Monitoring the Migrations of Snake River Wild Spring/Summer Juvenile Chinook Salmon Stocks

OVERALL PERFORMANCE WORK STATEMENT:  Assess the migrational characteristics and estimate parr-to-smolt survival for Snake River wild spring/summer Chinook salmon smolts at Lower Granite Dam.  Characterize parr and smolt survival and movement out of natal rearing areas of selected streams and examine the relationships between fish movement, environmental conditions within the streams, and weather and climate data.  Collect parr-to-smolt growth information on previously PIT-tagged wild Chinook salmon parr at Lower Granite Dam each spring.

OVERALL MAJOR STUDY OBJECTIVE

Characterize the outmigration timing of wild spring/summer Chinook salmon smolts at Lower Granite Dam over a period of years.

-Null Hypothesis (Ho):  Run-time distributions at Lower Granite Dam are not significantly different within years among wild spring/summer Chinook salmon smolt populations in the Snake River drainage.

-Corollary:  If the null hypothesis is rejected, it is highly likely that run-timing to Lower Granite Dam is different among wild populations within years in the Snake River and that these differences may be influenced by factors such as temperature, flow, or genetics.

-Criteria for Rejecting Ho:  The null hypothesis will be rejected if run-timing is significantly different among populations by re-sampling methods (Efron 1982).  Significance will be set at (P<0.05).

-Null Hypothesis (Ho):  Run-time distributions for individual streams or tributaries at Lower Granite Dam are not significantly different among years.

-Corollary:  If the null hypothesis is rejected, it is highly likely that run-timing of individual streams or tributaries is different among years and that these differences may be influenced by environmental  factors such as temperature or flow and climatic/weather conditions.

-Criteria for Rejecting Ho:  The null hypothesis will be rejected if run-timing of individual streams or tributaries is different among years by re-sampling methods.  Significance will be set at (P<0.05).

Background

In 1988, the NOAA Fisheries, National Marine Fisheries Service (NMFS) began a pilot study to PIT tag wild/natural spring/summer Chinook salmon parr for transportation research. Out-migrating smolts from this marking effort were detected at Lower Granite, Little Goose, and McNary Dams in spring 1989 (Matthews et al. 1990). Preliminary information from this initial effort showed that various wild stocks exhibited very different run timing from each other as well as from hatchery stocks.

The project continued as a transportation research pilot study for 2 additional years (Achord et al. 1992; Matthews et al. 1992). Thereafter, we determined the technique was not currently practical for use in transportation research due to low population abundance and the high numbers of wild fish required for statistically credible results.  However, the transportation research pilot study continued to provide useful and interesting wild smolt timing information.  With the Endangered Species Act listings of wild Snake River Chinook salmon stocks, the continuation of this work became critical for proper in-season water management, particularly since river flows alone were a poor predictor of wild smolt migrational timing.  In addition, more data, including annual environmental information was required before we could determine with precision which factors were exerting primary control over wild smolt migrational timing. Therefore, the study was continued as a long-term, wild-smolt migrational timing study cooperatively funded by NMFS and BPA in 1991.

Prior to 1992, fisheries managers relied on branded hatchery fish, index counts, and flow patterns for information to guide their passage decisions.  A more complete approach now integrates mark information for a broad mixture of the Columbia River Basin's wild/natural and hatchery stocks. The Northwest Power Planning Council (NWPPC) has stated "... major gaps remain in understanding Columbia Basin stocks, their life patterns and survival at different points in their life cycles." Our research directly addresses filling these major gaps for wild Snake River spring/summer Chinook salmon stocks during their parr-to-smolt life stage.

In addition, to addressing several Sections of previous Fish and Wildlife Programs; our research also addresses some of the "Reasonable and Prudent Alternatives (RPA's)" in the 2000 NMFS Biological Opinion (NMFS 2001). Section 9.6.5.2, Action 180 advocates a regional monitoring effort on the population status of wild fish stocks and the environmental status of their natal streams and tributaries. Section 9.6.5.5, Action 199 and Appendix H Research Action 1193 calls for "...research to produce information on the migrational characteristics of Columbia and Snake River basin salmon and steelhead". The smolt monitoring program produces information on the migrational characteristics of various salmon and steelhead stocks...and provides management information for implementing flow and spill measures designed to improve passage conditions in the mainstem lower Snake and Columbia Rivers". More recently, the "Final Updated Proposed Action for the FCRPS Biological Remand", (a section of the 2004 BIOP), stated in Updated Proposed Actions, "Implement and maintain the Columbia River Basin PIT Tag Information System. Expand the system to systematically plan PIT Tag efforts in the pilot study basins such that production and survival can be estimated throughout the system for wild and hatchery fish. Also, continue development and implementation of new fish detection and tagging techniques.

