on NOR steelhead	9/30/2009	9/30/2009
40846	D: 157	Multi-locus DNA genotypes will be determined for 150 HOR & NOR steelhead	9/30/2009	9/30/2009
40846	E: 162	Genetic change will be estimated	9/30/2009	9/30/2009
40846	T: 161	Present information from project formally at meetings	12/16/2009	12/16/2009
40846	U: 183	Communicate results to scientific community via peer reviewed publications	12/16/2009	12/16/2009
40846	Q: 157	Determine multilocus, microsatellite DNA genotypes for steelhead and rainbow trout	12/16/2009	12/16/2009
40846	K: 157	Monitor physiological status of steelhead at AFTC and emigrating steelhead	12/16/2009	12/16/2009
40846	S: 157	Collect tissues, conduct analysis; distinguish resident and anadromous o. mykiss	12/16/2009	12/16/2009
40846	M: 162	Determine population estimates of NOR/HOR steelhead in Abernathy Creek	12/16/2009	12/16/2009
40846	R: 162	Produce genetic pedigrees to determine success of the NOR/HOR steelhead	12/16/2009	12/16/2009
40846	P: 176	Produce/rear 100 full-sib families from 140 HOR and 60 NOR steelhead	12/16/2009	12/16/2009

View full Project Summary report (lists all Contracted Deliverables and Quantitative Metrics)

Explanation of Performance:

One contract deliverable is marked Red; however, a discrepancy occurred between the statement of work(SOW) due date for the annual report (February) and the date set in the PISCES status reporting page (December).  The Annual Report was attached in February as opposed to December as was outlined in the SOW.  This action was approved by BPA.

Results: Reporting, Accomplishments, and Impact

Please do the following to help the ISRP and Council assess project performance:
List important activities and then report results.
List each objective and summarize accomplishments and results for each one, including the projects previous objectives. If the objectives were not met, were changed, or dropped, please explain why. For research projects, list hypotheses that have been and will be tested.
Whenever possible, describe results in terms of the quantifiable biological and physical habitat objectives of the Fish and Wildlife Program, i.e., benefit to fish and wildlife or to the ecosystems that sustain them. Include summary tables and graphs of key metrics showing trends. Summarize and cite (with links when available) your annual reports, peer reviewed papers, and other technical documents. If another project tracks physical habitat or biological information related to your project’s actions please summarize and expand on, as necessary, the results and evaluation conducted under that project that apply to your project, and cite that project briefly here and fully in the Relationships section below. Research or M&E projects that have existed for a significant period should, besides showing accumulated data, also present statistical analyses and conclusions based on those data. Also, summarize the project’s influence on resource management and other economic or social benefits. Expand as needed in the Adaptive Management section below. The ISRP will use this information in its Retrospective Review of prior year results. If your proposal is for continuation of work, your proposal should focus on updating this section. If yours is an umbrella project, click here for additional instructions. Clearly report the impacts of your project, what you have learned, not just what you did.

All Proposals:

Umbrella Proposals:

We have successfully developed a “native” or “endemic” hatchery broodstock of steelhead by producing hatchery-origin (HOR) progeny of natural-origin (NOR) captively-reared adults from Abernathy Creek. We have released approximately 20,000 smolts annually. Our results demonstrate that a “native” or “endemic” hatchery broodstock of steelhead can be obtained by capturing age 0+ NOR juvenile steelhead and rearing them to sexual maturity. NOR juveniles accepted commercial salmonid rations and became sexual mature at age-3. Our results suggest a minimum of 380 age-0+ NOR juveniles be collected to ensure production of 100 full-sib families.

Our study suggests that demographic changes are occurring within the steelhead populations in Abernathy creek compared to our control streams. Smolt to adult return rates have begun to increase. The first returning adult F₁ HOR steelhead were trapped at AFTC in 2005, showing successful adult returns from a broodstock derived from captured 0+ NOR juveniles. NOR and HOR steelhead trout began immigrating into Abernathy Creek during January continuing until May. Male and female steelhead immigrated into Abernathy Creek on similar dates. Age determination from scale reading indicates the majority of adults returned as two and three-salt adults. Adult returns began to increase in 2007and have continued to be relatively high when compared to previous rates. Although, steelhead smolt production has declined in the last few years in all three creeks decreases within Abernathy Creek are not related to hatchery supplementation (Figure 1). Thus this supplementation strategy appears not have imparted negative consequences on NOR populations. To ensure that our observed changes are due to supplementation and not other factors, data will need to be collected into the future to account for the inherent variability associated with our observed demographic changes.

New Picture

Demographic changes with steelhead recruitment to the smolt life history stage may be strongly related to the differences we have consistently observed in steelhead physiology and morphology. Although the majority of both HOR and NOR steelhead appear to undergo smoltification, HOR smolts have had lower levels of gill Na⁺, K⁺ ATPase activity than the NOR fish (Figure 2). Saltwater challenges confirm the gill Na⁺, K⁺ ATPase sampling results suggesting that NOR fish performed better in saltwater when compared to HOR fish. In addition, morphometric data on the released fish suggest that HOR fish have been consistently larger and shaped differently than NOR fish. These results suggest that NOR fish expressed smolt-related characteristics that may provide a survival advantage over that expressed by HOR fish. NOR emigrants displayed an enhanced ability to tolerate seawater which may increase survival in the estuary and ocean. Improper synchrony of HOR physiological processes associated with smolt transformation may increase the percent of HOR fish that elect to remain in freshwater or reduce survival for those released from the hatchery. The consistent differences we have observed in HOR and NOR steelhead physiology and morphology may be positively related to the proportion of HOR fish that remain in Abernathy Creek (residualize) annually.

New Picture (1)

Figure 2- Box plots of gill Na⁺, K⁺ ATPase activity for HOR and NOR steelhead migrants captured at the Abernathy screwtrap. Numbers below each box plot denote its sample size and the letters above denote significant (P < 0.05) differences between HOR and NOR groups within a release block.

To determine causative agents behind reproductive success of HOR and NOR fish we evaluated spatial and seasonal overlap in habitat use and behavior between yearling HOR steelhead released from the AFTC and NOR salmonids. During spring, the majority of HOR smolts migrated downstream and left the system soon after each of three releases, whereas NOR smolt migration was more protracted following a normal distribution with one central peak. Both groups moved downstream at night and median emigration dates were similar. This suggests that the highest potential for ecological interactions between NOR and HOR at the smolt life stage only occurs downstream of the release location and within the first few days after each release. Possible interactions could arise during nighttime hours when migration peaked or could take place during the day during resting or feeding periods and could include predation, behavioral displacement, or premature emigration of NOR fish. Hill (2004) found little evidence that NOR steelhead changed habitat use during daytime periods after release of HOR. Our results suggest that there is a potential for hatchery fish to affect wild steelhead populations due to dietary overlap and salmonid fry predation. However, diet composition appears to be more strongly affected by seasonal and yearly differences in prey abundance and presence rather than differences in rearing environments. Hatchery and wild steelhead showed small but important foraging differences. Hatchery smolts did not consume as many fry as wild fish and hatchery residuals showed relatively stronger surface oriented feeding behavior than wild parr. Because most hatchery smolts emigrated shortly after release and the overall number of residuals in the study creek was low, we speculate that there is low dietary and predatory-based risk of hatchery steelhead in Abernathy Creek negatively impacting wild salmonids.

Similar to many systems where HOR anadromous fish are released, a proportion did not migrate but residualized in the system during summer increasing the spatial and temporal overlap of HOR fish and wild populations. HOR and NOR steelhead had summer longitudinal distributions where HOR fish were generally only abundant near the AFTC release site, whereas NOR fish were more evenly distribution throughout the creek. This pattern indicates that the greatest potential for negative interactions between NOR and HOR occurs in a small section of stream close to the release location. Both HOR residuals and NOR parr were observed to feed and act aggressively toward other fish. Additionally, residual fish had lower gill Na⁺, K⁺ ATPase activities and higher GSI values than either NOR and HOR emigrants at the time of release. The sex ratio of residual parr was significantly skewed towards males, whereas the sex ratio of HOR migrants and HOR fish before release was a 1:1 ratio of males to females. Examination of the frequency distribution of residual male GSI’s reveals a distribution that is highly positively skewed, suggesting the presence of a notable proportion of male residuals that are undergoing early maturation. Collectively these results suggest that HOR fish that elect to residualize are 1) not ready to undergo the smolt transformation, and 2) a large proportion of HOR males are electing to undergo early maturation instead of smoltification. Since few HOR steelhead emigrate in years subsequent to their release, presumably residuals forego smoltification and either die or become obligate resident fish that may partially explain the observed differences in smolt recruitment between Abernathy and the control creeks. What effect these precocious spawners may have on the reproductive success of the HOR and NOR populations has yet to be assessed.

Since the inception of this project we have been assessing whether or not the HOR and NOR steelhead populations in Abernathy Creek are substantially genetically differentiated from one another, it is important to remember that allele frequencies in both of these populations will vary year to year due to differences among brood years. Thus we have assessed this by addressing the question, “Is the divergence between HOR and NOR populations greater than the divergences among years within each of these populations?” Our results suggest an increasing degree of family structure and a decrease in genetic diversity in the HOR population in recent years. Increased departures from Hardy-Weinberg equilibrium and genotypic linkage disequilibrium observed in recent HOR samples suggest that the number of effective breeders contributing to the HOR population has decreased, relative to the 2004 HOR population and to the NOR population. Increased family structure and concomitant effects of increased genetic drift are common, if not universal, in HOR populations. Limited availability of returning adults to use as broodstock has lead to a decreasing number of crosses contributing to HOR smolts which may have lead to acceleration of genetic drift in the HOR population. Unequal representation of the crosses by returning adults based on selection or stochastic forces may have intensified this effect. Additionally, contributions to the anadromous NOR population by resident fish (rainbow trout), stray steelhead from neighboring creeks and Abernathy steelhead that spawn below the electric weir may all contribute to a larger effective size for that population. It is possible that the specimens used for genetic analyses represent an admixed collection (i.e. fish that spawn below the weir, contributions from resident fish not previously sampled, or that it represents only a few families) and is thus different by chance.

Determination of the relative reproductive success or productivity of HOR vs. NOR steelhead in Abernathy Creek is one of the main goals of this study that directly addresses RPAs 63 and 64. Evaluation #6. Relative reproductive success can be determined from both a family type and individual type perspective. Among all progeny genotyped 20.7% were matched to a parent pair. Assignment of progeny to an anadromous NOR parent (23.7%) exceeded anadromous HOR assignments (7.7%). Assignment of progeny to a residual NOR parent (9.6%) exceeded residual HOR assignments (0.2%). The number of progeny per family was quite variable with the majority (13) of families represented by fewer than 10 progeny. Many half-sib family clusters, both maternal and paternal, were observed.

In this study there are four different family types: HxH, HxN, NxH, NxN, where H and N indicate HOR and NOR respectively, and the origin of the female is listed first. The relative reproductive success of families involving two hatchery origin parents (HxH) is greater than that of either mixed family type (HxN or NxH), but less than that of family types involving two NOR parents. This suggests that there is some selective disadvantage to crosses of mixed origin, either they don’t occur as often, or they are less successful. When comparing relative reproductive success based on the origin and migratory status of individual parents, HOR parents have reduced relative reproductive success compared to NOR parents, but this difference is ten times greater in residual parents (HOR/NOR = 0.01) than in anadromous parents where relative reproductive success of HOR is 10% that of NOR parents.

Our most meaningful measure of relative reproductive success will be based on the number of naturally produced progeny parented by NOR and HOR steelhead that return to Abernathy Creek as adult fish (Araki et al. 2007). However, the information necessary for a complete evaluation of adult-to-adult survival for the 2007-2008 run year will not be available until all F₂’s have returned in the 2011-2012 run year (Figure 3).

New Picture (2)

Figure 3-Time-line of adult to adult production following the first year of implementation of the AFTC steelhead hatchery program (1999). Based on a predominately age 2-salt life history, the majority of adult F₁ progeny will have returned in 2005 and will have been included in that year’s broodstock (t the largest proportion of F₂ progeny would likewise return after two years; in 2008). The F₂ progeny that returned as age 1-salt would have been observed during the 2006-2007 collection year. Production by HOR fish evaluated in the 2007 report is depicted through time and indicated by gray boxes; total age is given in parentheses. All subsequent years' evaluations will follow the same pattern for each year of original NOR broodstock collection (i.e. 2000, 2001).

We assessed the maternal origin of steelhead progeny in Abernathy Creek using otolith microchemistry to determine the potential reproductive contribution of anadromous and non-anadromous females. Overall, the majority of fish sampled had anadromous maternal parents versus resident maternal parents. However, this difference was lower in Mill Creek compared to Germany and Abernathy Creeks. The differences in the number of fish with resident maternal parents between Abernathy Creek and Mill Creek could be due to a number of factors including stream size, habitat complexity, or genetic origin of the population. Mill Creek drains from a smaller watershed with stream gradients that are much lower than Abernathy Creek. This could promote more favorable conditions for a resident population of fish or could promote unfavorable conditions for anadromous fish. Either situation could explain the pattern we observed. In Abernathy Creek, the large majority of fish sampled were found to have an anadromous maternal parent. Of the fish found with a resident parent, all but one were located in or near a small tributary near the confluence of Abernathy Creek and Columbia River. The one remaining fish with a resident maternal parent was found upstream of Abernathy Fish Technology Center and could have come from a female resident spawner.

Our continued plan for parentage analysis as part of this overall project is to conduct comprehensive analyses over the next 2-3 years. This will entail consideration of all categories of potential candidate parents in Abernathy Creek including: out-of-basin strays, fish intercepted at the WDFW weir, and hatchery broodstocks from 2005 to the present. Using the SPAN baseline that is now available (multi-lab standardized steelhead microsatellite baseline) we plan to 1) test whether or not it is possible to identify the source of the stray steelhead, and 2) compare divergence among steelhead in Mill, Germany, and Abernathy creeks to divergence of other populations at comparable geographic scales in the Columbia River watershed. Analysis of samples collected from each watershed in more recent years (following the return of AFTC HOR steelhead) would also be helpful in understanding the relationships among steelhead populations in these three creeks.

In addition to monitoring genetic variation in the HOR and NOR anadromous populations, genetic characterization of the resident population, a clearer understanding of resident contributions to diversity in the NOR anadromous population, and further analysis of the fish not captured in the screw trap will be critical in understanding genetic divergence between HOR and NOR populations in Abernathy Creek. Because production by resident fish appears to be occurring, we will continue to monitor the relative contribution made by this group of fish to overall production in Abernathy Creek. Genetic markers that distinguish the sex of an individual were recently published (Brunelli et al. 2008). We plan to use sex markers to determine the male/female ratio among our resident fish samples. Understanding mating schemes and the rate of geneflow among resident and anadromous O. mykiss will provide information about interbreeding and population structure (e.g. panmixia) that may prove to be invaluable for the management of the hatchery program, and how broodstock are selected.

