Short Description

This Statement of Work covers the completion of Phase 1 of our research project entitled "Evaluating relative reproductive success of natural- and hatchery-origin Snake River fall Chinook spawners upstream of Lower Granite Dam".  The goal for Phase 1 is to determine whether genetic variation between wild and hatchery origin Snake River fall Chinook spawner populations is large enough to allow accurate estimates of their relative contributions to natural production, and if so, to estimate wild and hatchery contributions to annual samples of natural origin fall Chinook.  Results from Phase 1 will determine whether proceeding with Phase 2 (the research application phase from mid-2005 to 2008) is justified.  The long-term study evaluates whether hatchery-reared fall Chinook are contributing to recovery of the ESA-listed Snake River population, which addresses concerns documented in Federal Columbia River Power System (FCRPS) Biological Opinion Action 182.

Completion of Phase 1 during funding year 2005 (FY05) will include collecting microsatellite DNA data for wild Chinook sampled at Lower Granite dam and the Snake River in 2004, performing statistical tests and data analyses, estimating stock contribution and admixture proportions, interpreting analytical results, database management, writing final Phase 1 report, and presenting study results and conclusions to managers and scientists at appropriate meetings or conferences.  We also plan for Phase 2 project sampling activities that need to occur in 2005, in case Phase 2 implementation is approved.

Background

Production of fall Chinook at Lyons Ferry Hatchery (LFH) began as a mitigation program for the impacts of the four dams of the Lower Snake River Project (LSRP).  In early years, adult Snake River fall Chinook were trapped at Snake River dams for broodstock, and subsequently, hatchery-origin adults returning to LFH or trapped at Lower Granite Dam formed the broodstock.  Due to straying of non-Snake River Chinook into LFH, broodstock integrity has been managed by using only marked, known-origin adult spawners (1990-2003) and 100% marking of all on-station juvenile releases.  Snake River fall Chinook were designated as an Evolutionarily Significant Unit (ESU) and were ESA-listed as a threatened species in 1992.  The National Marine Fisheries Service's 1999 Biological Opinion on Artificial Propagation in the Columbia River Basin documented that the LFH Snake River fall Chinook program is intended to provide fish for mitigation, compensation, natural production (recovery above Lower Granite Dam), and Tribal Trust responsibilities.  In recent years the LFH program has become a supplementation program to enhance Snake River fall Chinook production.

The Nez Perce Tribe (NPT) has used LFH-reared fall Chinook for Clearwater River (upstream of Lower granite Dam) supplementation activities since 1997.  These fish have been released as both marked and unmarked smolts from their Clearwater River Big Canyon acclimation site.  The new NPT hatchery will be producing fall Chinook derived from LFH-stock and Clearwater/Snake origin fall chinook .  LFH fall Chinook also have been released from Snake River mainstem acclimation sites since 1996 to supplement natural production near release locations.

Wild Snake River fall Chinook were not included in LFH broodstocks from 1990 to 2003.  However, hatchery-origin fall Chinook have been accessing natural spawning grounds in varying proportions from year to year.  Fall Chinook passing Lower Granite Dam into upper Snake River spawning grounds have increased in abundance significantly since 1995, especially the numbers of wild origin fish.  Relative proportions of LFH-origin fish in escapements have also increased, from approximately 0% in 1995 to as high as 64% in 1998.  Based on wild juvenile fall Chinook sampled in the Snake River, genetic variation among natural spawner broodyears has been analyzed and compared to LFH and Columbia River fall Chinook.  In years when LFH fall Chinook were not abundant in escapements above Lower Granite Dam, natural origin juveniles were particularly genetically divergent from LFH broodstocks (Marshall et al. 2000).  The wild spawner population appeared to be an important and distinguishable component of genetic diversity within the ESU.

Productivity of Snake River Basin fall chinook is currently estimated from trends in redd counts for the mainstem and several sub-basins.  Although hatchery-origin fish are most likely spawning naturally in these areas, wild- and hatchery-origin fish productivity cannot be estimated separately via redd counts.  It is unknown what contribution hatchery-origin fish have provided to the recent increase in natural origin spawner abundance.  Determining reproductive success of natural spawners has been identified as a priority in the NMFS Biological Opinion for the FCRPS.  Our study is evaluating whether genetic differentiation between wild and hatchery spawner components can be used to estimate their relative contributions to natural production, and whether reproductive contributions correspond with proportional abundance.

We are using a genetic mixture analysis approach for estimating relative reproductive success of wild and hatchery origin fall Chinook spawning naturally in the upper Snake River, and will test whether it is an effective methodology.  We are using a time-series of existing samples of Snake River wild fall chinook juveniles, LFH broodstock adults, and natural origin adults to collect microsatellite DNA genotype data.  We also have baseline samples for Columbia Basin fall chinook populations that are known to stray into the Snake River and may also participate as spawners.  We are testing several statistical mixture analysis procedures to estimate contributions to annual production from each potential spawner group.  If genetic divergence allows, we plan to produce estimates of relative reproductive success of wild and hatchery origin spawners from several older broodyears.

