Natural subyearling fall Chinook salmon in the Clearwater River emerge later, grow slightly slower, and become subyearling smolts later in the year than those in the Snake River.  Natural fall Chinook salmon produced in the Clearwater River frequently exhibit the reservoir-type life history (e.g., 60-85% without accounting for winter passage) and it is assumed that these subyearlings commonly pass dams undetected during the winter while the Passive Integrated Transponder (PIT)-tag monitors are not in operation.  Ignoring detections of yearlings that occur in the spring following release, a typical “survival” estimate to the tailrace of Lower Granite Dam (LGR) made for Clearwater fish made by use of Cormack-Jolly-Seber (CJS) methods might be 16%.  This estimate is a product of the probability of migrating as a subyearling smolt and passing the dams when the PIT-tag monitors are operated (e.g., 40%) and the probability of surviving to the tailrace of Lower Granite Dam (e.g., 40%).  That is, 16% = 40% x 40%.  The joint probability estimate in this example is 24 percentage points lower than actual survival.

The Comparative Survival Study (CSS) study design calculates smolt to adult returns (SARs) for inriver migrants (i.e., those that are not transported) as the number of returning adults divided by the number of smolts estimated to have passed Lower Granite Dam. The number of smolts estimated to have passed Lower Granite Dam is called a "Lower Granite Equivalent."  For simplicity, let's use the 16% CJS estimate of survival described above to illustrate bias in the calculation of SARs.  If we released 1000 smolts the Lower Granite Equivalent would be 160 (i.e., .16 x 1000).  If 16 adults returned, the SAR would be 10% (i.e., 16/160).  In reality, the true survival was 40%.  Therefore, the true Lower Granite Equivalent was 400 (i.e., .4 x 1000) and the true SAR was only 4%    In contrast to the inriver group, the Lower Granite Equivalent for the transport group is known with 100% certainty.  For example, if 1000 smolts are released and 400 are detected as they are routed to a barge, the Lower Granite Equivalent will be 400.  If 16 adults return the SAR for the transport group would be 4%.  So, under the CSS study design the inriver group (SAR = 10%) wins over the transport group (SAR = 4%) because the Lower Granite Equivalent for the transport group was biased low.  Note that this is example is oversimplified.  However, no one has modeled a range of "what if" scenarios to illustrate this situation for managers.  This is an important objective of our study.   The field tasks that follow will move us toward better estimating LGR equivalents.

During this study, we will assume that fish from the Clearwater will represent late migrants from the lower Hells Canyon reach of the Snake River.  This will allow us to focus our work on the Clearwater.  Migratory delay is one mechanism that contributes to a fish adopting a reservoir-type life history.  One related question is where does migratory delay occur?  The answer is significant because if fish delay near the confluence as we observed in 2006, then these fish will not benefit from management actions such as summer spill and transportation.  The timing of delay and the reinitiation of downstream movement will be of interest to managers in regard to these actions. Radio telemetry ( RT)  and acoustic telemetry (AT) tasks will identify when and where fish delay.  A related question will address the magnitude of delay in a release group and the fate of those fish.  It is currently assumed that fish that are not detected at Lower Granite are mortalities in survival estimation.  The first step is to determine the fates of fish in the lower Clearwater and upper reservoir to determine how much mortality is incurred by fish that delay in this area.  The mark-recapture data collected by RT will address this need.  The next step is to determine the fate of fish that reinitiate downstream movement in late summer and fall and determine the survival and fate of those fish.  AT will address this need by determining how many fish survive to reach the forebay of LGR and of those fish, how many will pass the dam, how many will stay in the forebay, and how many will not survive.  This is a critical piece of information needed to estimate LGR equivalents for SAR determination.  Finally, we need to relate the data we collect to potential environmental data that might influence the behaviors we see.  People always ask whether flow augmentation has something to do with the reservoir-type life history.  Putting hydraulic data together with the fish data will further our understanding of why fish delay and reinitiate downstream movement.

FY 2007/2008 through FY2010/2011 update:

In the 2007 and 2009 years of this study, hatchery juvenile fall Chinook salmon from the Clearwater River implanted with acoustic and radio transmitters experienced migration delay and relatively low probabilities of migrating and surviving through the Clearwater/Snake River transition zone and confluence (survival probability = 0.30–0.60 in 2007 and 0.30–0.35 in 2009).  Hydrologic conditions at the Snake-Clearwater confluence change drastically compared to the free-flowing Clearwater River.  Water velocity decreases and water temperature increases moving downstream through the transition and confluence zones; velocity and temperature differences are especially pronounced during late summer when cold water is released from Dworshak Dam and as river discharge decreases.  These changes in water quality may be related to the migration delay and low survival of transmittered juvenile salmon and perhaps wild migrating juvenile salmon; however, the exact causative mechanism is not yet known.      

Wild juvenile fall Chinook salmon captured in the lower Clearwater River (within a few km of the Snake River) in summer 2008 displayed visible signs of gas bubble disease (GBD) despite relatively low concentrations of total dissolved gas (TDG; 101% to 109%) recorded by a USACE-operated gage in the Clearwater River about 7 km upstream of the confluence.  Field measurements of total dissolved gas concentrations by PNNL in the lower Clearwater River from May–September 2009 verified that TDG fluctuated diurnally and peaked at about 110% in late afternoons of the August sampling period.  Because juvenile salmon have a relatively low probability of experiencing GBD when chronic TDG exposure is less than about 120% (Backman et al. 2002), additional hypotheses were explored that might explain the incidence of GBD in juvenile Chinook salmon caught in the lower Clearwater River.  

