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 Little Goose 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

Before 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

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 in summer 1988.  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.  These run-timing differences appear typical for most streams for the first year's marking and recovery effort.  It should be pointed out that environmental conditions were unusual and rather severe for these groups of fish.  The wild fish had endured back-to-back drought years followed by a severe winter and late, cold spring.
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.  For example, during the second year, we again found the outmigration timing of wild stocks was much more protracted than for their hatchery counterparts and that wild smolts from summer Chinook salmon streams out-migrated much earlier than those from spring Chinook salmon streams.  Overall, however, the wild smolt out-migrations were much earlier than during the first year, coincidental with a much warmer, late winter and early spring period.  During the third year, we found little variability in the timing of hatchery stocks from the previous 2 years, even though environmental conditions differed considerably.  Wild stocks, on the other hand, out-migrated much later than during the first 2 years of study, even though flows were similarly low during all 3 years.  This final year of study was characterized by a cold, late winter and early spring.  
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.  
The present study began with the 1992 migration of wild Chinook salmon smolts (Achord et al. 1994).  Warm weather and high water temperatures in late winter and spring appeared to elicit an early migration timing of all wild smolts in 1992.  The migration timing of wild spring Chinook salmon smolts was earlier in 1992 than in the previous 3 years.  Also, most wild summer Chinook salmon smolts migrated earlier than wild spring Chinook salmon smolts.  However, as was observed during previous years, wild stocks exhibited protracted and variable timing at Lower Granite Dam.
           In 1993, cold weather and low water temperatures from late winter to early summer appeared to elicit a late migration timing; however, high flows during the third week of May moved a large portion of wild spring/summer Chinook salmon through the dams (Achord et al. 1995a).  As observed in previous years, wild stocks exhibited variable migration timing at Lower Granite Dam; however, the middle 80% passage time of wild fish stocks at the dam was more compressed in 1993 than in earlier years.
           In 1994, migration timing of wild spring/summer Chinook salmon smolts at Lower Granite Dam was similar to timing in 1990, and 1992, with peak passage in all 3 years occurring in April; however, peak detections of fish from individual streams in 1994 occurred from late April to late May (Achord et al. 1995b).  As observed in 1990 and 1992, 1994 was also warm during late winter and spring.
           Before 1995, we observed a 2-week shift in timing of wild fish at Lower Granite Dam between relatively warm and relatively cold years.  In the cold years of 1989, 1991, and 1993, 50% of all wild fish passed the dam by mid-May, while 90% passed by mid-June (except in 1993, when high flows moved 90% through the dam by the end of May).  In the warm years of 1990, 1992, and 1994, 50% of all wild fish passed this dam from 29 April to 4 May, and 90% passed by the end of May.  In 1995, we experienced intermediate weather conditions in late winter and early spring (compared to the previous 6 years) and observed intermediate passage timing at the dam, with 50 and 90% passage occurring on 9 May and 5 June, respectively (Achord et al. 1996a).  Sustained high flows from mid-May to early June in that year moved the later half of the wild fish migration through the dam at a more uniform rate than in previous years, and over 90% passed by the time peak flows occurred at the dam on 6 June.
            Due to extremely low adult spawning escapements in summers 1994, 1995, and 1996 parr abundance was at low levels in summers 1995, 1996, and 1997, with the exception of streams in the South Fork of the Salmon River.  As a result, the Idaho Department of Fish and Game requested that we greatly reduce any potentially negative handling impacts in summers 1995, 1996, and 1997 by restricting PIT tagging of wild parr to only a few streams.
            In 1996 and 1997, as observed in all previous migration years from 1989 to 1995, peak detections of wild spring/summer Chinook salmon smolts at Lower Granite Dam were highly variable and generally independent of river flows before 9 May; however, in all years, peak detections of wild fish coincide with peak flow at the dam from 9 May to the end of May.  In both 1995 and 1996, well over 90% of the wild fish had migrated passed Lower Granite Dam by the time peak flows occurred in June.  In 1997, high river flows from mid-April to mid-May moved most wild fish through the dam (Achord et al. 1998).  In 1989, we observed a period of peak detections of wild fish that coincided with peak flows at the dam in June (Achord et al. 1996b).  These data suggest that water reserved for fish during the outmigration may benefit more wild spring/summer Chinook salmon smolts if it is initiated around mid-May in most years and may be especially important in drought years.