This is a brief summary of past results. All data have been made accessible through annual reports, peer reviewed publications, and presentations at scientific and professional meetings.

Past Council Recommendations and ISRP Reviews

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Review: 2018 Research Project Status Review

Council Recommendation

Assessment Number:	2003-063-00-NPCC-20210302
Project:	2003-063-00 - Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington
Review:	2018 Research Project Status Review
Approved Date:	12/20/2018
Recommendation:	Implement
Comments:	This set of projects [200303900, 200305400, 200306300 and 201003300] went through a policy review in 2017, and this review by the ISRP for progress. Studies to date have revealed that RRS between hatchery and naturally spawning fish can be reduced in a variety of ways. Because of this complexity, a more detailed conceptual framework is needed to predict how different species or populations will respond to hatchery supplementation and to allow managers to make better case-specific decisions. The ISRP believes that an updated synthesis is needed to make progress toward such a framework. They suggest that any new effort to synthesize results across the RRS studies should consider the history of hatchery influence prior to and during each study. Many of the projects reviewed are expected to report their most valuable results over the next few years. At that time, an updated synthesis of findings will be especially valuable. The ISRP is reassured that the RRS studies are on track and that proponents are collaborating and sharing information effectively. The Council concurs and asks that the sponsors work together on a synthesis report to be submitted and reviewed by the Council and the ISRP ahead of the start of the 2021 Anadromous Habitat and Hatchery Review process. Recommendation: Bonneville to work with the sponsors on a coordinated reporting of results as a “synthesis” review. Bonneville and the sponsors are requested to present this progress report/results to the Council and ISRP in summer of 2020; close to when these projects will be wrapping up, and ahead of the 2020 Anadromous Habitat and Hatchery Review.

Review: RME / AP Category Review

Council Recommendation

Assessment Number:	2003-063-00-NPCC-20110125
Project:	2003-063-00 - Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington
Review:	RME / AP Category Review
Proposal:	RMECAT-2003-063-00
Proposal State:	Pending BPA Response
Approved Date:	6/10/2011
Recommendation:	Fund (Qualified)
Comments:	Implement through FY 2014. Implementation beyond 2014 based on ISRP and Council review of the results report and/or outcome of a regional hatchery effects evaluation process.
Conditions:
	Council Condition #1 Programmatic Issue: RMECAT #6 Research projects in general—.
	Council Condition #2 Programmatic Issue: RMECAT #4 Hatchery Effectiveness—.

Independent Scientific Review Panel Assessment

Final Round ISRP Comment:
Assessment Number:	2003-063-00-ISRP-20101015
Project:	2003-063-00 - Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington
Review:	RME / AP Category Review
Proposal Number:	RMECAT-2003-063-00
Completed Date:	12/17/2010
Final Round ISRP Date:	12/17/2010
Final Round ISRP Rating:	Meets Scientific Review Criteria
The proponents provided much more detailed data to address the ISRP’s questions, and these data were very useful. In particular proponents have responded favorably to our suggestion to develop methods to include adult steelhead abundance estimates in Abernathy and extrapolated to Germany and Mill Creek for an evaluation of supplementation. One question that was not addressed, and perhaps we failed to emphasize it, was the actual number of individuals that were assigned to single or parent pairs in the parentage analysis, and how many individuals that were genotyped were not assigned to a parent. The numbers (and proportion) of fish not assigned needs to be presented and adequately discussed in any future proposal for completion of this project. The challenge with this project is not executing the lab work but the logistics of the field work, namely, to meet the sample sizes required to have sufficient data. From the ISRP perspective, the question posed circa 2000, about establishing a broodstock using wild parr and producing smolts and subsequent anadromous adults from them has been answered. The questions for which support is currently being provided are the relative reproductive success of hatchery versus natural origin steelhead and the demographic consequences of supplementation. Since Germany, Mill, and Abernathy Creeks are intended to serve as reference and treatment locations respectively, the near genetic equilibrium among them, with the conclusion they have large amounts of gene flow, complicates any analysis. The challenge is twofold: First, for a demographic analysis you need a reasonable estimate of the adult progeny produced from natural spawning. If the three streams are functionally panmictic, adults attributed to one stream based on redd counts may have originated in one of the other streams. Second, if the implied large proportion of unassigned adults or juveniles is owing to adults that avoided capture at the electric weir, effort is being expended on genotyping individuals for which no useful conclusion can be reached. Unless all of these logistical challenges can be resolved in future proposals, this project should be designed to complete the RRS and supplementation evaluation tasks over the next few years, and then be concluded. The project should be included in the Columbia River Hatchery Effects Evaluation project as part of consideration of basinwide evaluation. If the data are not suitable for meaningful evaluation the project should be brought to a reasonable conclusion. If the logistic challenges can be resolved this study will provide an important replicate of the relative reproductive success of hatchery steelhead developed from a local broodstock, adding to the range of locations to help meet BiOp needs.
First Round ISRP Date:	10/18/2010
First Round ISRP Rating:	Response Requested
First Round ISRP Comment:
The ISRP requests a response that provides two primary items. 1. The response should provide a succinct, yet complete, presentation of the accomplishments of all facets of the project. This includes: • the number of parr collected each year to establish broodstocks the smolts released from these initial broodstocks • the estimates of smolts leaving the system from these releases and those residualized in the stream • natural smolt yield before beginning supplementation • adult returns to the stream from natural and hatchery production (by release year) • estimates of steelhead spawning below the hatchery weir site • numbers of hatchery and natural steelhead passed above the weir for natural spawning • estimates of juvenile (parr or smolt) production from natural spawning by natural and hatchery-origin adults, and • estimates of RRS of hatchery and natural-origin adults. The presentation should include the primary data (actual counts of fish), analysis of the primary data, interpretation of the analysis, and use of this interpretation to justify the approach to completing the study design in the 2003 proposal. The submitted proposal and presentation to the ISRP often provide conclusions without transparent supporting data. Portions of the proposal and presentation are contradictory. And within the proposal, conclusions in various places are often contradictory or cannot be easily associated with specific data. As an example, in the proposal in the accomplishments section there is a statement: steelhead smolt production has declined in the last few years in Abernathy Creek, whereas Germany and Mill Creeks (control streams) have been more variable (figure 1). These results suggest that this supplementation strategy may have negative consequences from either HOR smolt release or HOR adults spawning in the wild. Slide 9 in the presentation has bullet points stating that smolt production is equivalent between pre- and post-hatchery production years and that HOR emigration rates, timing, and patterns are similar to NOR fish. The text accompanying the presentation states: “These results suggest that smolt production within Abernathy Creek has not been negatively effected by hatchery production thus far.” A second example: the proposal accomplishments section states that, “Improper synchrony of HOR physiological processes associated with smolt transformation may increase the percent of HOR fish that elect to remain in fresh water or reduce survival. The consistent differences we have observed in HOR and NOR steelhead physiology and morphology may be positively related to the proportion of HOR fish that remain in Abernathy Creek (residualize) annually.” But in the next paragraph: “we evaluated spatial and seasonal overlap in habitat use and behavior between yearling HOR steelhead released from the AFTC and NOR salmonids. During spring, the majority of HOR smolts migrated downstream and left the system soon after each of three releases, whereas NOR smolt migration was more protracted following a normal distribution with one central peak. This suggests that the highest potential for ecological interaction between NOR and HOR at the smolt life states occurs downstream of the release location and within the first few days after each release.” Later in the same paragraph: “Our results suggest that there is a potential for hatchery fish to affect wild steelhead populations due to dietary overlap and salmonid fry predation.” In the adaptive management section the proposal states: “Our results suggest that a small portion (1% - 7%) of HOR released smolts did not emigrate.” For most of the essential production, demographic, and genetic objectives there is similar inconsistency within the proposal. 2. The response should also address the qualifications identified by the ISRP in the 2007 review. The 2007 ISRP review summary stated: “The sponsors made a diligent effort to rapidly respond to the ISRP’s questions. For the most part, however, their answers are only partially satisfactory. One major difficulty with this project lies with the comparison of adult abundance estimates in the reference streams (Germany and Mill Creeks) and the treatment stream (Abernathy Creek). The sponsor’s are apparently unable to verify (with presently collected data) assumptions involved with redd counts, which will be used to assess adult abundance in the reference streams. The response lacks a description of how the error associated with the abundance estimates will be assessed, and there is difficulty in accurately assessing other demographic characteristics such as sex ratio, age structure, and redds per female. The sponsors fail to plainly explain how they will account for confounding effects, such as habitat restoration actions, planned sometime in the future for Germany and Mill Creeks.” The recently submitted proposal continues to emphasize the opportunity to contrast production, demography, and genetic evaluations in reference and treatment streams. The proposal executive summary states: “We have started to compare the reproductive success and demographic changes (to both juvenile steelhead production and adult returns) occurring within Abernathy Creek to two control streams (i.e. Germany and Mill creeks) to determine whether supplementation was successful...” However, the accomplishment section provides no data on adults in Germany and Mill creeks. None of the objectives identify a demographic comparison of adults in reference streams to a treatment stream, and there are no objectives to obtain data on adult steelhead in Germany and Mill creeks. The ISRP raised concerns in the 2007 review about the sufficiency of data to assess and interpret relative reproductive success (for a variety of reasons), and demographic consequences of supplementation (for a variety of reasons) (see 2007 review). These concerns need to be resolved during this response loop.
Documentation Links:	Proponent Response (11/15/2010)

Response to past ISRP and Council comments and recommendations:

The project received ISRP and Council comments in 2007 (<a href="http://www.nwcouncil.org/library/isrp/isrp2007-5.htm" target="_blank">http://www.nwcouncil.org/library/isrp/isrp2007-5.htm</a>) and five major points needed. They were: to provide a more thorough treatment of the reporting of the reproductive success work-to-date in the project history section of the proposal; clarify and explain how the use of Mill and Germany creeks as reference locations can be used to evaluate the demographic effects of hatchery-origin steelhead in Abernathy Creek, when no adults are being counted in the reference streams; clarify and explain how Mill and Germany creeks can serve as reference locations if these streams are part of an Intensively Monitored Watershed project and are receiving habitat improvement treatments different from each other and Abernathy Creek; describe how the physiological data on out-migrating hatchery steelhead smolts will be interpreted and subsequently used to modify hatchery practices; and, describe how the behavioral studies on residual steelhead and steelhead smolts can be used to estimate the population level effects of steelhead hatchery programs on natural steelhead, coastal cutthroat trout, and coho salmon production. We submitted our responses to each of the comments provided by the Independent Scientific Review Panel (ISRP) on April 10, 2007 to Dr. Loudenslager. Overall the ISRP indicated that the proposed ongoing project was scientifically supportable and has potential systemwide application. The additional clarification of these five points was primarily due to page limit and word count restrictions and formatting constraints when submitting a proposal electronically. Therefore our responses included additional analysis and explanations not permissible during the original electronic submittal process. The additional information illustrated and addressed the concerns raised by the ISRP. As a result the project received favorable ratings from both the ISRP and Council.

Adaptive Management

Management Changes:

Our results suggest that steelhead produced from an integrated program differ morphologically and physiologically from emigrating wild fish. HOR steelhead were significantly larger, but had similar condition factors as NOR fish.  HOR smolts consistently displayed a reduced readiness to transition to the seawater environment based on lower levels of Na+, K+ ATPase activity than NOR steelhead.  Improper synchrony of HOR physiological processes associated with smolt transformation may increase the percent of HOR fish that elect to remain in fresh water or reduce survival. Although the physiological differences we have observed have a significant effect on NOR and HOR smolt survival it is still unknown how this may be related to adult return rates.  As a result, future work will continue to monitor indicators of seawater readiness in migrating HOR and NOR fish as well as examining how these indicators relate to smolt to adult survival and the relative reproductive success of HOR and NOR adults.  Additionally, physiological analyses will be expanded to determine carry over of non-genetic maternal effects (stress, egg quality) between generations.

Our results suggest that a small portion (1%-7%) of HOR released smolts did not emigrate.  Instead they residualized and remained near their release location for the duration of the summer.  HOR residuals that survive winter probably have undergone early sexual maturation.  What effect these precocious spawners may have on the reproductive success of the HOR and NOR populations has yet to be assessed.  Therefore, we will expand our assessment of the impacts of residualized steelhead through increased electrofishing and PIT tagging efforts.

The genetic analyses suggest an increasing degree of family structure due to decreased numbers of effective breeders contributing to the HOR population in recent years relative to the 2004 HOR collection and the NOR population with decreased allelic diversity and increased genotypic disequilibrium within HOR collections.  Analyses of genetic diversity among collections indicate significant divergence of HOR and NOR populations, and significantly greater divergence among HOR collections relative to that among NOR collections.  Increased family structure and concomitant effects of genetic drift within the HOR populations, and divergence of HOR and NOR populations in recent years appears to be due to limited availability of returning adults to use as brood stock, and decreasing representation of NOR steelhead within brood stock.  Hatchery protocols will be adapted by strict adherence to spawning protocols as outlined in the proposal, equalizing families (200 per family), and varying the total number of HOR steelhead released from the program dependent on the number of families produced each year (in years of low adult returns, fewer HOR steelhead will be released).

In addition to the above modifications, to address the overall low proportion of total juveniles collected each year that we can assign to known parents we will work to improve our control of upstream passage of both adults and juveniles, thus limiting the fish present in the experimental reach above AFTC to those parents and offspring that are part of the program.  This increased control along with increased sampling and PIT tagging of juveniles should improve our ability to assign parentage.