Our working theory is that juvenile Chinook salmon (hatchery and wild) migrating through the Clearwater/Snake River transition zone and confluence in late summer may incur GBD due to the great difference in water temperature between the two rivers, which can produce gas supersaturation as the cold water is warmed.  Just upstream of the confluence in late summer, the Clearwater River is about 10–12°C and TDG varies from about 100–110%.  In contrast, the surface layer temperature of the Snake River at the confluence can approach 25°C.  Based on the physical properties of water and dissolved gas, fish acclimated to 10°C and 100% TDG that are warmed to 25°C would experience a difference in partial pressure (?P) of 250.2 mm Hg or 135% TDG (assuming barometric pressure = 760 mm Hg and salinity = 0.0 ppt; Colt 1984).  A total dissolved gas concentration of 135% exceeds the “safe” concentration of 120% by Backman et al. (2002) yet still does not account for supersaturated waters of the Clearwater or Snake rivers produced from daily photosynthetic activity (which would further increase total dissolved gas concentrations that fish experience).  Consequently, these conditions may be directly lethal to juvenile salmon or may increase the probability of indirect mortality (e.g., predation susceptibility) related to the sublethal effects of GBD.    

Temperature increases alone are known to cause mortality of juvenile Chinook salmon; however, we know of no studies that have evaluated gas bubble disease following an increase in temperature and its relationship to mortality in juvenile fall Chinook salmon.  In a previous study, groups of juvenile spring Chinook salmon acclimated to 10°C and supersaturated (125-130%) TDG and exposed to 25°C had mean times to death of 7.5 min (Ebel et al. 1971).  Although the authors mention in their methods that gas bubble disease was evaluated for fish that died, no results of gas bubble disease and its effect on mortality were reported or discussed.  Thus, it is uncertain what the causative mechanism of death was for fish exposed to the increased temperature.  Further, spring Chinook salmon were used in Ebel et al. (1971) and may have differential thermal and gas bubble disease tolerance than fall Chinook salmon (Sauter et al. 2001), which should be evaluated to understand the probability of mortality of fall Chinook salmon.  

Behavioral data of transmittered, hatchery juvenile fall Chinook salmon in August 2009 indicates that fish made repeated upstream forays back to the lower Clearwater River after encountering the Clearwater/Snake confluence and many fish “mulled” just upstream of the confluence until the thermal difference between the rivers dissipated in mid-September (Tiffan et al. 2010).  Based on the potential for fish to incur gas bubble disease due to the temperature difference between these two rivers in late summer, it is plausible that juvenile salmon elect to stay in the Clearwater River until these conditions dissipate.  This may be the reason that wild juvenile salmon caught by Tiffan et al. (2009) in the lower Clearwater River had GBD despite the relatively low measured concentrations of total dissolved gas in the Clearwater River.  To evaluate the potential for juvenile fall Chinook salmon to incur gas bubble disease through the Clearwater/Snake transition zone and confluence in summer, we will perform a controlled laboratory study in FY11/12 to simulate acclimation and challenge conditions experienced by fish in the wild.  

FY11/12 study update:

Results on the FY11/12 experiment to acclimate fish at Clearwater River conditions and expose them to conditions that they may experience when migrating through the Snake River are still being analyzed.  However, preliminary results indicate that the largest temperatures change from 10 to 25 C resulted in the highest proportion of mortality, which was expected based on other previous studies.  We are still analyzing the data to determine if the interaction between fish acclimated to 110% TDG that undergo a 5,10, or 15 degree Celsius increase in temperature have higher rates of GBD than control fish.  

Interestingly, our field measurements of total dissolved gas in the summer of 2011 documented gas concentrations of 122.5% (at 6-m depth) in early August in the Snake River immediately downstream of the Clearwater River confluence.  This high concentration of total dissolved gas was present near the thermocline at the river-right bank of the Snake River immediately downstream of the confluence.  However, the difference in temperature between the Snake and Clearwater rivers was only about 8 degrees Celsius during this period.  Thus, we can reasonably assume that at higher differences in water temperature between the two sources, total dissolved gas concentrations would be even higher than 122.5%.  Although this gas concentration was recorded at 6-m depth, these high concentrations of total dissolved gas have the potential to be dangerous to migrating juvenile salmonids if they acclimate to this gas level and then swim to the surface.  Juvenile salmonids acclimated to high gas concentrations are considered "safe" if they remain below the gas compensation depth, which is about 1-m depth depending on the total dissolved gas concentration of the water, but if fish acclimated to these levels swim to the water surface, this gas could be released from solution (due to decreased barometric pressure) and has the potential to cause mortal injuries.

Based on the above preliminary results, and further diagnosis of data collected in FY11/12 from both the laboratory and field components, we will conduct a laboratory study in FY12/13 to assess the combined effects of low total dissolved gas concentration acclimation (100% and 105%) and temperature change (5, 10, and 15C) on the predator-avoidance ability of juvenile Chinook salmon.  Other studies have documented the effects of temperature changes on juvenile Chinook salmon predator avoidance, however, no known studies have studied the combined effect of slightly supersaturated total dissolved gas and drastic temperature changes on predator avoidance.  

The PNNL objective for Project 2002-032-00 in FY2012/2013 is:

1.  Evaluate predation susceptibility of juvenile fall Chinook salmon acclimated to Clearwater River conditions (105% TDG and 10degC) and exposed to predators in Snake River conditions (105% TDG and 15, 20, or 25 C) with varying levels of temperature increase (e.g., 0 C (control), 5 C, 10 C, and 15 C).