Clearly, important migratory aspects of wild fish (e.g., run timing/survival) should continue to be considered. To this end, marking wild/natural parr with PIT tags in their natal streams during the summer of their first year of life provides the opportunity to precisely track these stocks through in-stream PIT-tag monitors, traps, and the hydroelectric complex during their parr/smolt migrations from late summer to spring. We believe that migrational characteristics of wild spring/summer Chinook salmon smolts should be examined over several years.  A goal of this study is to characterize run-timing of wild fish over a sufficient number of years to determine if consistent patterns are apparent and to determine if the data are useable for providing daily information for real-time management decisions during the smolt out-migrations. Wild spring/summer Chinook salmon parr will be captured and PIT-tagged in their natal streams during the summer. The fish will then be returned to the stream in the same area from which they were sampled. This will allow exposure to all environmental factors that affect behavior and survival from that point forward. As the smolts migrate downstream the following spring, those that enter the collection facility at Lower Granite Dam will be detected automatically and the information will be incorporated daily into the smolt monitoring data base along with hatchery fish recoveries.

Project Summary Update

Since 1993, we have observed varying parr-to-smolt survival for wild spring/summer Chinook salmon from Idaho and Oregon streams ranging from an estimated 8.1% in 2004 to 24.4% in 1998, with an overall average parr-to-smolt survival rate of 16.0%.  Most recent years (2009-2013) show a gradual decline in parr-to-smolt survival with the most recent survival rate being 11.0% in 2013.
Over the last 21 years, we have found a direct correlation with the parr density and parr-to-smolt survival.  Years with much higher parr density (2004 and 2005) end up having the lowest parr-to-smolt survival rates (8.1 and 8.4% respectively).  Returns of wild adults to the Snake River basin from 2001 to 2003 were more than one order of magnitude greater than those from 1994 to 1996, when we measured the highest rates of parr-to-smolt survival (20.6 and 24.4%).  
    
In 2013, like other years, we observed that wild fish detected at Lower Granite dam early in the migration season have been significantly larger at release than fish detected later in the season.  Fish that passed the dam in April were on average 4.2 mm larger at the time of release than those fish passing in May and June.  This data suggests that fish size may influence migration timing or overwintering locations.

From 2011 through 2013, fish collected in locations with in-stream PIT detection (Secesh River, Lake, Valley, and Big Creek) were tagged using both standard 12-mm TX1400SST(PL) and 9-mm TX49011B9(PL) PIT tags.  Based on detections at downstream dams, we are able to look at the efficiency of the in-stream monitors for each of the tag types.  Comparison of detection efficiencies varied at the different locations with Valley Creek having an estimated 74.2% and 49% efficiency for 12-mm and 9-mm tags during the 2012-2013 out migration.  Based on these efficiencies, an estimated 43.1% of all parr marked with a 12-mm tag survived to migrate past the Valley Creek monitors and an estimated 43.2% of all parr marked with a 9-mm tag survived to pass these monitors.  Survival from the Valley Creek monitors to Lower Granite Dam was 22.4% and 13.6% respectively, for the 12-mm and 9-mm tagged parr.

Since 2008, we have had sufficient detection numbers at the Big Creek monitors to estimate survival to Lower Granite Dam.  However, detection rates at these monitors ranged only 9.2 12.9% during 2008 to 2012.  In 2013, improved detection efficiencies lead to a detection rate of 29.2% for fish tagged at Big Creek, providing us with more precise survival estimates.  Continued development and maintenance of the Big Creek monitoring sites, as well as, all other in-stream arrays in the Salmon River Basin is being conducted by the ISEMP Project.  

Timing patterns for individual populations and groups of populations have emerged over the years and range from early to late spring. During 2013, the 80th percentile passage (Lower Granite Dam) for fish from all Idaho and Oregon streams ranged from 9 to 33 days.  Annual climatic conditions appear directly related to the 2- to 3-week (average) passage-distribution shifts in timing of combined populations of wild fish over the years. Complex yearly interrelationships between flow and annual climatic conditions are primary factors contributing to passage timing. However, water temperatures in streams above the dam, turbidity, physiological development, variability in stock behavior, fish size, and yet unknown factors may all contribute substantially to wild smolt passage timing.

This study continues to supply managers with in-season information for management decisions related to flow augmentations, dam operations including spill, and transportation. Environmental monitoring in streams and climate/weather monitoring is continuing and relationships to parr and smolt movements will be developed in the future.