Project Documents & Reports

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Public Attachments in CBFish

ID	Title	Type	Period	Contract	Uploaded
00016522-1	Natural Reproductive Success and Demographic Effects of Hatchery Origin Steelhead in Abernathy Creek	Progress (Annual) Report	01/2004 - 12/2004	16522	12/1/2004 12:00:00 AM
00016522-2	Natural Reproductive Success and Demographic Effects of Hatchery Origin Steelhead in Abernathy Creek	Progress (Annual) Report	01/2005 - 12/2005	16522	12/1/2005 12:00:00 AM
P104265	NATURAL REPRODUCTIVE SUCCESS AND DEMOGRAPHIC EFFECTS OF HATCHERY-ORIGIN STEELHEAD IN ABERNATHY CREEK, WASHINGTON	Progress (Annual) Report	01/2006 - 12/2006	25708	10/30/2007 8:56:07 AM
P105449	NATURAL REPRODUCTIVE SUCCESS AND DEMOGRAPHIC EFFECTS OF HATCHERY-ORIGIN STEELHEAD IN ABERNATHY CREEK, WASHINGTON	Progress (Annual) Report	01/2007 - 12/2007	36369	2/1/2008 11:49:23 AM
P109560	NATURAL REPRODUCTIVE SUCCESS & DEMOGRAPHIC EFFECTS OF HATCHERY-ORIGIN STEELHEAD IN ABERNATHY CREEK, WASHINGTON	Progress (Annual) Report	01/2008 - 12/2008	36369	12/30/2008 7:47:42 AM
P114605	aKennedy2009fieldid	Other	-	40846	12/22/2009 10:32:33 AM
P114607	aSimpson2009piscivory	Other	-	40846	12/22/2009 10:33:31 AM
P115359	Natural reproductive success and demographic effects of hatchery origin steelhead in Abernathy Creek, Washington	Progress (Annual) Report	01/2009 - 01/2010	40846	2/24/2010 8:39:16 AM
P119190	NATURAL REPRODUCTIVE SUCCESS AND DEMOGRAPHIC EFFECTS OF HATCHERY-ORIGIN STEELHEAD IN ABERNATHY CREEK, WASHINGTON	Progress (Annual) Report	01/2010 - 12/2010	45565	12/27/2010 10:16:59 AM
P124372	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/11 - 12/11	Progress (Annual) Report	01/2011 - 12/2011	51233	12/29/2011 2:04:32 PM
P131735	Natural Reproductive Success and Demographic Effects of Hatchery - Origin Steelhead in Abernathy Creek, Washington	Progress (Annual) Report	01/2012 - 12/2012	59842	4/15/2013 5:24:36 PM
P137626	2014 Hatchery Genetic Management Plan	Management Plan	-	64022	5/13/2014 9:49:40 AM
P136786	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington	Progress (Annual) Report	01/2013 - 12/2013	64022	5/27/2014 10:08:27 AM
P142760	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/14 - 12/14	Progress (Annual) Report	01/2014 - 12/2014	67795	4/16/2015 9:00:26 AM
P148481	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/15 - 12/15	Progress (Annual) Report	01/2015 - 12/2015	71238	4/19/2016 1:16:04 PM
P154496	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington	Progress (Annual) Report	01/2016 - 12/2016	74723	5/19/2017 1:13:19 PM
P158652	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/17 12/17	Progress (Annual) Report	01/2017 - 12/2017	78003	1/8/2018 10:10:00 AM
P163716	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/18 12/18	Progress (Annual) Report	01/2018 - 12/2018	81000	1/28/2019 2:53:59 PM
P171286	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/19 - 12/19	Progress (Annual) Report	01/2019 - 12/2019	84082	2/27/2020 1:20:57 PM
P175410	Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; 1/11 - 12/11	Photo	-		5/7/2020 5:44:05 PM

Project Relationships

The Project Relationships tracked automatically in CBFish provide a history of how work and budgets move between projects. The terms "Merged" and "Split" describe the transfer of some or all of the Work and budgets from one or more source projects to one or more target projects. For example, some of one project's budget may be split from it and merged into a different project. Project relationships change for a variety of reasons including the creation of efficiency gains.

Project Relationships:	None

Additional Relationships Explanation:

Our study is related to a number of projects within the Columbia River basin because it has basinwide applicability. Specifically, our study is related to the projects titled “Reproductive success study for spring/summer Chinook salmon in the Snake River” (BPA 198909600), “Reproductive success study for spring Chinook salmon in the Wenatchee River watershed (BPA 200303900), “Reproductive success study for steelhead in the Willapa River (BPA 200305000), “Reproductive success study for kelt steelhead (related to objective 8; BPA 200305200), “Reproductive success study for steelhead in the Hood River (BPA 200305400) “Reproductive success study for chum salmon (related to objective 8; BPA 200305600), “Reproductive success study for fall Chinook salmon in the Snake River (BPA 200306000), and “Reproductive success study for kelt steelhead in the Yakima basin (BPA 200306200). Our project is similar to these other projects only in regards to their examination of salmonid reproductive success ascertained via genetic contributions to naturally spawning populations.

Our study differs from these listed BPA projects because we initiated the program with juveniles that were captively reared to sexual maturity and because we are simultaneously examining potential mechanisms that may be responsible for differing reproductive success between hatchery and naturally produced fish. In addition, we are also assessing and quantifying actual hatchery practices that have direct relevance to current hatchery operating procedures. None of the related BPA studies listed above are examining the entire processes including hatchery production, ecological interactions, residualism, behavior, and their relationship to adult return rates and domestication selection.

Focal Species

Primary Focal Species

Steelhead (O. mykiss) - Lower Columbia River DPS (Threatened)

Secondary Focal Species

Coho (Oncorhynchus kisutch) - Lower Columbia River ESU (Threatened)

Cutthroat Trout, Coastal (O. c. clarkii) - Southwest Washington/Columbia River ESU

Threats to program investments and project success:

Our project’s focal species and its habitat is vulnerable to potential impacts arising from emerging limiting factors and threats such as climate change, non-native species, predation increases, or toxics.

Climate change: Climate change is expected to cause chaotic weather resulting in floods and droughts. Floods and droughts will change water temperatures and disrupt habitats and thus may adversely impact the survival of our species by affecting migration, disturbing or dewatering redds, and reducing the availability of natural food. We will ensure the continued success of our project by annually producing enough HOR fish to ensure a return of adult steelhead to AFTC.
Chaotic weather will also make it difficult to recover steelhead from Abernathy Creek for biological and genetic sampling. To ensure the continued success of our project, we are prepared to use a variety of techniques to to collect fish including fishing, electrofishing, ladder and screw traps, and electric and picket weirs.

Non-native species: Non-native species may affect the survival and habitat of the focal species. However, unless an invasion of a particularly deadly species occurs, non-native species should not impact the continued success of our project.

Predation increases: Our project has already documented increases in avian predation on HOR steelhead from Abernathy Creek (Kennedy et al. 2007). We will ensure the continued success of our project by annually producing enough HOR fish to ensure a return of adult steelhead to AFTC.

Toxics: There is no reason to believe that the continued success of our project should be affected by a toxic. AFTC is located in a non-industrial rural area with little opportunity to be affected by toxics. in addition, each steelhead year class at AFTC is located in a separate location on a separate water source. If an unavoidable toxic event occurred, we would at most lose a single year class and the whole project would not be affected.

Types of Work

Work Classes

Work Elements

RM & E and Data Management:

70. Install Fish Monitoring Equipment
157. Collect/Generate/Validate Field and Lab Data
158. Mark/Tag Animals
160. Create/Manage/Maintain Database
161. Disseminate Raw/Summary Data and Results
162. Analyze/Interpret Data
183. Produce Journal Article

Hatchery:

176. Produce Hatchery Fish

Anadromous Fish Hatchery

Program Name:

winter steelhead

Type:

Integrated

HSRG Recommendations Summary

Not applicable. This is not a production stock. The stock was produced from natural-origin Abernathy Creek stock for this research. Not associated with HSRG recommendations.

HSRG Implementation Explanation

Not applicable. This is not a production stock. The stock was produced from natural-origin Abernathy Creek stock for this research. Not associated with HSRG recommendations.

Fish Species:

Steelhead (O. mykiss) - Lower Columbia River DPS (Threatened)

	pNOB	pHOS	PNI
Target	<div class="userEnteredValue">0.30</div>	<div class="userEnteredValue">0.70</div>	0.30
Realized	<div class="userEnteredValue">0.03</div>	<div class="userEnteredValue">0.97</div>	0.03

Links to Hatchery Genetic Management Plan (HGMP) documents

Abernathy Creek Hatchery Genetic Management Plan

Tagging

Please explain why the tagging technology used in this project was selected. Include a discussion of how the cost and applicability of the selected tagging technology influenced your selection. Enter "NA" if not applicable to your project.

Data from passive integrated transponder (PIT) tagged HOR and NOR steelhead will be reported to PTAGIS. Data from PIT tagged HOR and NOR steelhead moving through remote monitoring antenna will be uploaded to PTAGIS.  PIT tags were selected because they provide information about individuals. PIT tag information may be used to correlate information derived from an individual over time. For example, a single individual may be collected and weighed several times. However, relatively few fish were PIT tagged because PIT tags are expensive and time consuming to insert.

Annual releases of coded-wire tagged (CWT) HOR steelhead will be reported to RMIS through USFWS Fish and Wildlife office. CWTs with adipose clips are used primarily to provide visual verification that fish are HOR (adipose clips) and to identify their origin (CWTs). In our case we need to segregate NOR from HOR steelhead and to verify that the HOR returning adults are in fact from AFTC, and are not strays from other hatcheries. Different tag numbers may be used within a single population in order to identify fish who have received special treatment. CWTs are relatively inexpensive and easy to insert, allowing an entire year class to be tagged.

Describe any of the innovative approaches that your projects proposes that are in direct support of the ISAB/ISRP's recommendations to improve techniques for surgical insertion of internal tags, or external attachment of acoustic, radio, or data storage tags that reduce handling time, fish injury and stress. Enter "NA" if not applicable to your project.

This project has indirectly supported two evaluations of innovative approaches and refinements to fish tagging that are in direct support of the ISAB/ISRP's recomendations and is unique in that it employes 19mm PIT tags as opposed to 12 mm tags.  The first evaluation is summarized in Kennedy et al. 2007 Northwest Science paper that examines sedation techniques, concentrations, and handling effort and processing time for PIT tagged salmonids.  The second is summarized in Ostrand et al. 2010, AFS Fish Marking Techniques that examines the long-term retention and survival and physiological effects of juvenile bull, steelhead, cutthroat trout, and coho salmon tagged with 9, 12, and 19 mm PIT tags.

For specific tagging technologies, please address the tagging report's recommendations for genetic markers, otolith thermal marking, PIT tags, acoustic tags and radio tags for improving technologies in any way applicable. Enter "NA" if not applicable to your project.

This project has employed otolith microchemistry and fatty acid composition to determine juvenile salmonids maternal life history (i.e. was she anadromous or resident).  In addition, this project continually employes various techniques and innovations when upgrading stream-width PIT tag antenna arrays.

If your project involves ocean port sampling and lower river sampling for coded wire tag (CWT) recovery, address the tagging and tag recovery issues (statistical validity of tagging rates, tag recovery rates, and fishery sampling rates) presented in the Pacific Salmon Commission's Action Plan to Address the CWT Expert Panel (PSC Tech. Rep. No. 25, March 2008).

Not applicable.

Explain how your tagging and tag recovery rates ensure a statistically valid result for your project. Enter "NA" if not applicable to your project.

1) PIT tagging is conducted on a relatively large proportion (5% or greater) of the wild and hatchery populations annually. Thus, increasing the probaility of recapture events.

2) Fish are held 24 to 48 hours after tagging to evaluate potential delayed mortality.

3) Stream-width PIT tag antenna arrays are established at three different sites on Abernathy Creek. Again, increasing the probability of recapture events.

4) A screwtrap also operates on Abernathy Creek near the mouth and all captured fish are scanned for PIT tags.

5) Abernathy Creek is PIT-Packed (mobile backpack PIT tag reader) annually.

6) Abernathy Creek is electrofished annually from the mouth to the headwaters and all fish are checked for PIT tags.

7) Lastly we employ peer-reviewed published statistical techniques specifically designed to deal with open systems such as streams and rivers. In short, a priori models of survival and recapture are created using programs such as MARK (White and Burnham 1999) and test the assumptions underlying the Cormack-Jolly-Seber analysis with programs like RELEASE (Lebreton et al. 1992; Burnham et al. 1987).

Data Management

What tools (e.g., guidance material, technologies, decision support models) are you creating and using that support data management and sharing?

Describe the process used to facilitate receiving and sharing of data, such as standardizing data entry format through a template or data steward, including data exchange templates that describe the data collection methods, and the provision of an interface that makes data electronically accessible.

Please describe the sources from which you are compiling data, as well as what proportion of data is from the primary source versus secondary or other sources?

Please explain how you manage the data and corresponding metadata you collect.

Describe how you distribute your project's data to data users and what requirements or restrictions there may be for data access.

RM&E

What type(s) of RM&E will you be doing?

Uncertainties Research (Validation Monitoring and Innovation Research)

Where will you post or publish the data your project generates?

PTAGIS Website

RMIS - Regional Mark Information System

Location

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Layers

Legend

Name (Identifier)	Area Type	Source for Limiting Factor Information
Name (Identifier)	Area Type	Type of Location	Count
Elochoman River-Frontal Columbia River (1708000305)	HUC 5	EDT (Ecosystem Diagnosis and Treatment)	161

Project Deliverables

Project Deliverables:

Perform activities necessary to maintain a conservation hatchery broodstock of steelhead juveniles until release at 1 year post-fertilization (DELV-1)

1a: Produce Hatchery Fish
Annually, rear up to 20,000 HORxHOR and HORxNOR steelhead juveniles, the progeny of adult HOR and NOR steelhead returning to Abernathy Creek, for approximately 1 year. Feed, clean and maintain hatchery, water lines, intake, tanks and raceways; treat disease outbreaks, and care for juvenile steelhead following AFTC hatchery protocols. Weigh and obtain fork lengths for fish in order to adjust feeding rate to produce a 1 year smolt phenotypically similar at release to outmigrating Abernathy Creek NOR steelhead smolts. Each year, release up to 20,000 HOR steelhead yearlings into Abernathy Creek directly from AFTC. Steelhead smolts will be divided into three equal groups and up to 7,000 will be force released in mid-April, the beginning of May, and the end of May. Fish health will be checked prior to release.

1b: Collect/Generate/Validate Field and Lab Data
Maintain records during rearing of feeding rate, fish weight and fork length, treatments performed, and coded-wire tag (CWT) retention information. Additional weight, fork length, and CWT retention information will be collected at release.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data

Hatchery

176. Produce Hatchery Fish

Estimate genetic change associated with producing an integrated steelhead broodstock in a conservation hatchery; collect genetic samples from HOR (DELV-2)

2a: Collect/Generate/Validate Field and Lab Data
Fin clips will be collected annually from 150 HOR steelhead smolts (stratified into three groups of 50 fish by spawning time of the parents) just prior to their release in the spring from AFTC. Multi-locus DNA genotypes at ten or more microsatellite loci will be determined for those 150 HOR steelhead smolts and for samples from 150 NOR steelhead collected at the screw trap during out-migration in the spring. All genotypes will be archived at AFTC using PROGENY software.

2b: Analyze/Interpret Data
Annual comparisons of multi-locus DNA genotype information from 150 HOR and 150 NOR steelhead will be used to estimate genetic change between HOR and NOR steelhead from Abernathy Creek. Selectively-neutral DNA marker information will be used to determine the amount of genetic change occuring in a HOR/NOR integrated steelhead stock produced and reared in a conservation hatchery compared to NOR steelhead.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data
162. Analyze/Interpret Data

Perform activities necessary to estimate emigration for steelhead including fish tagging, data collection, and installation of tag detection devices (DELV-3)

3a: Mark/Tag Animals
Up to 4,500 steelhead will be PIT tagged annually with 19 mm long-range PIT tags. Previously marked (CWT/adipose clipped) HOR steelhead (N = 1,500) reared at AFTC will be PIT tagged prior to release from AFTC. NOR steelhead parr (N = 3,000) in Abernathy Creek will be PIT tagged. Biological data on PIT tagged fish including release location, fork length, weight, and PIT tag recapture information will be collected. Fin clips will be collected for genetic analysis. Information about PIT tagged fish will be transferred to PSMFC's PIT tag information database, PTAGIS. In addition, all young of year (YOY) HOR steelhead (up to N= 20,000) reared at AFTC in up to 3 raceways will be marked with a CWT and adipose fin clip. Each raceways will be given a separate CWT code.

