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 up to 2008) is justified.  The long-term goal is to evaluate whether hatchery-origin fall Chinook are affecting productivity and recovery of the ESA-listed Snake River population, which addresses concerns documented in Federal Columbia River Power System (FCRPS) Biological Opinion Action 182.

Work during funding year 2006 (FY06) will include 1) completing analytical work on previously collected samples and data, 2) collecting microsatellite DNA data for wild adult and juvenile Chinook sampled in the Snake River in the fall of 2005 and during 2006, 2) performing statistical tests and data analyses, estimating stock contribution and admixture proportions, and interpreting results for sample groups that include new samples, 3) database management, 4) writing project reports and presenting study results to managers and scientists at meetings or conferences.  Project cooperators will conduct sampling activities in 2006.

We have already collected DNA genetic data for a time series of annual wild fall Chinook juvenile samples that includes broodyears that vary widely in potential contributions of hatchery-origin fish.  We have sampled and genetically analyzed unmarked adults at Lower Granite Dam in recent years in order to get samples of surviving adults from natural spawning in brood years two to five years previously, and to sample potential parents of current brood year.  In 2004, management practices for hatchery production changed, and state, tribal and federal agencies agreed that wild Chinook could be used in Lyons Ferry Hatchery (LFH) broodstocks.  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 hatchery spawners.  Thus, wild origin adults trapped at Lower Granite Dam were not all passed upstream and our samples of trapped, but removed, fish do not contain potential naturally spawning parents.  Because of this, we are sampling adults on upper Snake River spawning grounds in fall 2005 and plan to continue this in 2006.   We will discontinue project sampling at Lower Granite Dam in 2006.  Field work for spawning ground sampling will be carried out by U.S. Fish and Wildlife Service (USFWS) staff and other cooperators, and conducted under a separate, but companion contract.

Hypothesizes and General Approach

Phase 1 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.

Background: 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.  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 Phase 1 results indicate that the long-term application phase is feasible, Phase 2 could be implemented.

Phase 2 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.)