Quantifying the Behavioral Response of Spawning Chum Salmon to Elevated Discharges from Bonneville Dam, Columbia River : Annual Report 2005-2006.

In unimpounded rivers, Pacific salmon (Oncorhynchus spp.) typically spawn under relatively stable stream flows, with exceptions occurring during periodic precipitation events. In contrast, hydroelectric development has often resulted in an artificial hydrograph characterized by rapid changes in discharge and tailwater elevation that occur on a daily, or even an hourly basis, due to power generation (Cushman 1985; Moog 1993). Consequently, populations of Pacific salmon that are known to spawn in main-stem habitats below hydroelectric dams face the risks of changing habitat suitability, potential redd dewatering, and uncertain spawning success (Hamilton and Buell 1976; Chapman et al. 1986; Dauble et al. 1999; Garland et al. 2003; Connor and Pflug 2004; McMichael et al. 2005). Although the direct effects of a variable hydrograph, such as redd dewatering are apparent, specific effects on spawning behavior remain largely unexplored. Chum salmon (O. keta) that spawn below Bonneville Dam on the Columbia River are particularly vulnerable to the effects of water level fluctuations. Although chum salmon generally spawn in smaller tributaries (Johnson et al. 1997), many fish spawn in main-stem habitats below Bonneville Dam near Ives Island (Tomaro et al. 2007; Figure 1). The primary spawning area near Ives Island is shallow and sensitive to changes in water level caused by hydroelectric power generation at Bonneville Dam. In the past, fluctuating water levels have dewatered redds and changed the amount of available spawning habitat (Garland et al. 2003). To minimize these effects, fishery managers attempt to maintain a stable tailwater elevation at Bonneville Dam of 3.5 m (above mean sea level) during spawning, which ensures adequate water is provided to the primary chum salmon spawning area below the mouth of Hamilton Creek (Figure 1). Given the uncertainty of winter precipitation and water supply, this strategy has been effective at restricting spawning to a specific riverbed elevation and providing minimum spawning flows that have the greatest chance of being maintained through egg incubation and fry emergence. However, managing the lower Columbia River for a stable tailwater elevation does not provide much operational flexibility at Bonneville Dam, which has little storage capacity. When river discharges increase due to rain events, the traditional approach has been to pass excess water at night to maintain stable tailwater elevations during the daytime. The underlying assumption of this strategy, referred to as reverse load following, is that fish do not spawn at night. However, Tiffan et al. (2005) showed that this assumption is false by documenting nighttime spawning by chum salmon in the Ives Island area. Similarly, McMichael et al. (2005) reported nighttime spawning by Chinook salmon (O. tshawytscha) in the Columbia River, indicating that diel spawning may be a common occurrence in Pacific salmon. During the latter portion of the chum spawning period in December 2003 and 2004, discharges from Bonneville Dam increased from an average of 3,398 m3/s (tailwater elevation {approx} 3.5 m above mean sea level) during the day to over 5,664 m3/s (tailwater elevation {approx} 5.1 m) at night, with peak discharges of 7,080 m{sup 3}/s (tailwater elevation {approx} 6.1 m). This caused concern among fishery managers regarding the potential effects of these high discharges on this population of spawning chum salmon, which is listed under the Endangered Species Act (National Oceanic and Atmospheric Administration 1999). We hypothesized that increased water velocities associated with elevated tailwaters might alter chum salmon spawning behavior if water velocities at redd locations increased beyond the range of suitability (>0.8 m/s; Salo 1991). In 2005, we investigated the movement and behavioral responses of spawning chum salmon at Ives Island to increased tailwater elevations at Bonneville Dam. We used acoustic telemetry to determine if the higher velocities associated with increased tailwater elevations caused fish to leave their redds. We related the duration fish were away from redds and the distances moved to water velocities estimated from a two-dimensional hydrodynamic model. Finally, we described specific changes in spawning behavior (e.g., nest digging; swimming activity) during elevated-tailwater tests using a dual-frequency identification sonar (DIDSON)

Post-Release Attributes and Survival of Hatchery and Natural Fall Chinook Salmon in the Snake River : Annual Report 1999.

This report summarizes results of research activities conducted in 1999 and years previous. In an effort to provide this information to a wider audience, the individual chapters in this report have been submitted as manuscripts to peer-reviewed journals. These chapters communicate significant findings that will aid in the management and recovery of fall chinook salmon in the Columbia River Basin. Abundance and timing of seaward migration of Snake River fall chinook salmon was indexed using passage data collected at Lower Granite Dam for five years. We used genetic analyses to determine the lineage of fish recaptured at Lower Granite Dam that had been previously PIT tagged. We then used discriminant analysis to determine run membership of PIT-tagged smolts that were not recaptured to enable us to calculate annual run composition and to compared early life history attributes of wild subyearling fall and spring chinook salmon. Because spring chinook salmon made up from 15.1 to 44.4% of the tagged subyearling smolts that were detected passing Lower Granite Dam, subyearling passage data at Lower Granite Dam can only be used to index fall chinook salmon smolt abundance and passage timing if genetic samples are taken to identify run membership of smolts. Otherwise, fall chinook salmon smolt abundance would be overestimated and timing of fall chinook salmon smolt passage would appear to be earlier and more protracted than is the case

Identification of the Spawning, Rearing, and Migratory Requirements of Fall Chinook Salmon in the Columbia River Basin, Annual Report 1995.