3b: Collect/Generate/Validate Field and Lab Data
Smolt emigration will be monitored directly in Abernathy Creek using a rotary screw trap operated by Washington Department of Fish & Wildlife biologists (Mara Zimmerman, WDFW) and an AFTC biologist. WDFW work is currently being conducted with "in-kind" funding from the Washington Salmon Recovery Board. Biologists will enumerate emigrating smolts of each rearing type each spring. Biologists will collect biological data on tagged and recaptured fish including fork length, weight, and PIT tag recapture information. Fin clips will be collected for genetic analysis and gill biopsies will be collected for ATPase activity. Diel and seasonal movement patterns will be determined for PIT tagged fish.

3c: Analyze/Interpret Data
Steelhead smolt emigration in Abernathy Creek will be estimated using standard methods. A portion of the smolts trapped each day will be marked with unique fin clips and released upstream to generate a Cormack-Jolly-Seber model estimate. The information collected will be used to examine HOR smolt production and its effect on NOR smolt production in Abernathy Creek.

3d: Install Fish Monitoring Equipment
Purchase and install upgraded equipment including software as needed to operate three PIT tag antenna arrays for remote detection of fish with PIT tags in Abernathy Creek. PIT tag antenna arrays will be located just upstream of the AFTC electric barrier, in the hatchery fish ladder (for monitoring steelhead releases during April and May), and at the mouth of Abernathy Creek. All information about PIT tagged fish will be transferred to PSMFC's PIT tag information database, PTAGIS. Maintain the units as necessary including replacing units damaged by winter flooding.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

70. Install Fish Monitoring Equipment
157. Collect/Generate/Validate Field and Lab Data
158. Mark/Tag Animals
162. Analyze/Interpret Data

Compare HOR and NOR steelhead smolt quality (DELV-4)

4a: Collect/Generate/Validate Field and Lab Data
Pysiological variables will be sampled annually from a total of 495 juvenile HOR and NOR steelhead (HORXHOR, NORxHOR). These fish will be sampled at AFTC in January, February, March, and at release (20 fish per raceway x up to 3 raceways x 4 time periods = 240 total fish). In addition HOR and NOR smolt gill tissue will be collected from the smolt trap throughout the emigration season (every 5th steelhead collected from the beginning of April through mid-June). Gill Na+, K+-ATPase for those fish will be determined as an indication of readiness to emigrate and compared between HOR and NOR smolts.

4b: Collect/Generate/Validate Field and Lab Data
Collect tissues (egg, blood) from maternal steelhead (N=30) prior to artificial spawning to determine carry over of non-genetic maternal effects (stress, egg quality) between generations. Offspring (up to N=10 per family depending upon fish size and physiological variable) will be sampled at multiple time periods across development for tissues (blood, white muscle) and whole organism (swimming performance, growth rates) as indicators of condition. Offspring condition will be linked back to maternal condition and origin (HOR vs. NOR) to further refine spawning practices given that our current results suggest that HOR fish differ physiologically from NOR fish, regardless of their similar genomic make-up.

4c: Analyze/Interpret Data
Gill Na+, K+, ATPase activity will be determined from gill biopsies using the method of McCormick (1993). Kruskal-Wallis tests will be used to compare differences among sampling dates and between NOR and HOR steelhead physiological parameters and Tukey-type post hoc comparisons will be performed to determine pairwise differences where appropriate. All analyses will be performed in the statistical package JMP v 7.0 (SAS Institute, Cary, North Carolina) and the level of significance for all tests (a) will be assessed at 0.05.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data
162. Analyze/Interpret Data

Capture returning HOR & NOR steelhead; release some for relative reproductive success determination; retain some for conservation hatchery broodstock (DELV-5)

5a: Collect/Generate/Validate Field and Lab Data
The electric barrier weir, a USFWS "in-kind" contribution, will be operated annually from mid-October to the end of June to help capture immigrating steelhead. Non-Abernathy Creek stray steelhead captured will be euthenized. Two-thirds of adult NOR steelhead captured will be released above AFTC and allowed to spawn naturally within Abernathy Creek; one-third will be retained for broodstock at AFTC. Captured HOR originating from AFTC will also be released; one-third to one-half as many HOR as NOR will be released above AFTC to spawn naturally. However, twice as many HOR as NOR will be retained for broodstock at AFTC. The total number of NOR and HOR steelhead retained for broodstock will not exceed 33 and 67, respectively. These numbers may be adjusted if the number of NOR steelhead captured exceeds 100. Fin clips and information such as return date, weight, and fork length will be collected from all HOR and NOR steelhead handled.
5b: Analyze/Interpret Data
Based on the number of HOR smolts released and number of HOR adults returning, a smolt to adult return rate will be calculated for the integrated conservation hatchery stock of steelhead.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data
162. Analyze/Interpret Data

Spawn returning HOR and NOR Abernathy Creek steelhead to continue development of a conservation hatchery broodstock that is genetically integrated (DELV-6)

6a: Produce Hatchery Fish
Use returning adult HOR and NOR Abernathy Creek steelhead to continue development of a conservation hatchery broodstock that is genetically integrated with the natural spawning population in Abernathy Creek. Two-thirds of adult NOR steelhead captured will be released above AFTC. The remaining one-third of captured NOR will be retained for broodstock at AFTC and twice as many HOR as NOR will also be retained for broodstock. Progeny produced will be derived from at least one-third NOR steelhead. This proportion will be strictly maintained in order to retain an integrated broodstock (Ford 2002). If no NOR are retained for broodstock, then no broodstock will be produced. The total number of NOR and HOR steelhead retained for broodstock will not exceed 33 and 67, respectively. These numbers may be adjusted if the number of NOR steelhead captured exceeds 100.

Adult steelhead retained for broodstock will be spawned in 2x2 factorial crosses where each NOR adult will be paired, as much as possible, with two HOR adults to produce HORxHOR and HORxNOR crosses. We will cull the up to 100 factorially derived families (where one male x one female is considered a family) to equal numbers of eyed eggs after shocking with the goal of producing 200 yearling smolts per family for release. Families produced using factorial mating designs have been shown to increase the effective population size under artificial production circumstances (Busack and Knudsen 2007). Fertilized eggs from each family will be incubated and hatched separately in Heath trays at AFTC. Initial rearing tasks will include cleaning and maintaining hatchery, water lines, intake, tanks and raceways; treating disease outbreaks, preventing disease, and care for steelhead eggs and fry following AFTC hatchery protocols.
6b: Collect/Generate/Validate Field and Lab Data
Collect biological information on all HOR and NOR steelhead used for broodstock including: spawn date egg size, egg survival to eye. Collect fin clips from all steelhead used for broodstock for genetic analysis.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data

Hatchery

176. Produce Hatchery Fish

Determine the relative reproductive success of HOR and NOR steelhead. (DELV-7)

7a: Collect/Generate/Validate Field Data
Multilocus, microsatellite nuclear DNA genotypes will be determined from up to 300 NOR and HOR adult steelhead and 1500 NOR and HOR juveniles collected from Abernathy Creek. All of the fish samples will be genotyped at the set of microsatellite loci used for parentage analysis. Multilocus genotypes for all of the adult steelhead trout caught will be entered into the database of potential parents. All genotypes will be archived at AFTC using PROGENY software.

7b: Analyze/Interpret Data
Using a set of highly variable, mircosatellite nuclear DNA loci and parentage analysis we will determine the relative reproductive success of the NOR and HOR steelhead. Reproductive success will be estimated by determining the proportion of juveniles (parr and smolts), sampled from Abernathy Creek that were parented by each adult fish type.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data
162. Analyze/Interpret Data

Manage and administer project and disseminate results through presentations at professional meetings and publication in peer reviewed journals (DELV-8)

Supervise and oversee all aspects of the project including budget and personnel. Prepare statement of work (SOW) for upcoming year in PISCES 90 days before expiration of contract. Includes administrative work in support of on the ground efforts and in support of BPA's programmatic requirements such as metric reporting, financial reporting (e.g., accruals), and development of an SOW package (includes draft SOW, budget, spending plan, and property inventory). Prepare and submit summary report to BPA each year. Provide progress reports to COTR on a quarterly basis via PISCES. These will be due within 15 days after the reporting period ends.

8a: Disseminate Raw/Summary Data and Results
Present results at a variety of annual meetings including the Northwest Pacific Culture Conference, American Fisheries Society national and regional meetings, and the FWS Hatchery Management Workshop.

8b: Produce journal article
Write papers and submit to peer reviewed journals for publication.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

161. Disseminate Raw/Summary Data and Results
183. Produce Journal Article

Perform activities necessary to ennumerate adult steelhead returns to Abernathy Creek; validate redd counts as surrogate for adult returns (DELV-9)

Redd counts have been used as a surrogate for estimating adult steelhead returns in Abernathy, Germany and Mill creeks. In order to validate redd counts as a reasonable surrogate, adult steelhead returning to Abernathy Creek will be captured and ennumerated using a picket weir installed and operated by Washington Department and Wildlife (WDFW) through the steelhead migration season. WDFW's work will be funded via a contract with AFTC. Biologists will collect data from captured steelhead before releasing them alive above the weir. The data collected will help to provide demographic information such as sex ratio, age structure and redds per female. A quantitative comparison of adult returns to redd numbers will determine whether a using redd counts as a surrogate is reasonable.

9a: Collect/Generate/Validate Field and Lab Data
Adult returns will be monitored directly in Abernathy Creek using a picket weir operated by WDFW biologists (Mara Zimmerman, WDFW) and an AFTC biologist from October through June. Biologists will enumerate returning adult steelhead: NORs, AFTC HORs, and strays. Biologists will collect data from captured steelhead including sex, weight, and length, and scales and fin clips will be taken for age and genetic analyses, respectively. Tags and mark information will also be noted.

9b: Analyze/Interpret Data
The data collected on migrating adult steelhead will help to provide demographic information such as sex ratio, age structure, and redds per female. A quantitative comparison of adult returns to redd numbers will determine whether a using redd counts as a surrogate is reasonable.

Types of Work:

Work Class

Work Elements

Research, Monitoring, and Evaluation + Data Management

157. Collect/Generate/Validate Field and Lab Data
162. Analyze/Interpret Data

Objectives & Project Deliverables

Objective: Maintain a conservation hatchery broodstock of steelhead using protocols to minimize effects of artificial rearing on an integrated broodstock (OBJ-1)

Project Deliverables	How the project deliverables help meet this objective*


Perform activities necessary to maintain a conservation hatchery broodstock of steelhead juveniles until release at 1 year post-fertilization (DELV-1)

Objective: Use selectively-neutral, DNA markers to determine the amount of genetic change associated with captive rearing of NOR steelhead. (OBJ-2)

Project Deliverables	How the project deliverables help meet this objective*


Estimate genetic change associated with producing an integrated steelhead broodstock in a conservation hatchery; collect genetic samples from HOR (DELV-2)

Objective: Estimate total annual smolt emigration and behavior of steelhead in Abernathy, Germany, and Mill Creeks (OBJ-3)

Project Deliverables	How the project deliverables help meet this objective*


Perform activities necessary to estimate emigration for steelhead including fish tagging, data collection, and installation of tag detection devices (DELV-3)

Objective: Assess physiological status of HOR and NOR steelhead smolts (OBJ-4)

Project Deliverables	How the project deliverables help meet this objective*


Compare HOR and NOR steelhead smolt quality (DELV-4)

Objective: Control passage of HOR and NOR for evaluation of relative reproductive success; retain some steelhead for conservation hatchery broodstock (OBJ-5)

Project Deliverables	How the project deliverables help meet this objective*


Capture returning HOR & NOR steelhead; release some for relative reproductive success determination; retain some for conservation hatchery broodstock (DELV-5)

Objective: Develop conservation hatchery broodstock of steelhead that is genetically integrated (OBJ-6)

Project Deliverables	How the project deliverables help meet this objective*


Spawn returning HOR and NOR Abernathy Creek steelhead to continue development of a conservation hatchery broodstock that is genetically integrated (DELV-6)

Objective: Determine the relative, natural reproductive success of hatchery-origin (HOR) and natural-origin (NOR) steelhead in Abernathy Creek above AFTC (OBJ-7)

Project Deliverables	How the project deliverables help meet this objective*


Determine the relative reproductive success of HOR and NOR steelhead. (DELV-7)

Objective: Manage and administer project and communicate work and results to BPA and the scientific community (OBJ-8)

Project Deliverables	How the project deliverables help meet this objective*


Manage and administer project and disseminate results through presentations at professional meetings and publication in peer reviewed journals (DELV-8)

Objective: Validate steelhead redd count surveys (OBJ-9)

Project Deliverables	How the project deliverables help meet this objective*


Perform activities necessary to ennumerate adult steelhead returns to Abernathy Creek; validate redd counts as surrogate for adult returns (DELV-9)