            In 1996 and 1997, 50 and 90% passage dates of wild stocks combined (Idaho and Oregon streams) at Lower Granite Dam occurred on 3 and 22 May and 24 April and 21 May, respectively (Achord et al. 1997, 1998).  However, unlike previous years, few wild fish were marked as parr in 1995 and 1996 from Idaho streams; therefore, the 1996 and 1997 detections at the dam were composed of 91% and 73.5% fish from Oregon streams, respectively.  Therefore, we caution against comparing migration timing in 1996 and 1997 to previous years, since in all previous years less than 50% were from Oregon streams.
In 1998, we observed a warm late winter and spring period and the overall wild fish timing at Lower Granite Dam was similar to 1992 with the 50 and 90% passing by 1 and 25 May, respectively (Achord et al. 2000).  Beginning in 1998, statistical methods were developed to estimate parr-to-smolt survival of wild fish stocks to Lower Granite Dam and were used as a basis to determine stock timings (Sandford and Smith, 2002).  The overall average estimated parr-to-smolt survival for the combined stocks averaged 24.4% (range 16.1-48.4% depending on stream of origin).
In 1999, we observed different climatic conditions than in all previous migration years. In late winter, a near-record snow pack in the Snake River basin resulted in high flows during early spring in March.  However, the ensuing flows were moderated by very dry and cold conditions during the remaining spring and early summer period.  The fluctuating medium to high flows throughout the spring moved the wild fish through Lower Granite Dam as observed in warmer years, with 50% passing by 3 May and 90% passing by 30 May (Achord et al. 2001a).  The overall average estimated parr-to-smolt survival to the dam for the combined stocks averaged 19.9% (range 14.3-46.7% depending on stream of origin).
In 2000, we had a slightly below normal flow year with our highest flows occurring in April at Lower Granite Dam; along with more seasonal temperatures and climatic conditions throughout the spring.  Consequently, we observed a wild fish migration pattern similar to a warm year with 50% passing the dam by 6 May and 90% passing by 29 May (Achord et al. 2001b).  The overall average estimated parr-to-smolt survival to the dam for the combined stocks averaged 17.7% (range 11.2-35.5% depending on stream of origin).
In 2001, we had the lowest flow year since 1977 at Lower Granite Dam accompanied by a warmer-than-normal spring period.  Estimated parr-to-smolt survival to the dam averaged 19.5% (range 13.7-34.8%).  Peak detections of all wild fish at the dam occurred during low flows of 57.4 kcfs on 28 April, with a lesser peak on 14 May under moderate flows of 71.6 kcfs, just prior to peak flows for the year.  The 50th and 90th percentile passage occurred on 9 and 26 May, respectively.  In addition, length and weight measurements on 420 recaptured wild fish from six streams were conducted at Little Goose Dam in 2001.  These fish had grown an average of 43.3 mm in length and 11.4 g in weight over an average of 274 days. Their mean condition factor declined from 1.30 at release (parr) to 1.02 at recapture (smolt)(Achord et al. 2002).  This baseline growth information on these wild fish are important for nutrient and ecosystem studies in natal rearing areas started in 2002.
In 2002, the peak detections of wild fish at Lower Granite Dam occurred during moderate flows of 86.7 kcfs on 4 May (Achord et al. 2003).  The 50th and 90th percentile passage occurred on 3 and 29 May, respectively.  However, in 2002, we had slightly lower than normal temperatures and cooler than normal climatic conditions throughout the spring.
The estimated parr-to-smolt survival of wild fish to Lower Granite Dam average 14.3% (range 6.6-38.1% depending on stream of origin) in 2002.  Lengths and weights were taken on 483 recaptured fish (smolts) from 11 Idaho streams at Little Goose Dam in 2002.  Fish had grown an average of 39.7 mm in length and 9.0 g in weight over an average of 275 days.  Their mean condition factor declined from 1.28 at release (parr) to 1.00 at recapture (smolt).
In 2003, the peak detections at Lower Granite Dam of parr tagged during the late summer in 2002 (from the 15 streams in Idaho and 4 streams in Oregon) occurred during high and rapidly increasing flows of 146.7 kcfs on 26 May (Achord et al. 2004).  The 10th, 50th, and 90th percentile passage occurred on 18 April and 11 and 29 May, respectively.  Climatic conditions were similar to 2002 in 2003, with cooler than normal conditions throughout the spring and below normal flows until the last week of May when high flows occurred.  Therefore, although our previous observations support the importance of annual climatic conditions influencing overall migration timing of the stocks at the dam; clearly, complex interrelationships of several factors drive the annual migrational timing of the stocks (Achord et al. 2003).  