Our current set of annual wild production samples includes broodyears that vary widely in potential contributions of hatchery-origin fish.  Unmarked adults sampled at Lower Granite Dam in 2003 include Chinook naturally-produced in the 1998, 1999, and 2000 broodyears.  In these three broodyears proportions of LFH-origin fish were very high in Lower Granite Dam interceptions, in contrast to 1993, 1994 and 1995 when they were very low.  We expect the genetic profile of a natural origin broodyear sample to reflect contributions of hatchery and wild stocks in proportions that occurred in the parent spawner population if relative reproductive success is similar.  We assume that annual hatchery and wild proportions in the spawner population are the same as those estimated in fall Chinook intercepted and sampled at the Dam.

If the proportion of LFH-origin natural spawners increases and their reproductive success is high, we expect the genetic profile of wild-origin fall Chinook in future years to become very similar to that of LFH broodstocks.  A time-series of broodyear-based genetic data for Snake River fall Chinook should permit effective monitoring of change in the wild population as recovery efforts continue.  The long-term study is expected to determine whether hatchery-reared fall Chinook are contributing to recovery of the Snake River population.  If our study continues through Phase 2 and accurately determines LFH fall Chinook relative reproductive success, our results will inform management regarding the ratio of wild and hatchery Chinook that most effectively meets population growth criteria for a healthy and recovered wild population.

A change in management practice for hatchery production occurred in 2004.  State, tribal and federal agencies agreed that wild Chinook could be used in LFH broodstocks to reduce genetic divergence from the wild spawning population.  In order to acquire wild-origin adults it was agreed that Chinook intercepted at Lower Granite Dam, transported to LFH, and determined by lack of marks and scale pattern analysis to be wild-origin would be used as spawners for the 2004 broodyear.  Thus, potential wild origin adults (recognized as such by the lack of marks) that were trapped at Lower Granite Dam were not passed upstream as had occurred in previous years.  We took genetic samples from these fish for our Phase 1 study.  However, because they did not have the opportunity to spawn naturally, we do not have samples of wild-origin potential parents of the 2004 wild brood.  We can only assume that sampled fish accurately represent those that did pass upstream.  Because of this situation, we plan to try sampling adults on upper Snake River spawning grounds in 2005 with the assistance of U.S. Fish and Wildlife Service (USFWS) staff and other cooperators already involved in natural production research.

References

Marshall, A. R., H. L. Blankenship, and W. P. Connor.  2000.  Genetic Characterization of Naturally Spawned Snake River Fall-Run Chinook Salmon.  Transactions of the American Fisheries Society 129:680-698.



Hypothesizes and General Approach

For Phase 1, we are testing the following hypothesis:

Ho:  Genetic variation among wild and hatchery origin spawner components is large enough to allow accurate estimates of relative contributions to natural production of Snake River fall Chinook during the period of our study.

Using microsatellite DNA loci data we will determine the magnitude of differentiation between and among wild and hatchery-origin fall Chinook population samples.  We will test mixture analysis methodologies with sample data.  If analytical results are positive (i.e., genetic differences are large enough for reliable estimates), we will calculate annual contributions by wild and hatchery-origin populations to natural production in a set of study samples.

If Phase 1 results indicate that the long-term application phase is feasible, we will recommend that Phase 2 be implemented.  To be adequately prepared to advance to Phase 2, we plan to collect DNA and scale samples from adults accessing upper Snake River spawning areas in 2005.  Adults may be sampled at the adult trap at Lower Granite Dam or on spawning grounds.  We will request assistance from USFWS staff in Idaho with spawning ground sampling because they are actively involved with annual fall Chinook survey work.  We will also plan to genetically analyze naturally-produced 2005 offspring that will be sampled by USFWS over a period of months in 2005 during their out-migration.  We will only proceed with Phase 2 tasks that need to occur in the latter half of 2005 upon review of Phase 1 results and approval by BPA.

In Phase 2, we will be testing the following hypothesis:

Ho:  There is no difference in the generation of F2 progeny by naturally spawning wild and hatchery origin Snake River stock fall chinook.  (In this case, "F2" progeny are offspring of the first generation offspring of hatchery-origin adults that spawned naturally.)

Objectives

Objective 1:  Complete statistical data analyses on samples' genetic data collected in FY04
Objective 2:  Complete mixture analyses tests and produce contribution estimates as appropriate
Objective 3:  Collect genetic data on wild origin adults and juveniles sampled in 2004
Objective 4:  Estimate wild and hatchery relative reproductive contributions for 2004 samples
Objective 5:  For Phase 2, collect genetic data on wild juveniles sampled in 2005 by USFWS
Objective 6:  For Phase 2, sample wild adults returning to spawn in 2005
Objective 7:  Produce progress reports
Objective 8:  Produce final report on Phase 1 work and annual progress report
Objective 9:  Manage and administer contracting and budget process
Objective 10:  Prepare draft manuscript for submission to peer-reviewed journal