*This section was not available on proposals submitted prior to 9/1/2011

RM&E Protocols and Methods

RM&E Protocol	Deliverable	Method Name and Citation
ExpireDetermine multi-locus DNA genotypes for hatchery- and natural-origin steelhead smolts and estimate genetic change for the integrated broodstock. v1.0		Estimation of Hatchery Strays v1.0 (Jeremy Trump 2017) Adult Run Timing v1.0 (Crawford, E., Peven, C, and Hillman, T. 2014) Calculating Relative Contribution v1.0 (PNAMP Support 2014) Size at return v1.0 (Beasley, C.A., Berejikian, B.A., Carmichael, R.W., Fast, D.E., Galbreath, P.F., Ford, M.J., Hesse, J.A., McDonald, L.L., Murdoch, A.R., Peven, C.M., & Venditti, D.A. 2008) Calculating the smolt to adult return rate (SAR) v1.0 (Coordinated Assessments Data Exchange Standard Development Team 2014) Fish Salvage v1.0 (Brian D. Mahoney Michael B. Lambert Travis J. Olsen Eric Hoverson Paul Kissner and Jesse D.M. Schwartz 2006) Adult Sex Ratio v1.0 (Crawford, E. & Stark, E. 2014)
Expired Estimate total annual smolt emigration of steelhead, coho, and cutthroat trout in Abernathy, Germany, and Mill Creeks (2003-063-00) v1.0		Electrofishing - Determine Electrofisher Settings v1.0 (Temple, G.M, & Pearsons, T.N. 2007) Electrofishing - Site Selection v1.0 (Temple, G.M., & Pearsons, T.N. 2007) Electrofishing - Fish Processing and Recovery v1.0 (Temple, G.M., & Pearsons, T.N. 2007) Electrofishing - Backpack - Mark v1.0 (Temple, G.M., & Pearsons, T.N. 2007) Electrofishing - Backpack - Recapture v1.0 (Temple, G.M. & Pearsons, T.N. 2007) Rotary Screw Trap Deployment and Operation v1.0 (Volkhardt, G.C., Johnson, S.L., Miller, B.A., Nickelson, T.E., & Seiler, D.E. 2007) Trap Efficiency Testing v1.0 (Volkhardt, G.C., Johnson, S.L., Miller, B.A., Nickelson, T.E., & Seiler, D.E. 2007) Weirs v1.0 (Zimmerman, C.E., & L.M. Zabkar 2007) Mark Retention v1.0 (Peter Cleary) Size-at-Emigration v1.0 (Beasley, C.A., Berejikian, B.A., Carmichael, R.W., Fast, D.E., Galbreath, P.F., Ford, M.J., Hesse, J.A., McDonald, L.L., Murdoch, A.R., Peven, C.M., & Venditti, D.A. 2008) Number of Hatchery Smolts v1.0 (Patricia Crandell 2014) Adult Sex Ratio v1.0 (Crawford, E. & Stark, E. 2014) Cormack-Jolly-Seber (CJS) Model v1.0 (Burnham, K. P., D. R. Anderson, G. C. White, C. Brownie, and K. H. Pollock. 1987) Fin tissue sampling for genetic analysis v1.0 (Ewann Berntson 2013)
Expired Obj-4. Assess physiological status of HOR and NOR steelhead smolts (2003-063-00) v1.0		Number of Hatchery Smolts v1.0 (Patricia Crandell 2014) Hatchery Propagation v1.0 Hatchery Fish Marking and Tagging v1.0 (Vander Haegen, G. and L. Blankenship 2010) Juvenile fish survival v1.0 (Johnson et al. 2007 2007) Gill Na+/K+ATPase activity v1.0 (McCormick, S.D. 1993)
Expired Obj-7. Determine the relative reproductive success of HOR and NOR steelhead (2003-063-00) v1.0		Estimation of Hatchery Strays v1.0 (Jeremy Trump 2017) Adult Run Timing v1.0 (Crawford, E., Peven, C, and Hillman, T. 2014) Calculating Relative Contribution v1.0 (PNAMP Support 2014) Size at return v1.0 (Beasley, C.A., Berejikian, B.A., Carmichael, R.W., Fast, D.E., Galbreath, P.F., Ford, M.J., Hesse, J.A., McDonald, L.L., Murdoch, A.R., Peven, C.M., & Venditti, D.A. 2008) Calculating the smolt to adult return rate (SAR) v1.0 (Coordinated Assessments Data Exchange Standard Development Team 2014) Fish Salvage v1.0 (Brian D. Mahoney Michael B. Lambert Travis J. Olsen Eric Hoverson Paul Kissner and Jesse D.M. Schwartz 2006) Number of Breeders/Hatchery Population Size v1.0 (Patricia Crandell) Hatchery Propagation v1.0 Adult Sex Ratio v1.0 (Crawford, E. & Stark, E. 2014) Hatchery Fish Marking and Tagging v1.0 (Vander Haegen, G. and L. Blankenship 2010) Estimating relative reproductive success (RRS) v1.0 (Kalinowski, ST, Taper, ML & Marshall, TC 2007)
Expired Obj-9. Validate steelhead redd surveys (2003-063-00) v1.0		Estimating Adult Spawner Abundance v1.0 (Crawford, B.A. 2011) Statistical Testing for Changes in Adult Abundance v1.0 (Crawford, B.A. 2011) Estimation of Hatchery Strays v1.0 (Jeremy Trump 2017) Adult Run Timing v1.0 (Crawford, E., Peven, C, and Hillman, T. 2014) Calculating Relative Contribution v1.0 (PNAMP Support 2014) Size at return v1.0 (Beasley, C.A., Berejikian, B.A., Carmichael, R.W., Fast, D.E., Galbreath, P.F., Ford, M.J., Hesse, J.A., McDonald, L.L., Murdoch, A.R., Peven, C.M., & Venditti, D.A. 2008) Calculating the smolt to adult return rate (SAR) v1.0 (Coordinated Assessments Data Exchange Standard Development Team 2014) Fish Salvage v1.0 (Brian D. Mahoney Michael B. Lambert Travis J. Olsen Eric Hoverson Paul Kissner and Jesse D.M. Schwartz 2006) Adult Sex Ratio v1.0 (Crawford, E. & Stark, E. 2014) Hatchery Fish Marking and Tagging v1.0 (Vander Haegen, G. and L. Blankenship 2010)

Project Deliverables & Budget

Project Deliverable	Start	End	Budget
Perform activities necessary to maintain a conservation hatchery broodstock of steelhead juveniles until release at 1 year post-fertilization (DELV-1)	2012	2016	$440,084
Estimate genetic change associated with producing an integrated steelhead broodstock in a conservation hatchery; collect genetic samples from HOR (DELV-2)	2012	2016	$223,309
Perform activities necessary to estimate emigration for steelhead including fish tagging, data collection, and installation of tag detection devices (DELV-3)	2012	2016	$686,880
Compare HOR and NOR steelhead smolt quality (DELV-4)	2012	2016	$189,055
Capture returning HOR & NOR steelhead; release some for relative reproductive success determination; retain some for conservation hatchery broodstock (DELV-5)	2012	2016	$237,436
Spawn returning HOR and NOR Abernathy Creek steelhead to continue development of a conservation hatchery broodstock that is genetically integrated (DELV-6)	2012	2016	$319,333
Determine the relative reproductive success of HOR and NOR steelhead. (DELV-7)	2012	2016	$338,618
Manage and administer project and disseminate results through presentations at professional meetings and publication in peer reviewed journals (DELV-8)	2012	2016	$534,195
Perform activities necessary to ennumerate adult steelhead returns to Abernathy Creek; validate redd counts as surrogate for adult returns (DELV-9)	2012	2016	$280,695
		Total	$3,249,605

Requested Budget by Fiscal Year

Fiscal Year	Proposal Budget Limit	Actual Request	Explanation of amount above FY2010
2012		$602,793	This estimate is based on the 2010 budget with the addition of travel costs, additional PIT tags, the ISRP recommended OBJ 9, and cost of living increases of approximately 3% for 2010 and 2011; adjustments have also been made to more accurately reflect changes in costs for laboratory chemicals, pers
2013		$626,871	This estimate is based on the 2012 budget with the addition of cost of living increases of approximately 3%.
2014		$650,376	This estimate is based on the 2013 budget with the addition of cost of living increases of approximately 3%.
2015		$676,513	This estimate is based on the 2014 budget with the addition of cost of living increases of approximately 3%
2016		$693,052	This estimate is based on the 2015 budget with the addition of cost of living increases of approximately 3%
Total	$0	$3,249,605

Item	Notes	FY 2012	FY 2013	FY 2014	FY 2015	FY 2016
Personnel	Personnel costs have been adjusted to more accurately reflect the highly professional personnel we h	$332,425	$346,881	$361,014	$377,100	$385,433
Travel		$0	$0	$0	$0	$0
Prof. Meetings & Training	Although project personnel have made many presentations about this project, in the last several year	$5,150	$5,305	$5,464	$5,628	$5,796
Vehicles		$0	$0	$0	$0	$0
Facilities/Equipment	(See explanation below)	$11,845	$12,200	$12,566	$12,943	$13,332
Rent/Utilities	Increases due to cost-of-living only.	$7,638	$8,138	$8,382	$8,632	$8,892
Capital Equipment		$0	$0	$0	$0	$0
Overhead/Indirect	FWS overhead of 26.1% (and 6% for pass-thru on WDFW contract).	$116,298	$121,028	$125,631	$130,772	$133,917
Other	This category includes: WDFW contract (OBJ 9), fish feed, coded-wire tagging, hatchery and field sup	$118,695	$122,255	$125,923	$129,700	$133,592
PIT Tags	This reflects an increase in the number of NOR PIT tagged allowing us to better understand differenc	$10,742	$11,064	$11,396	$11,738	$12,090
Total		$602,793	$626,871	$650,376	$676,513	$693,052

Major Facilities and Equipment explanation:
AFTC, located 100 miles downstream from Bonneville Dam, has 30 staff in conservation genetics, nutrition, and ecological physiology. AFTC is equipped with the components necessary for a self-sufficient steelhead hatchery including an electric weir, ladders and holding pond for trapping and enumerating upstream-migrating adults. Additionally, AFTC has fully equipped conservation genetics, nutrition, and ecological physiology laboratories. Access to Abernathy Creek and neighboring streams, Germany and Mill creeks (that serve as natural controls), allows AFTC to test new culture and recovery strategies in a natural stream without the constraints imposed by dams, mitigation, and urban impacts. Facilities: a 4,000 sq. ft. building with a 1,500 sq. ft. Nutrition laboratory and a 1,600 sq. ft. feed processing room with extruder; 3 houses (2 offices/1 residence); a 1,500 sq. ft. building with a 925 sq. ft. Conservation Genetics laboratory; and a 3,100 sq. ft. building with a 1,216 sq. ft. Ecological Physiology laboratory and a 252 sq. ft. wet laboratory.a shop, storage sheds, fish ladder, settling & pollution abatement ponds, degassing tower, well house with generator 12 8’x80’ raceways, and 10 above-ground 10’ tanks. The hatchery building contains 109 4’ tanks, 24 2.5’ tanks, 8 troughs, & 40 incubator stacks. Equipment: vehicles appropriate for activities including boat, pick-up trucks, back hoe, SUVs etc.; fully equipped, state-of-the-art laboratories have ABI sequencers, robopipetters, thermocyclers, PCR machines, etc. with warranties and maintenance agreements. Water: Abernathy Creek water right of 45 cfs and well water right of 3,000 gpm (temperature 11.7-12.1o C). Information Technology: a full-time computer specialist; more than 60 computers (20 for laboratory equipment), 6 servers. New equipment: equipment for remote detection of PIT tags purchased annually. AFTC has been subsidising this expense. It is now accurately reflected in our budget.

Cost Share

Source / Organization	Fiscal Year	Proposed Amount	Type	Description
Washington Department of Fish and Wildlife (WDFW)	2012	$75,000	In-Kind	WDFW staff perform screwtrap monitoring for salmonids in Abernathy, Germany, and Mill creeks, and PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead. smolts.
US Fish and Wildlife Service (USFWS)	2012	$35,000	In-Kind	Provide additional staff to conduct field sampling in Abernathy Creek (GS 9, STEP, volunteers). Staff PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
US Fish and Wildlife Service (USFWS)	2012	$2,500	In-Kind	Annual operating and service costs for electrical weir installed in Abernathy Creek to allow the capture of returning adult HOR and NOR steelhead and to block access above AFTC to stray HOR steelhead.
US Fish and Wildlife Service (USFWS)	2012	$29,879	In-Kind	Provide additional staff time/equipment to perform PIT tag antenna, IT, and facility maintenance (2xGS9, GS11, WG6, WG10). Staff not paid for time include electrical engineer and computer specialist.
Washington Department of Fish and Wildlife (WDFW)	2013	$77,250	In-Kind	WDFW staff perform screwtrap monitoring for salmonids in Abernathy, Germany, and Mill creeks, and PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
Washington Department of Fish and Wildlife (WDFW)	2014	$79,568	In-Kind	WDFW staff perform screwtrap monitoring for salmonids in Abernathy, Germany, and Mill creeks, and PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
Washington Department of Fish and Wildlife (WDFW)	2015	$81,955	In-Kind	WDFW staff perform screwtrap monitoring for salmonids in Abernathy, Germany, and Mill creeks, and PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
Washington Department of Fish and Wildlife (WDFW)	2016	$84,413	In-Kind	WDFW staff perform screwtrap monitoring for salmonids in Abernathy, Germany, and Mill creeks, and PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
US Fish and Wildlife Service (USFWS)	2013	$36,050	In-Kind	Provide additional staff to conduct field sampling in Abernathy Creek (GS 9, STEP, volunteers). Staff PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
US Fish and Wildlife Service (USFWS)	2014	$37,132	In-Kind	Provide additional staff to conduct field sampling in Abernathy Creek (GS 9, STEP, volunteers). Staff PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
US Fish and Wildlife Service (USFWS)	2015	$38,245	In-Kind	Provide additional staff to conduct field sampling in Abernathy Creek (GS 9, STEP, volunteers). Staff PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
US Fish and Wildlife Service (USFWS)	2016	$39,393	In-Kind	Provide additional staff to conduct field sampling in Abernathy Creek (GS 9, STEP, volunteers). Staff PIT tag and collect biological data, scales, and genetic samples from HOR and NOR steelhead.
US Fish and Wildlife Service (USFWS)	2013	$2,575	In-Kind	Annual operating and service costs for electrical weir installed in Abernathy Creek to allow the capture of returning adult HOR and NOR steelhead and to block access above AFTC to stray HOR steelhead.
US Fish and Wildlife Service (USFWS)	2014	$2,652	In-Kind	Annual operating and service costs for electrical weir installed in Abernathy Creek to allow the capture of returning adult HOR and NOR steelhead and to block access above AFTC to stray HOR steelhead.
US Fish and Wildlife Service (USFWS)	2015	$2,732	In-Kind	Annual operating and service costs for electrical weir installed in Abernathy Creek to allow the capture of returning adult HOR and NOR steelhead and to block access above AFTC to stray HOR steelhead.
US Fish and Wildlife Service (USFWS)	2016	$2,814	In-Kind	Annual operating and service costs for electrical weir installed in Abernathy Creek to allow the capture of returning adult HOR and NOR steelhead and to block access above AFTC to stray HOR steelhead.
US Fish and Wildlife Service (USFWS)	2013	$30,775	In-Kind	Provide additional staff time/equipment to perform PIT tag antenna, IT, and facility maintenance (2xGS9, GS11, WG6, WG10). Staff not paid for time include electrical engineer and computer specialist.
US Fish and Wildlife Service (USFWS)	2014	$31,699	In-Kind	Provide additional staff time/equipment to perform PIT tag antenna, IT, and facility maintenance (2xGS9, GS11, WG6, WG10). Staff not paid for time include electrical engineer and computer specialist.
US Fish and Wildlife Service (USFWS)	2015	$32,650	In-Kind	Provide additional staff time/equipment to perform PIT tag antenna, IT, and facility maintenance (2xGS9, GS11, WG6, WG10). Staff not paid for time include electrical engineer and computer specialist.
US Fish and Wildlife Service (USFWS)	2016	$33,629	In-Kind	Provide additional staff time/equipment to perform PIT tag antenna, IT, and facility maintenance (2xGS9, GS11, WG6, WG10). Staff not paid for time include electrical engineer and computer specialist.