The estimated parr-to-smolt survival of wild fish at the dam averaged 8.8% (range 2.8-19.3% depending on stream of origin in 2003.  Lengths and weights were taken on 426 recaptured fish (smolts) from 15 Idaho streams at Little Goose Dam in 2003.  Fish had grown an average of 42.4 mm in length and 8.9 g in weight over an average of 282 days.  The mean condition factor declined from 1.41 at release (parr) to 1.00 at recapture (smolt).
In July 2002, two in-stream PIT-tag monitoring systems were installed in lower Valley Creek near Stanley, Idaho.  Of the 2,266 Chinook salmon parr, PIT tagged and released in Valley Creek above these monitors in summer 2002, 3.2% (72) were detected at the two monitoring systems in summer-fall, 2002 and spring 2003.  Of these stream-detected fish, 9.7% (7) were detected as smolts at downstream dams in 2003.  Development and improvements of the in-stream PIT-tag monitoring systems continued throughout 2002, 2003, and 2004.
In 2003-2004, estimated parr-to-smolt survival of wild fish at the dam averaged 8.1% (range 4.1-18.0% depending on stream of origin) (Achord et al. 2005).  The 10th, 50th, and 90th percentile estimated passage dates for these wild fish at the dam were 16 April, 3 May, and 26 May, respectively.
In a preliminary evaluation of PIT-tag in-stream monitoring on Valley Creek in 2003-2004; an estimated 28 to 40% of the summer-tagged Chinook salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 13.2%.  The proportions of parr/pre-smolts/smolts leaving Valley Creek were 58.7% in late summer/fall (August, September, October), 32.8% in winter (November, December, January, February), and 8.5% in spring (March, April, May, June).  The estimated parr-to-smolt survival to the dam for each of these groups was 6.6% for the late-summer/fall group, 16.9% for the winter group, and 43.9% for the spring group.  Wild fish parr-to-smolt growth rates as measured at Little Goose Dam in 2004 were very similar to growth rates observed in 2003.
In 2004-2005, estimated parr-to-smolt survival of wild fish at the dam averaged 8.4% (range 3.7-13.3% depending on stream of origin) (Achord et al. 2006).  The 10th, 50th, and 90th percentile estimated passages dates for these wild fish at the dam were 25 April, 7 May, and 24 May, respectively.
In a preliminary evaluation of PIT-tag in-stream monitoring on Valley Creek in 2004-2005; an estimated 41.5 to 46.4% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 13.9%.  The proportions of parr/pre-smolts/smolts leaving Valley Creek were 77.3% in late summer/fall, 14.0% in winter, and 8.7% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 10.9% for the late summer/fall group, 22.7% for the winter group, and 32.9% for the spring group.
Lengths and weights were taken on 656 recaptured fish (smolts) from 15 Idaho streams at Little Goose Dam in 2005.  Fish had grown an average of 44.5 mm in length and 9.6 g in weight over an average of 282 days.  The mean condition factor declined from 1.24 at release (parr) to 0.96 at recapture (smolt).
In 2005-2006, estimated parr-to-smolt survival of wild fish at Lower Granite Dam averaged 14.4% (range 6.8-37.1% depending on stream of origin) (Achord et al. 2007).  The 10th, 50th, and 90th percentile estimated passages dates for these wild fish at the dam were 18 April, 2 May, and 22 May, respectively.
In a preliminary evaluation of PIT-tag in-stream monitoring on Valley Creek in 2005-2006; an estimated 58.4% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 20.6%.  The proportions of parr/pre-smolts/smolts leaving Valley Creek were 45.6% in late summer/fall, 36.8% in winter, and 17.6% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 7.7% for the late summer/fall group, 44.3% for the winter group, and 18.1% for the spring group.
Lengths and weights were taken on 557 recaptured fish (smolts) from 15 Idaho stream populations at Little Goose Dam in 2006.  Fish had grown an average of 35.1 mm in length and 8.2 g in weight over an average of 266 days.  The mean condition factor declined from 1.27 at release (parr) to 1.07 at recapture (smolt).
In 2006-2007, estimated parr-to-smolt survival of wild fish (Idaho and Oregon) at Lower Granite Dam averaged 16.3% (range 4.5-29.7% depending on stream of origin) (Achord et al. 2008).  The 10th, 50th, and 90th percentile estimated passages dates for these wild fish at the dam were 15 April, 30 April, and 14 May, respectively.
In evaluation of PIT-tag in-stream monitoring on Valley Creek in 2006-2007; an estimated 28.9% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 37.0%.  The proportions of parr/pre-smolts/smolts leaving Valley Creek were 48.4% in late summer/fall, 43.2% in winter, and 8.4% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 17.6% for the late summer/fall group, 49.2% for the winter group, and 86.1% for the spring group.
