Title: Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Lower Columbia River

Since June 2007, the project team has collected monthly beach seine samples and associated environmental data to identify juvenile salmon migration characteristics and associations between fish and habitat in various shallow, tidal freshwater areas of the Columbia River near the Sandy River delta.  This time series of data on fish community structure, salmonid density, genetic stock identification, fish diet, habitat vegetation, substrate, bathymetry, and other monitored indicators is addressing the importance of tidal freshwater habitats to listed salmonids, especially during fall and winter periods.  This information will be applied by resource managers and other decision-makers to guide habitat restoration efforts to increase salmon survival and adult return rates.  The scope of work for Year 3  (May 2009 through April 2010) of the study titled “Ecology of Juvenile Salmonids in Shallow Tidal Freshwater Habitats in the Lower Columbia River” (or the Tidal Freshwater Monitoring [TFM] Study for short) is presented herein.

UPDATE:  The contract is being amended for a NCTE to extend the end date to 12/31/10 to allow enough time to complete a final report and to make the transition to ACOE funding for this work starting in 2010-2011.

UPDATE (5/5/10):  The contract will be modified to add $36,000 for processing and anlysis of genetics samples from juvenile salmon collected in tidal freshwater habitats.  background and justificatioon follow.
What is the TFM project?  Project 2005-001-00, the Tidal Freshwater Monitoring (TFM) project, has been working to resolve the critical uncertainty about use of tidal freshwater habitats by upriver stocks, e.g., Snake River fall Chinook salmon.  Genetics analysis is fundamental to this research because it provides an estimate of the stock of origin.  We are working to relate the genetics data to data collected year-round on juvenile Chinook spatial and temporal distribution, length, weight, and diet.  We also study residence times of tagged juvenile Chinook salmon during winter in tidal freshwater; knowing the genetic stock of the tagged fish is essential to interpreting residence time data.  And, when TFM data for June 2007 through April 2010 are synthesized during summer 2010, the genetics component will be essential to the findings and their management implications.  
Which BiOp RPAs does the TFM project address?  The TFM project directly addresses 4 of the 16 estuary RME subactions.  
• RPA Action 59: Monitor and Evaluate Migration Characteristics and Estuary/Ocean Conditions.  
o Subaction 59.4: Evaluate migration through and use of a subset of various shallow-water habitats from Bonneville Dam to the mouth toward understanding specific habitat use and relative importance to juvenile salmonids.
• RPA Action 60: Monitor and Evaluate Habitat Actions in the Estuary.  
o Subaction 60.2: Evaluate the effects of selected individual habitat restoration actions at project sites relative to reference sites and evaluate post-restoration trajectories based on project-specific goals and objectives.
• RPA Action 61: Investigate Estuary/Ocean Critical Uncertainties.  
o Subaction 61.1 Continue work to define the ecological importance of the tidal freshwater, estuary, plume, and nearshore ocean environments to the viability and recovery of listed salmonid populations in the Columbia River Basin.  
o Subaction 61.3: Investigate the importance of early life history of salmon populations in tidal fresh water of the lower Columbia River.
How did we end up with 600 fin clips and no money to analyze them?  The TFM project has been collecting and analyzing genetics data since its inception in 2007.  However, during 2009/2010 sampling from Cowlitz to the Lewis rivers and in the Sandy River delta and vicinity, we captured more juvenile Chinook salmon than we had budgeted for genetics analysis.  But, since the fish were in hand and the effort had been expended to capture them, we decided the prudent course of action was to collect the fin clip because we were aware of the shortage of genetics data on salmon in tidal freshwater habitats.  
What will the additional 600 data points tell us that we don’t already know?  Associations between juvenile salmon and habitat usage are hampered by high variability in fish abundance, much less variability in genetic stock.  Increasing the sample size by 600 will provide an 40% increase for the TFM project 2007-2010.  Importantly, more 300 of the samples we would add are from unmarked Chinook sampled in January and February 2010.  No genetic data currently exists for fish sampled in Reaches D-G during these months.  This will strengthen the TFM data set and the inferences that can be drawn from it during the 2010 synthesis.  
What other BiOp-related work funded by BPA will benefit from this additional analysis?  The Habitat Restoration Strategy project by Simenstad and Trask would be interested in these data.  In general terms, their strategy is to target restoration to locations and habitats being used by specific upriver stocks of interest.  The strategy relies on genetics data from multiple sources.
To summarize, why is this work necessary to meet the BiOp?  Without genetic stock identification, managers will not know if restoration actions will be benefiting listed upriver stocks.