Project References or Citations

REPORTS HAVE BEEN SUBMITTED ANNUALLY AND ARE AVAILABLE:

2009
https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P115359
2008
https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P109560
2007
https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P105449
2006
https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=P104265
2005
https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00016522-2
2004
https://pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00016522-1 

MASTERS OF SCIENCE DEGREE COMPLETED AS PART OF THIS PROJECT:

Hill, Megan S. (2004): Habitat Use and Physiology of Pit-Tagged Htachery and Wild Steelhead Trout Smolts (M.S.). http://www.sees.wsu.edu/GraduateStudies/ESRP/past_theses.html#h

SCIENTIFIC PAPERS THAT HAVE BEEN PUBLISHED, IN REVIEW, IN PRESS IN PEER REVIEWED JOURNALS.  THE MANUSCRIPTS ARE AS FOLLOWS:

Simpson, W. G., B. M. Kennedy, and K. G. Ostrand.  2009.  Seasonal Foraging and Piscivory by Sympatric Wild and Hatchery-reared Steelhead from an Integrated Hatchery Program.  Environmental Biology of Fishes (In Press). http://www.springerlink.com/content/wv47471u01v34u73/fulltext.pdf

Ostrand, K. G., G. B. Zydlewski, W. L. Gale, and J. D. Zydlewski.  2009.  Long Term Retention, Survival, Growth, and Physiological Indicators of Salmonids Marked with Passive Integrated Transponder Tags. In: Symposium Proceedings Advances in Fish Tagging and Marking Technology. American Fisheries Society, Bethesda, Maryland. (In Review).

Kennedy, B. M., J. Baumsteiger, W. L. Gale, W. R. Ardren, and K. G. Ostrand.  2009.  Morphological, physiological, and genetic techniques for improving field identification of steelhead trout, coastal cutthroat trout, and hybrid smolts.  Marine and Costal Fisheries: Dynamics, Management, and Ecosystem Science 1:45-56.
http://www.bioone.org/doi/pdf/10.1577/C08-006.1

Kennedy, B. M., W. L. Gale, and K. G. Ostrand.  2007. Relationship between smolt gill Na+, K+, ATPase activity and migration timing to avian predation risk of steelhead trout (Oncorhynchus mykiss) in a large estuary.  Canadian Journal of Fisheries and Aquatic 
Sciences. 64:1506-1516.
http://article.pubs.nrc-cnrc.gc.ca/ppv/RPViewDoc?issn=1205-7533&volume=57&issue=10&startPage=2086

Kennedy, B. M., W. L. Gale, and K. G. Ostrand.  2007.  Evaluation of clove oil concentrations for use as an anesthetic during field processing and passive integrated transponder (PIT tags) implantation of juvenile steelhead.  Northwest Science 81(2):147-154.
www.bioone.org/doi/pdf/10.3955/0029-344X-81.2.147

Hill, M. S., G. B. Zydlewski, J. D. Zydlewski, and J. M. Gasvoda.  2006.  Development and evaluation of portable PIT tag detection units: PITpacks.  Fisheries Research 77:102-109
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T6N-4H6XKR5-1&_user=2075862&_coverDate=01%2F31%2F2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1374270091&_rerunOrigin=google&_acct=C000056106&_version=1&_urlVersion=0&_userid=2075862&md5=7d40b2b479b4850b8caf84f73533547b

Hill, M. S., G. B. Zydlewski, and W. L. Gale.  2005.  Comparisons between hatchery and wild steelhead trout (Oncorhynchus mykiss) smolts:  Physiology and habitat use.  Canadian Journal of Fisheries and Aquatic Sciences 63:1627-1638.
http://article.pubs.nrc-cnrc.gc.ca/ppv/RPViewDoc?issn=1205-7533&volume=63&issue=7&startPage=1627

PEER REVIEWED REFERENCES CITED IN THIS PROPOSAL:

Araki, H.., W. R. Ardren, E. Olsen, B. Cooper, and M. S. Blouin. 2007a. Reproductive success of captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the Hood River. Conservation Biology 21:181-190.

Ardren, W. R., Borer, S., Thrower, F., Joyce, J. E., and Kapuscinski, A. R.  1999. Inheritance of 12 microsatellite loci in Oncorhynchus mykiss.  Journal of Heredity 90: 529-536.

Banks, M. A., Blouin, M. S., Baldwin, B. A., Rashbrook, V. K., Fitzgerald, H. A., Blankenship, S. M., and Hedgecock, D. 1999.  Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha).  Journal of Heredity 90: 281-288.

Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N., and Bonhomme, F.  2004.  GENETIX Version 4.05, logiciel sous Windows TM pour la génétique des populations.  Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France). 

Brunelli, J.P., Wertzler, K.J., Sundin, K., and Thorgaard, G.H.  2008.  Y-specific sequences and polymorphisms in rainbow trout and Chinook salmon.  Genome 51:739-48.

Burnham, K.P., D.R. Anderson, G.C. White, C. Brownie, and K.H. Pollock. 1987. Design and analysis methods for fish survival experiments based on release-recapture. Monograph 5 American Fisheries Society. Bethesda, Maryland.

Busack, C. and Knudsen, C.M. 2007. Using factorial designs to increase the effective number of breeders in fish hatcheries. Aquaculture 273:24-32.

Cairney, M., Taggart, J. B., and Hoyheim, B.  2000.  Atlantic salmon (Salmo salar) and cross-species amplification in other salmonids.  Molecular Ecology 9: 2175-2178.

Campton, D.E. 1995. Genetic effects of hatchery fish on wild populations of Pacific salmon and steelhead: What do we really know? Edited by H.L.Jr. Schramm and R.G. Piper. American Fisheries Society, Bethesda, Maryland pp. 337-353.

Cavalli-Sforza, L.L., and Edwards, A.W.  1967.  Phylogenetic analysis. Models and estimation procedures.  American Journal of Human Genetics 19:233-257.

Excoffier, L., Smouse, P. E., and Quattro, J. M.  1992.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data.  Genetics 131: 479-491.

Excoffier, L., Laval, G., and Schneider, S.  2005.  ARLEQUIN Version 3.0: An integrated software package for population genetics data analysis.  Evolutionary Bioinformatics Online 1: 47-50.

Ford, M. J.  2002.  Selection in captivity during supportive breeding may reduce fitness in the wild.  Conservation Biology 16:815-825.

Hill, M. S.  2004.  Habitat use and physiology of PIT tagged hatchery and wild steelhead trout smolts.  Masters Thesis.  Washington State Univeristy, Vancouver WA.

Hindar, K., Ryman, N., and Utter, F. 1991. Genetic Effects of cultured fish on natural fish populations. Canadian Journal of Fisheries and Aquatic Sciences 48: 945-957.

IMST (Independent Multidisciplinary Science Team) 2000. Conservation Hatcheries and Supplementation Strategies for Recovery of Wild Stocks of Salmonids: Report of a Workshop. IMST, Portland, OR.

Kalinowski, S.T., Taper, M.L., and Marshall, T.C.  2006.  Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16:1099-1106.

Kennedy, B.M., W.L. Gale, and K.G. Ostrand.  2007. Relationship between smolt gill Na+, K+, ATPase activity and migration timing to avian predation risk of steelhead trout (Oncorhynchus mykiss) in a large estuary.  Canadian Journal of Fisheries and Aquatic Sciences. 64:1506-1516.

Lebreton, J.D., Burnham, K.P., Clobert, J., and D.R. Anderson. 1992. Modeling survival and testing biological hypotheses using marked animals-a unified approach with case studies. Ecological Monographs 62:67-118.

Marshall, T.C., Slate, J., Kruuk, L.E.B. and Pemberton, J.M. 1998.  Statistical confidence for likelihood-based paternity inference in natural populations.  Molecular Ecology 7: 639-655.

McConnell, S. K., O'Reilly, P., Hamilton, L., Wright, J. M., and Bentzen, P.  1995. Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): Genetic differentiation of North American and European populations.  Canadian Journal of Fisheries and Aquatic Sciences 52: 1863-1872.

McCormick, S. D.  1993.  Methods for nonlethal gill biopsy and measurement of Na+, K+ ATPase activity. Canadian Journal of Fisheries and Aquatic Science 50:656-658.

Nelson, R. J. and Beacham, T. D.  1999.  Isolation and cross species amplification of microsatellite loci useful for study of Pacific salmon.  Animal Genetics 30: 228–229.

NWWPC (Northwest Power Planning Council) 1999. Artificial Production Review, Council Document 99-15. Northwest Power Planning Council, Portland, OR.

Olsen, J. B., Bentzen, P., and Seeb, J. E.  1998.  Characterization of seven microsatellite loci derived from Pink salmon.  Molecular Ecology 7: 1087-1089.

Ostberg, C. O., and R. J. Rodriguez.  2002.  Novel microsatellite markers differentiate
Oncorhynchus mykiss (rainbow trout and steelhead) and the O. clarki (cutthroat trout) subspecies.  Molecular Ecology Notes 2: 197–202.

Ostberg, C. O., and R. J. Rodriguez.  2004.  Bi-parentally inherited species-specific markers identify hybridization between rainbow trout and cutthroat trout subspecies.  Molecular Ecology Notes 4: 26–29. 

Ostrand, K. G., G. B. Zydlewski, W. L. Gale, and J. D. Zydlewski.  2010.  Long Term Retention, Survival, Growth, and Physiological Indicators of Salmonids Marked with Passive Integrated Transponder Tags. In: Symposium Proceedings Advances in Fish Tagging and Marking Technology. American Fisheries Society, Bethesda, Maryland. (In Press).

Quinn, T.P. 1993. A Review of Homing and Straying of Wild and Hatchery-Produced Salmon. Fisheries Research 18: 29-44.

Raymond, M. and Rousset, F.  1995.  GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism.  Journal of Heredity 86: 248-249.

Rexroad, C. E. I., Lee, Y., Keele, J. W., Karamycheva, S., Brown, G., Koop, B., Gahr, S. A., Palti, Y., and Quackenbush, J.  2003.  Sequence analysis of a roinbow trout cDNA library and creation of a gene index.  Cytogenetic and Genome Research 102: 347-354.

Rice, W. R. 1989.  Analyzing tables of statistical tests.  Evolution 43: 223-225.

Ryman, N., Jorde, P.E., and Laikre, L. 1995. Supportive breeding and variance effective population size. Conservation Biology 9: 1619-1628.

Ryman, N. and Laikre, L. 1991. Effects of supportive breeding on the genetically effective population size. Conservation Biology 5: 325-329.

Scribner, K. T., Gust, J. R., and Fields, R. L. 1996.  Isolation and characterization of novel salmon microsatellite loci - cross-species amplification and population genetic applications.  Canadian Journal of Fisheries and Aquatic Sciences 53: 833-841.

Sharma, R., G. Morishima, S. Wang, A. Talbot, and L. Gilbertson. 2006. An evaluation of the Clearwater River supplementation program in western Washington. Canadian Journal of Fisheries and Aquatic Sciences 63:423-437.

Smith, C. T., Koop, B. F., and Nelson, R. J.  1998.  Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Molecular Ecology 7: 1614-1616.

Spies, I. B., Brasier, D. J., O’Reilly, P. T. L., Seamons, T. R., and Bentzen, P.  2005. Development and characterization of novel tetra-, tri-, and dinucleotide microsatellite markers in rainbow trout (Oncorhynchus mykiss).  Molecular Ecology Notes 5: 278-281.

Stephenson, J.J., Campbell, M.R., Hess, J.E., Kozfkay, C., Matala, A.P., McPhee, M.V., Moran, P., Narum, S.R., Paquin, M.M., Schlei, O., Small, M.P.; Van Doornik, D.M., and Wenburg, J.K.  2009.  A centralized model for creating shared, standardized, microsatellite data that simplifies inter-laboratory collaboration.  Conservation Genetics 10: 1145-1149.

Waples, R.S. 1991. Genetic interactions between hatchery and wild salmonids: lessons from the Pacific Northwest. Canadian Journal of Fisheries and Aquatic Sciences 48: 124-133.

Weir, B. S. and Cockerham, C. C.  1984.  Estimating F-statistics for the analysis of population structure.  Evolution 38: 1358-1370.

White, G.C. and K.P. Burnham. 1999. Program MARK: survival estimation from populations of marked animals. Bird Study 46 (supplement):S120-S139.

OTHER DOCUMENTS USED FOR PROPOSAL DEVELOPMENT:

Anadromous Salmonid Monitoring Strategy from the Columbia Basin Coordinated Anadromous Monitoring Workshop (ASMS) http://www.cbfwa.org/ams/FinalDocs.cfm

Beasley C.A, B.A. Berejikian, R.W. Carmichael, D.E. Fast, M.J. Ford, P.F. Galbreath J.A. Hesse, L.L. McDonald, A.R. Murdoch, C.M. Peven, and D.A. Venditti).  2008.  Recommendations for Broad Scale Monitoring to Evaluate the Effects of Hatchery Supplementation on the Fitness of Natural Salmon and Steelhead Populations. Final Report of the Ad Hoc Supplementation Monitoring and Evaluation Workgroup (AHSWG).  82 pages. (http://www.cbfwa.org/csmep/web/documents/general/Documents/FINAL%20REPORT%20AHSWG.pdf)

Council’s 2009 Fish and Wildlife Program: http://www.nwcouncil.org/library/2009/2009-09

Council’s website for general information: http://www.nwcouncil.org/fw

Draft Monitoring, Evaluation, Research and Reporting (MERR): http://www.nwcouncil.org/library/2010/2010-04.htm

Hatchery Scientific Review Group (HSRG)–Lars Mobrand (chair), John Barr, Lee Blankenship, Don Campton, Trevor Evelyn, Tom Flagg, Conrad Mahnken, Robert Piper, Paul Seidel, Lisa Seeb and Bill Smoker. 2004. Hatchery Reform: Principles and Recommendations of the HSRG. Long Live the Kings, 1305 Fourth Avenue, Suite 810, Seattle, WA 98101 (available from www.hatcheryreform.org).

Hatchery Scientific Review Group (HSRG)– Peter Paquet (chair), A. Appleby, P. Seidel, D. Campton, M. Delarm, D. Fast, T. Flagg, J. Gislason, P. Kline, G. Nandor, J. Barr (vice chair), H. Lee Blankenship (vice chair), T. Evelyn, L. Mobrand (chair, 2000-08), S. Smith.  2009.  Columbia River hatchery reform system-wide report. (http://www.hatcheryreform.us/hrp/welcome_show.action).