Lengths and weights were taken on 275 recaptured fish (smolts) from 12 Idaho stream populations at Little Goose Dam in 2007.  Fish had grown an average of 43.2 mm in length and 9.0 g in weight over an average of 272 days.  The mean condition factor declined from 1.30 at release (parr) to 0.98 at recapture (smolt).
In 2007-2008, estimated parr-to-smolt survival of wild fish (Idaho and Oregon) at Lower Granite Dam averaged 19.4% (range 6.2-38.4% depending on stream of origin) (Achord et al. 2009).  The 10th, 50th, and 90th percentile estimated passages dates for these wild fish at the dam were 30 April, 11 May, and 23 May, respectively.
In evaluation of PIT-tag in-stream monitoring on Valley Creek in 2007-2008; an estimated 40.8% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 26.5%.  The proportions of parr/pre-smolts/smolts leaving Valley Creek were 71.6% in late summer/fall, 11.9% in winter, and 16.5% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 15.5% for the late summer/fall group, 48.0% for the winter group, and 58.5% for the spring group.  However, monitoring operations on Valley Creek experienced intermittent outages throughout 2007-2008, partially due to the development of a new monitoring system for the new SST PIT tag.
Lengths and weights were taken on 505 recaptured fish (smolts) from 12 Idaho stream populations at Little Goose Dam in 2008.  Fish had grown an average of 40.1 mm in length and 10.6 g in weight over an average of 288 days.  The mean condition factor declined from 1.25 at release (parr) to 1.05 at recapture (smolt).
In 2008-2009, estimated parr-to-smolt survival of wild fish (Idaho and Oregon) at Lower Granite Dam averaged 17.7% (range 10.8-30.0% depending on stream of origin) (report in progress).  The 10th, 50th, and 90th percentile estimated passages dates for these wild fish at the dam were 23 April, 2 May, and 20 May, respectively.
In evaluation of PIT-tag in-stream monitoring on Valley Creek in 2008-2009; an estimated 34.8% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 27.3%.  The proportions of parr/pre-smolts/smolts leaving Valley Creek were 70.7% in late summer/fall, 20% in winter, and 9.3% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 21.8% for the late summer/fall group, 54.8% for the winter group, and 27.1% for the spring group.  
In evaluation of PIT-tag in-stream monitoring on lower Big Creek in 2008-2009; for fish tagged in upper Big Creek, an estimated 55.2% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 24.6%.  The proportions of parr/pre-smolts/smolts leaving upper Big Creek (and detected in lower Big Creek) were 65.3% in late summer/fall, 20.4% in winter, and 14.3% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 14.5% for the late summer/fall group, 0% for the winter group, and 106% for the spring group.  
               In evaluation of PIT-tag in-stream monitoring on lower Big Creek in 2008-2009; for fish tagged in lower Big Creek, an estimated 88.5% of the summer-tagged salmon parr survived to move out of this stream and their estimated survival from that point to the dam was 28.9%.  The proportions of parr/pre-smolts/smolts leaving lower Big Creek were 57.6% in late summer/fall, 36.4% in winter, and 5.9% in spring.  The estimated parr-to-smolt survival to the dam for each of these groups was 24.0% for the late summer/fall group, 41.2% for the winter group, and 0% for the spring group.  Although, we were able to make survival estimates from detections at the Big Creek monitors in 2008-2009; we only detected 9.2% of the tagged fish.  These low detection rates were responsible for the extreme variability observed when estimating survival rates for various groups of fish to Lower Granite Dam (0-106%).  Increasing the number of fish tagged and/or the number of antennas should provide better precision for these survival estimates in the future.  Future developments, improvements, operations, and maintenance of the in-stream PIT tag monitoring systems in both Big Creek and Valley Creek will be conducted under project 2003-017-00, the ongoing Integrated Status and Effectiveness Monitoring Program (ISEMP). The transition of these responsibilities from Project 1991-028-00 to 2003-017-00 occurred during the Contract year 2010-2011.
              Lengths and weights were taken on 763 recaptured fish (smolts) from 14 Idaho stream populations at Little Goose Dam in 2009.  Fish had grown an average of 36.1 mm in length and 8.1 g in weight over an average of 271 days.  The mean condition factor declined from 1.27 at release (parr) to 1.04 at recapture (smolt).
             Timing patterns for individual populations and groups of populations have emerged over the years and range from early to late spring. 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.