High level indicators: http://www.nwcouncil.org/fw/program/hli

Hinrichsen, R.A., and R. Sharma. 2010. The precision and accuracy of estimates of the proportion of hatchery-origin escapement. Draft Report, May 27, 2010, 52 pages. http://www.pnamp.org/node/2904

ISRP and ISAB Reports: http://www.nwcouncil.org/fw/science.htm

NOAA Fisheries Draft “Guidance for Monitoring Recovery of Salmon and Steelhead: Listed Under the Federal Endangered Species Act (Idaho, Oregon, and Washington)”. Bruce Crawford and Scott Rumsey 2009. http://www.nwr.noaa.gov/Salmon-Recovery-Planning/upload/Draft-RME-Guidance.pdf

Recommendations for Implementing Research, Monitoring and Evaluation for the 2008 NOAA Fisheries FCRPS BiOp (AA/NOAA/NPCC RM&E Workgroups, May 2010).  This document provides recommendations on RM&E that are needed to meet FCRPS BiOp RM&E Strategies and RPAs. http://www.salmonrecovery.gov/ResearchReportsPublications.aspx

Subbasin plans: http://www.nwcouncil.org/fw/subbasinplanning

Notes

None

RME / AP Category Review Assessments

Review: RME / AP Category Review

Independent Scientific Review Panel Assessment

Assessment Number:

2003-063-00-ISRP-20101015

Project:

2003-063-00 - Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington

Review:

RME / AP Category Review

Proposal Number:

RMECAT-2003-063-00

Completed Date:

12/17/2010

Final Round ISRP Date:

12/17/2010

Final Round ISRP Rating:

Meets Scientific Review Criteria

Final Round ISRP Comment:

The proponents provided much more detailed data to address the ISRP’s questions, and these data were very useful. In particular proponents have responded favorably to our suggestion to develop methods to include adult steelhead abundance estimates in Abernathy and extrapolated to Germany and Mill Creek for an evaluation of supplementation.

One question that was not addressed, and perhaps we failed to emphasize it, was the actual number of individuals that were assigned to single or parent pairs in the parentage analysis, and how many individuals that were genotyped were not assigned to a parent. The numbers (and proportion) of fish not assigned needs to be presented and adequately discussed in any future proposal for completion of this project.

The challenge with this project is not executing the lab work but the logistics of the field work, namely, to meet the sample sizes required to have sufficient data. From the ISRP perspective, the question posed circa 2000, about establishing a broodstock using wild parr and producing smolts and subsequent anadromous adults from them has been answered. The questions for which support is currently being provided are the relative reproductive success of hatchery versus natural origin steelhead and the demographic consequences of supplementation. Since Germany, Mill, and Abernathy Creeks are intended to serve as reference and treatment locations respectively, the near genetic equilibrium among them, with the conclusion they have large amounts of gene flow, complicates any analysis. The challenge is twofold: First, for a demographic analysis you need a reasonable estimate of the adult progeny produced from natural spawning. If the three streams are functionally panmictic, adults attributed to one stream based on redd counts may have originated in one of the other streams. Second, if the implied large proportion of unassigned adults or juveniles is owing to adults that avoided capture at the electric weir, effort is being expended on genotyping individuals for which no useful conclusion can be reached.

Unless all of these logistical challenges can be resolved in future proposals, this project should be designed to complete the RRS and supplementation evaluation tasks over the next few years, and then be concluded. The project should be included in the Columbia River Hatchery Effects Evaluation project as part of consideration of basinwide evaluation. If the data are not suitable for meaningful evaluation the project should be brought to a reasonable conclusion.

If the logistic challenges can be resolved this study will provide an important replicate of the relative reproductive success of hatchery steelhead developed from a local broodstock, adding to the range of locations to help meet BiOp needs.

First Round ISRP Date:

10/18/2010

First Round ISRP Rating:

Response Requested

First Round ISRP Comment:

The ISRP requests a response that provides two primary items. 1. The response should provide a succinct, yet complete, presentation of the accomplishments of all facets of the project. This includes: • the number of parr collected each year to establish broodstocks the smolts released from these initial broodstocks • the estimates of smolts leaving the system from these releases and those residualized in the stream • natural smolt yield before beginning supplementation • adult returns to the stream from natural and hatchery production (by release year) • estimates of steelhead spawning below the hatchery weir site • numbers of hatchery and natural steelhead passed above the weir for natural spawning • estimates of juvenile (parr or smolt) production from natural spawning by natural and hatchery-origin adults, and • estimates of RRS of hatchery and natural-origin adults. The presentation should include the primary data (actual counts of fish), analysis of the primary data, interpretation of the analysis, and use of this interpretation to justify the approach to completing the study design in the 2003 proposal. The submitted proposal and presentation to the ISRP often provide conclusions without transparent supporting data. Portions of the proposal and presentation are contradictory. And within the proposal, conclusions in various places are often contradictory or cannot be easily associated with specific data. As an example, in the proposal in the accomplishments section there is a statement: steelhead smolt production has declined in the last few years in Abernathy Creek, whereas Germany and Mill Creeks (control streams) have been more variable (figure 1). These results suggest that this supplementation strategy may have negative consequences from either HOR smolt release or HOR adults spawning in the wild. Slide 9 in the presentation has bullet points stating that smolt production is equivalent between pre- and post-hatchery production years and that HOR emigration rates, timing, and patterns are similar to NOR fish. The text accompanying the presentation states: “These results suggest that smolt production within Abernathy Creek has not been negatively effected by hatchery production thus far.” A second example: the proposal accomplishments section states that, “Improper synchrony of HOR physiological processes associated with smolt transformation may increase the percent of HOR fish that elect to remain in fresh water or reduce survival. The consistent differences we have observed in HOR and NOR steelhead physiology and morphology may be positively related to the proportion of HOR fish that remain in Abernathy Creek (residualize) annually.” But in the next paragraph: “we evaluated spatial and seasonal overlap in habitat use and behavior between yearling HOR steelhead released from the AFTC and NOR salmonids. During spring, the majority of HOR smolts migrated downstream and left the system soon after each of three releases, whereas NOR smolt migration was more protracted following a normal distribution with one central peak. This suggests that the highest potential for ecological interaction between NOR and HOR at the smolt life states occurs downstream of the release location and within the first few days after each release.” Later in the same paragraph: “Our results suggest that there is a potential for hatchery fish to affect wild steelhead populations due to dietary overlap and salmonid fry predation.” In the adaptive management section the proposal states: “Our results suggest that a small portion (1% - 7%) of HOR released smolts did not emigrate.” For most of the essential production, demographic, and genetic objectives there is similar inconsistency within the proposal. 2. The response should also address the qualifications identified by the ISRP in the 2007 review. The 2007 ISRP review summary stated: “The sponsors made a diligent effort to rapidly respond to the ISRP’s questions. For the most part, however, their answers are only partially satisfactory. One major difficulty with this project lies with the comparison of adult abundance estimates in the reference streams (Germany and Mill Creeks) and the treatment stream (Abernathy Creek). The sponsor’s are apparently unable to verify (with presently collected data) assumptions involved with redd counts, which will be used to assess adult abundance in the reference streams. The response lacks a description of how the error associated with the abundance estimates will be assessed, and there is difficulty in accurately assessing other demographic characteristics such as sex ratio, age structure, and redds per female. The sponsors fail to plainly explain how they will account for confounding effects, such as habitat restoration actions, planned sometime in the future for Germany and Mill Creeks.” The recently submitted proposal continues to emphasize the opportunity to contrast production, demography, and genetic evaluations in reference and treatment streams. The proposal executive summary states: “We have started to compare the reproductive success and demographic changes (to both juvenile steelhead production and adult returns) occurring within Abernathy Creek to two control streams (i.e. Germany and Mill creeks) to determine whether supplementation was successful...” However, the accomplishment section provides no data on adults in Germany and Mill creeks. None of the objectives identify a demographic comparison of adults in reference streams to a treatment stream, and there are no objectives to obtain data on adult steelhead in Germany and Mill creeks. The ISRP raised concerns in the 2007 review about the sufficiency of data to assess and interpret relative reproductive success (for a variety of reasons), and demographic consequences of supplementation (for a variety of reasons) (see 2007 review). These concerns need to be resolved during this response loop.

Documentation Links:

Proponent Response (11/15/2010)

Proponent Response:

Dr. Kenneth Ostrand, Technical Contact November 8, 2010

Abernathy Fish Technology Center

U.S. Fish and Wildlife Service

1440 Abernathy Creek Road

Longview, Washington 98632

Dear Independent Scientific Review Panel,

Enclosed are our responses to each of the Independent Scientific Review Panel (ISRP) comments for the proposal titled Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington; BPA Project No. 2003-063-00; Contract Number No. 45565).

We appreciate the time and thoroughness of the ISRP reviewers. We believe that we have addressed all of the reviewers’ comments. As a result of the ISRP comments an objective has been added to the 2012 proposal scope of work that focuses solely upon acquiring, analyzing, and interpreting adult return data within the treatment and control creeks.

Please contact me if you require any additional information. Thank you for your time and consideration.

Sincerely,

Kenneth Ostrand

Regional Ecologist

XC: Denise Hawkins, Patricia Crandell

Response to ISRP:

Primary Item 1:

Our results demonstrate that a “native” or “endemic” hatchery broodstock of steelhead useful for supplementation can be obtained by capturing age 0+ natural origin (NOR) juvenile steelhead and rearing them to sexual maturity. NOR juveniles collected in Abernathy Creek and reared at Abernathy Fish Technology Center (AFTC) accepted commercial salmonid rations and survival to sexual maturity at age-3 was high (Range = 79 to 97%) for the three collection years (1999, 2000, and 2001; Table 1). Once NOR steelhead reached sexual maturity, they were used as broodstock to produce hatchery origin (HOR) progeny that were released within Abernathy Creek. For example, NOR juveniles collected in 1999 reached sexual maturity in 2002 and produced 29,724 HOR F₁progeny that were released in 2003. Based on a predominately age 2-salt life history, the majority of adult HOR F₁ steelhead returned in 2005 and were subsequently included in that year’s broodstock. Subsequent NOR juvenile steelhead collection years (i.e. 2000, 2001) followed a similar rearing, release, and return pattern.

Table 1. NOR steelhead juveniles were collected annually (1999, 2000, and 2001), reared to sexual maturity, and subsequently used as broodstock. The broodstock produced HOR smolts (range = 29,724 to 19,049 smolts) that were released from Abernathy Fish Technology Center.

NOR Collection year	Number of salmonid juveniles collected	Number of NOR steelhead remaining after >5 mo rearing	HOR Brood year	Number HOR smolts released (year)
1999	556	427	2002	29,724 (2003)
2000	485	439	2003	20,009 (2004)
2001	365	240	2004	19,049 (2005)

We estimated the number of HOR steelhead smolts released from AFTC leaving the system and residualizing within Abernathy Creek to determine their potential reproductive contributions to the population (Table 2). Of the HOR steelhead smolts released annually (mean = 22,118, SE = 1,602) from AFTC, only 61% (mean = 13,600, SE = 1,200) survived and left Abernathy Creek. Additionally, 0 to 7% of HOR fish residualized and became residents (mean = 542, SE = 144); however, relatively few resident steelhead contributed reproductively to the population compared to those with an andromous life history (Table 7). The number of offspring produced per resident HOR fish (mean = 0.06) appeared to be far less than that of resident NOR fish (mean = 0.6; Table 7). Preliminary evidence, via otolith microchemistry, suggested that the supplementation program at AFTC had not increased the number of resident fish reproductively contributing to the population. Of the offspring (N = 87) collected within Abernathy Creek, only 11% had a resident mother, a result not statistically different (P > 0.05) from the two control streams (Germany Creek = 0% and Mill Creek = 34%). These results collectively suggested that the majority of juvenile steelhead had anadromous parents versus resident parents. Additionally, our results suggested that anadromous parents contributed far more offspring than did resident fish. However, the AFTC steelhead supplementation program will need to be monitored in succeeding generations, particularly if these life history forms are heritable;; the goals of conservation hatcheries will not be met by increasing the proportion of resident fish produced. Sampling of the progeny in succeeding generations and further genetic analyses will help to clarify this potential pitfall.

Table 2. The estimated number of smolts released from Abernathy Fish Technology Center, HOR smolts that emigrated out of and those that became residents within Abernathy Creek.

Release year	Number of HOR smolts released	Number of HOR smolts emigrating	HOR smolts emigrating (%)	Number of HOR resident (residual)	HOR resident (%)
2003	29,724	14,952	50	135	0
2004	20,009	11,090	55	488	2
2005	19,049	10,955	58	1,278	7
2006	17,660	11,769	67	241	1
2007	24,190	18,902	78	333	1
2008	19,657	11,130	57	673	3
2009	24,538	16,400	67	648	3

AFTC began to release adult HOR steelhead to spawn naturally above the electrical barrier weir in 2005; thus the effect of hatchery supplementation on natural smolt production first occurred in 2007. As a result 2002, 2003, 2004, 2005, and 2006 were considered pre-hatchery supplementation years and subsequent years were considered post-hatchery supplementation years (Table 3). Although within year estimates of variance are still being calculated for most years by the Washington Department of Fish and Wildlife (WDFW), preliminary estimates suggested that steelhead smolt yield had not been negatively affected by the hatchery supplementation program at AFTC or the removal of juveniles to create the broodstock. Our preliminary results suggested that smolt production declined within all the creeks (F₅, ₁₈ = 8.7, P < 0.05), and there was no significant increase or decrease in smolt yield due to supplementation (Stream × Treatment Interaction: F₅, ₁₈ = 1.43, P = 0.26) as compared to control streams. Once within year variance estimates are available, a more rigorous computation (e.g. paired BACI design) comparing smolt production pre-and post hatchery supplementation among creeks can be completed. Continuing to estimate smolt yield will allow the estimates to be more scientifically defensible since three years of post-supplementation data may not fully reflect annual variability within smolt yield and abiotic conditions. Acquiring more data will provide a broader scope of inference for determing the effects of hatchery supplementation and insights for use throughout the Columbia River Basin.

Table 3. Estimates of natural-origin (NOR) steelhead smolt yield within Abernathy, Germany, and Mill creeks. Smolt yield was obtained using rotary screw traps operated by Washington Department of Fish and Wildlife.

Emigration year	Abernathy NOR smolt yield	±95CI	Germany NOR smolt yield	±95CI	Mill NOR smolt yield		±95CI
2002	5,287	1,520	7,023	3,009		3,102	2,152
2003	4,141	509	5,936	700		1,383	747
2004	5,238	777	7,426	719		2,250	329
2005	2,400	TBD	6,350	TBD		1,200	TBD
2006	1,992	TBD	2,915	TBD		863	TBD
2007	1,638	TBD	4,008	TBD		1,110	TBD
2008	1,192	354	3,769	338		1,256	184
2009	1,544	TBD	4,488	TBD		1,944	TBD

One of our main objectives was to obtain a sufficient number of NOR and HOR adult steelhead for our broodstock so we could spawn adults randomly and equalize parental genetic contributions. The number of adult NOR steelhead returning to AFTC was relatively low from 2005 to 2009 but doubled in 2010. In contrast, the number of HOR adult steelhead returning to AFTC more than tripled since 2007 and remained relatively high through 2010. We propose to continue trapping adult steelhead at AFTC, and adhere to spawning protocols in hopes of minimizing genetic divergence between HOR and NOR populations. Moreover, due to the complex nature of population abundance patterns in relation to local and marine environmental conditions, additional years of data in conjunction with redd surveys in Abernathy, Mill, and Germany creeks are needed to assess the demographic change of Abernathy Creek steelhead due to supplementation practices. Although increasing trends in adult return rates in Abernathy Creek are promising, they have only been observed during the last few years. Continuing to determine the adult return rates should make the estimates more scientifically defensible given that adult salmonid return rates can fluctuate widely from year to year. Accounting for this inherent variability is imperative, particularly if management decisions will be based upon conclusions of this study.

Table 4. Adult natural origin (NOR) and hatchery origin (HOR) steelhead returns to AFTC. Electric barrier weir operation began in the fall of 2005 and has been operated each subsequent year from October through (at least) May.

Year	NOR	HOR	Stray-HOR
2005	34	38	36
2006	32	49	62
2007	26	58	50
2008	24	189	60
2009	40	148	67
2010	80	229	64

Estimates of the number of steelhead spawning in all of Abernathy Creek and in the creek below AFTC’s electric barrier weir, based on redd counts, have been estimated by WDFW (Table 5). Although the validation of redd counts as an appropriate surrogate for the number of adult steelhead has been beyond the scope of our study to date, we have included a new objective (OBJ 9) within the proposal to extend the duration of operation of an adult picket weir at the mouth of Abernathy Creek. The weir would be operated throughout the adult steelhead return season. We propose that by using redd counts collected on Abernathy, Germany, and Mill creeks and by operating the adult picket weir on Abernathy Creek throughout the adult steelhead return season, we will be able to validate current redd counts and more accurately assess demographic characteristics such as sex ratios, age structure, and redds per female. The addition of this objective to the proposal will provide additional information about adults in the treatment stream (Abernathy Creek) and the two control streams (Germany and Mill creeks).

Table 5. Adult steelhead escapement estimates for Abernathy Creek. Escapement counts include estimates from Cameron Creek (a tributary to Abernathy Creek). Escapement estimates were determined via redd counts (Bryce Glaser, WDFW).

Year	Total Steelhead escapement	Downstream of electric barrier weir
2005	116	84
2006	154	130
2007	200	82
2008	248	90
2009	302	86

To assess the relative reproductive success of HOR and NOR steelhead spawning in the natural environment, AFTC releases NOR and HOR adult steelhead into Abernathy Creek above the electric barrier weir to spawn naturally. The first year of upstream releases began in 2005 after the weir was built at AFTC to control upstream migration of steelhead. Additionally, 2005 was the first year of expected HOR adult returns from the first (2003) HOR smolt release. HOR and NOR natural spawners passed upstream in 2005 produced progeny that emigrated to the ocean in 2007 and returned in 2009. Thus, 2009 was the first year where returning adults consisted of those produced naturally in the stream by HOR and NOR adults spawning sympatrically. Over the next several years, we will have a number of adult fish returning that were produced by HOR and NOR spawners naturally in the creek. As mentioned previously, due to the complex nature of local and marine environmental conditions, it will be necessary to continue this project for the next several years in order to provide a robust assessment of relative reproductive success of HOR and NOR steelhead spawning in the natural environment across a broad spectrum of environmental conditions.

Table 6. Number of adult natural origin (NOR) and hatchery origin (HOR) steelhead passed above the electric barrier weir for natural spawning.

	NOR		HOR
Year	Male	Female	Male	Female
2005	2	4	4	1
2006	17	8	9	5
2007	11	7	9	5
2008	10	12	20	34
2009	18	20	8	9
2010	26	27	12	12
Total	84	78	62	66

The supplementation program at AFTC will follow these protocols for retaining broodstock and for passing adult steelhead: 1) retain 1/3 of all captured adult NOR steelhead for broodstock; retain twice as many HOR as NOR steelhead for a total of no more than 200 spawners, 2) spawn fish using a factorial mating design (2 males x 2 females), 3) release the other 2/3 of all captured NOR adult steelhead above the weir to spawn naturally and release HOR steelhead above the weir such that 1/3 to 1/2 of the adult steelhead passed upstream are HOR. The number of males and females passed upstream, of each origin (NOR or HOR), should be equivalent (equal numbers of HOR males and HOR females, equal numbers of NOR males and NOR females).

Our data show that the reproductive success of HOR adult steelhead spawning naturally in Abernathy Creek was lower than that of NOR adults for both anadromous and resident parents (Table 7). Two exceptions to this trend occurred when the reproductive success of HOR parents was nearly equal to that of NOR parents in a single group (resident parents in 2007 and anadromous parents in 2009). Despite this, the overall reproductive success of HOR fish (anadromous and resident) in those years was 40% (2007) and 50% (2009) that of NOR fish. The number of offspring produced per individual was highly variable for both NOR and HOR adults but anadromous parents of both types generally produced more offspring than did their resident counterparts (Table 8).

Table 7. Number of offspring per adult assigned to each parental type and relative reproductive success (offspring per parent) of hatchery (HOR) and natural (NOR) origin adults spawning naturally in Abernathy Creek (reproductive success analyses were not performed in 2006).

Brood Year	Life History	Number of offspring per adult		Relative reproductive success of HOR compared to NOR
		HOR	NOR	Relative reproductive success of HOR compared to NOR
2005	Total	1.40	5.83	0.24
2007	Anadromous	0.20	4.33	0.05
	Resident	0.19	0.18	1.06
	Total	0.19	0.45	0.42
2008	Anadromous	0.82	8.50	0.10
	Resident	0.02	1.45	0.01
	Total	0.38	3.55	0.11
2009	Anadromous	0.92	1.02	0.90
	Resident	0.00	0.10	0.00
	Total	0.21	0.40	0.52

The past two years of data have allowed (2008 and 2009) reproductive success to be assessed by family type as well as by parent of origin in order to evaluate the effect of HOR/NOR interbreeding (Table 8). Results indicate that HORxHOR crosses have lower reproductive success than natural NORxNOR crosses and crosses involving a HOR female and a NOR male (HORxNOR). The reproductive success of NOR female by HOR male (NORxHOR) crosses was very different between the two years (Table 8). These results appear to suggest there may be some selective disadvantage to crosses of mixed origin, but making a global statement about fitness based on family type would be inappropriate given the small sample sizes and variation in the results. Additional data from 2010 and 2011 may clarify these results.

Table 8. Relative reproductive success by family type for hatchery origin (H) and natural origin (N) adults spawning naturally in Abernathy Creek. Maternal origin is listed first.

Brood Year	Number of offspring per family				Reproductive success of HxH families relative to each cross
	Number of offspring per family
	HxH	NxN	NxH	HxN	NxN	NxH	HxN
2008	10.00	13.90	2.70	6.50	0.72	3.70	1.54
2009	1.30	2.30	8.00	1.00	0.57	0.16	1.30

Although an estimate of juvenile (parr or smolt) steelhead production from natural spawning adults was also requested by the ISRP, extrapolation of the offspring per family estimates to parr or smolt production in the system has not been conducted due to low assignment rates and small sample sizes of PIT tagged steelhead, and the associated high variance in these estimates. Smolt samples for this project were obtained from WDFW which operated a screw trap each spring below AFTC near the mouth of Abernathy Creek. HOR smolts were released from AFTC during the time of the outmigration of NOR smolts, so fish caught at the smolt trap included both NOR and HOR smolts. In addition, due to the screw trap’s location below the electrical barrier weir, the offspring of any spawning that occurred below the AFTC weir were also passed through the trap. NOR parr were caught in electrofishing surveys of Abernathy Creek each fall as part of this project. However, this sampling routine was intended to assess residualization of HOR smolts and to capture NOR fish for PIT tagging rather than assess total juvenile abundance, so data with which to estimate parr production per family has not been determined. Thus this estimate is dependent upon PIT tagged fish that have been assigned a parent. Given that only a handful of fish meet both these requirements coupled with large variance it has been difficult to determine this estimate with any confidence. Nevertheless, if sample sizes permit we may be able to estimate parr or smolt production by family type in future years for the study area located above the electrical barrier weir. In our proposal we have included an effort to increase our sample size by effectively doubling our electrofishing and marking efforts.

We agree that the proposal and presentation appear to have contradictory statements; we have added or altered text to more accurately reflect and clarify the unique results of our study. For example, our results suggested that smolt production had declined within all three creeks (F₅, ₁₈ = 8.7, P < 0.05), and there had been no significant increase or decrease in smolt yield due to supplementation in Abernathy Creek (Stream × Treatment Interaction: F₅, ₁₈ = 1.43, P = 0.26) as compared to control streams. As a result, we conclude that smolt production has not been negatively affected by hatchery supplementation.

In the second example in the accomplishment section within the proposal, it was our intent to suggest that a specific mechanism such as improper synchrony of chloride cell development at the time of progeny release (i.e. osmoregulatory ability) may be differentially affecting residual rates and survival. Osmoregulatory ability may be a mechanism that is mandating that fish die or residualize in the system. Those that do survive and become residents may negatively impact NOR fish but only for brief periods of time at specific locations within the creek. Nevertheless, we have altered the text to help clarify and reduce the appearance of contradictory statements.

Primary Item 2:

We agree, the comparisons of adult steelhead abundance between Abernathy Creek (treatment) and Germany and Mill creeks (controls) are logistically difficult. Water levels are too high and streams are too turbid to accurately conduct behavioral observations from the shore or via snorkeling. Constructing permanent barriers on Germany and Mill creeks similar to the electric barrier on Abernathy Creek is cost prohibitive. Steelhead redd counts on Abernathy, Germany and Mill creeks remain the only viable option for estimating relative adult abundance. However, adult redd counts and their associated estimates operate on various assumptions; capturing adults using a picket weir may help to refine redd count assumptions. As a result, we have come to an accord with WDFW (Mara Zimmerman); WDFW will operate an adult picket weir at the mouth of Abernathy Creek in order to help refine demographic characteristics for adult steelhead returns such as sex ratio, age structure, and redds per female. The refined estimates will be applied to all three creeks (treatment and two control streams). We argue that since redd counts are conducted by the same crews at the same time of year on all three creeks, any error in redd count data will be homogeneous among the streams. Therefore significant differences in adult returns due to hatchery supplementation will be apparent and valid. We have added an objective and increased the budget accordingly in order to accomplish this ISRP recommended task. The results provided from this objective combined with the genetic analyses should yield scientifically defensible information that can be applied to all future data and may be used to rigorously analyze past data.

In regards to the habitat restoration activities planned for the creeks, they remain only plans. Habitat restoration activities such as riparian projects such as sapling plantings will take years if not decades to impart any significant change to population demographics, well beyond the duration of this study.

We believe that the additional objective will provide us with the ability to use demographic analyses to assess and interpret relative reproductive success and demographic consequences of supplementation. As stated in the proposal, this study includes an evaluation of changes in production, demography, and genetic structure within Abernathy Creek and in reference to two control streams, Mill and Germany creeks. In line with these objectives, an evaluation of the level of gene flow between Abernathy Creek and the two control streams was done using 19 microsatellite loci (2009 Annual Report). The analysis included five years of smolt samples from Abernathy Creek (2002-2009), three years of smolt samples from Germany Creek (2002-2004) and four years of smolt samples from Mill Creek (2002-2005). A neighbor-joining dendogram (Figure 1) depicting the relationships among the creeks showed no evidence of major changes in the genetic structure of Abernathy Creek relative to Mill and Germany creeks, and only two branches of the tree (2008 Abernathy and 2008 Germany) and 2002 and 2003 Mill Creek samples had significant bootstrap values.

isrp1

isrp2

An additional analysis (2009 Annual Report) using 9 microsatellite loci showed Abernathy, Mill, and Germany creeks are part of a larger group of five genetically similar populations in the Lower Columbia River (Grays River, Elochoman River, Abernathy, Mill, and Germany creeks) which is distinct from a group of populations of winter steelhead farther upriver (Coweeman River, Green River, Kalama River, East and North Fork Lewis Rivers, North and South Fork Toutle Rivers, Washougal River). Genetic divergence among Abernathy, Mill and Germany creeks (F_ST =0.006) was not significantly different from divergence among the Elochoman and Grays River collections (F_ST=0.003, Weir and Cockerham, 1984). These results indicate that the three populations are genetically similar and that the divergence among them is comparable to that found among other populations in the Lower Columbia River (USFWS 2009).

The results of these analyses indicate that the there is a large amount of gene flow among the three streams, which likely represent a single panmictic population rather than three independent genetic groups. Although no strong genetic changes have been observed in the Abernathy Creek population relative to the other two since 2002 (USFWS 2009), our power to detect such changes is severely limited by the level of geneflow; any changes in the genetic structure of the Abernathy Creek steelhead due to hatchery supplementation are likely to affect that of steelhead in the other two creeks.

While our reports to date have not assessed changes in numbers of adult returns in Mill and Germany creeks, the inclusion of redd counts obtained from WDFW as a measure of population size in 2011 will allow us to compare changes in adult returns among the three creeks and assess any effect the supplementation program in Abernathy Creek has had on spawning population size. In 2011 additional smolt samples will also be collected from Mill and Germany creeks in order to update the baseline for the two populations. Additional analysis of these collections will assess patterns in genotypic disequilibrium, deviations from Hardy-Weinberg equilibrium and allelic richness relative to Abernathy Creek. Although these analyses will provide some insight into changes in the other two creeks relative to our “treatment” population, it is important to note that genetic results presented in 2009 and reiterated above indicate the three streams function as a single population, so changes observed in Mill and Germany creek population dynamics are unlikely to be independent of those observed in Abernathy Creek.

References

Cavalli-Sforza, L.L., and Edwards, A.W. 1967. Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics 19:233-257.

Saitou, N. and Nei., M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.

U.S. Fish & Wildlife Service, Abernathy Fish Technology Center, 1440 Abernathy Creek Road Longview, WA 98632. 2005. Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington Annual Report January 2005 – December 2005. (BPA Project No. 2003-063-00, Contract Number No. 016522).

U.S. Fish & Wildlife Service, Abernathy Fish Technology Center, 1440 Abernathy Creek Road Longview, WA 98632. 2007. Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington Annual Report January 2007 – December 2007. (BPA Project No. 2003-063-00, Contract Number No. 016522).

U.S. Fish & Wildlife Service, Abernathy Fish Technology Center, 1440 Abernathy Creek Road Longview, WA 98632. 2008. Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington Annual Report January 2008 – December 2008. (BPA Project No. 2003-063-00, Contract Number No. 016522).

U.S. Fish & Wildlife Service, Abernathy Fish Technology Center, 1440 Abernathy Creek Road Longview, WA 98632. 2009. Natural Reproductive Success and Demographic Effects of Hatchery-Origin Steelhead in Abernathy Creek, Washington Annual Report January 2009 – December 2009. (BPA Project No. 2003-063-00, Contract Number No. 016522).

Weir, B. S. and Cockerham, C. C. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.

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Dr. Kenneth Ostrand, Technical Contact November 8, 2010