This document is the 1995 annual progress report for selected studies of fall chinook salmon Oncorhynchus tshawytscha conducted by the Biological Resources Division (BRD) of the U.S. Geological Survey and the U.S. Fish and Wildlife Service. Activities were funded by the Bonneville Power Administration (BPA) through funding of Project 91-029. The decline in abundance of fall chinook salmon in the Snake River basin has become a growing concern. In 1992, Snake River fall chinook salmon were listed as {open_quotes}threatened{close_quotes} under the Endangered Species Act. Effective recovery efforts for fall chinook salmon cannot be developed until we increase our knowledge of the factors that are limiting the various life history stages. This study attempts to identify those physical and biological factors which influence spawning of fall chinook salmon in the free-flowing Snake River and their rearing and seaward migration through Columbia River basin reservoirs

Identification of the Spawning, Rearing, and Migratory Requirements of Fall Chinook Salmon in the Columbia River Basin, Annual Report 1993.

Recovery efforts for the endangered fall chinook salmon necessitates knowledge of the factors limiting the various life history stages. This study attempts to identify those physical and biological factors which affect spawning of the fish in the free-flowing Snake River and their rearing seward migration through Columbia River basin reservoirs. The spawning was generally a November event in 1993, with some activity in late Oct. and early Dec. Spawning habitat availability was assessed by applying hydraulic and habitat models to known fall chinook salmon spawning sites. Juveniles were seined and PIT tagged in the free-flowing Snake River, and in the Columbia River in he Hanford Reach and in McNary Reservoir. Subyearling fish were marked at McNary Dam to relate river flow and migration patterns of juveniles to adult returns. Hydroacoustic surveys were conducted on McNary and John Day reservoirs and in net pens

Identification of the Spawning, Rearing, and Migratory Requirements of Fall Chinook Salmon in the Columbia River Basin, Annual Report 1994.

Spawning ground surveys were conducted in 1994 as part of a five year study of Snake River chinook salmon Oncorhynchus tshawyacha begun in 1991. Observations of fall chinook salmon spawning in the Snake River were limited to infrequent aerial red counts in the years prior to 1987. From 1987-1990, red counts were made on a limited basis by an interagency team and reported by the Washington Department of Fisheries. Starting in 1991, the U.S. Fish and Wildlife Service (USFWS), and other cooperating agencies and organizations, expanded the scope of spawning ground surveys to include: (1) additional aerial surveys to improve red counts and provide data on the timing of spawning; (2) the validation (ground truthing) of red counts from aerial surveys to improve count accuracy; (3) underwater searches to locate reds in water too deep to allow detection from the air; and (4) bathymetric mapping of spawning sites for characterizing spawning habitat. This document is the 1994 annual progress report for selected studies of fall chinook salmon. The studies were undertaken because of the growing concern about the declining salmon population in the Snake River basin

Snake River Fall Chinook Salmon Life History Investigations, Annual Report 2007.

In 2007, we used radio and acoustic telemetry to evaluate the migratory behavior, survival, mortality, and delay of subyearling fall Chinook salmon in the Clearwater River and Lower Granite Reservoir. Monthly releases of radio-tagged fish ({approx}95/month) were made from May through October and releases of 122-149/month acoustic-tagged fish per month were made from August through October. We compared the size at release of our tagged fish to that which could have been obtained at the same time from in-river, beach seine collections made by the Nez Perce Tribe. Had we relied on in-river collections to obtain our fish, we would have obtained very few in June from the free-flowing river but by late July and August over 90% of collected fish in the transition zone were large enough for tagging. Detection probabilities of radio-tagged subyearlings were generally high ranging from 0.60 (SE=0.22) to 1.0 (SE=0) in the different study reaches and months. Lower detection probabilities were observed in the confluence and upper reservoir reaches where fewer fish were detected. Detection probabilities of acoustic-tagged subyearlings were also high and ranged from 0.86 (SE=0.09) to 1.0 (SE=0) in the confluence and upper reservoir reaches during August through October. Estimates of the joint probability of migration and survival generally declined in a downstream direction for fish released from June through August. Estimates were lowest in the transition zone (the lower 7 km of the Clearwater River) for the June release and lowest in the confluence area for July and August releases. The joint probability of migration and survival in these reaches was higher for the September and October releases, and were similar to those of fish released in May. Both fish weight and length at tagging were significantly correlated with the joint probability of migrating and surviving for both radio-tagged and acoustic-tagged fish. For both tag types, fish that were heavier at tagging had a higher probability of successfully passing through the confluence (P=0.0050 for radio-tagged fish; P=0.0038 for acoustic-tagged fish). Radio-tagged fish with greater weight at tagging also had a higher probability of migrating and surviving through both the lower free-flowing reach (P=0.0497) and the transition zone (P=0.0007). Downstream movement rates of radio-tagged subyearlings were highest in free-flowing reaches in every month and decreased considerably with impoundment. Movement rates were slowest in the transition zone for the June and August release groups, and in the confluence reach for the July release group. For acoustic-tagged subyearlings, the slowest movement rates through the confluence and upper reservoir reaches were observed for the September release group. Radio-tagged fish released in August showed the greatest delay in the transition zone, while acoustic-tagged fish released in September showed the greatest delay in the transition zone and confluence reaches. Across the monthly release groups from July through September, the probability of delaying in the transition zone and surviving there declined throughout the study. All monthly release groups of radio-tagged subyearlings showed evidence of mortality within the transition zone, with final estimates (across the full 45-d detection period) ranging from 0.12 (SE not available) for the May release group to 0.58 (SE = 0.06) for the June release group. The May and September release groups tended to have lower mortality in the transition zone than the June, July, and August release groups. Live fish were primarily detected away from shore in the channel, whereas all dead fish were located along shorelines with most being located in the vicinity of the Memorial Bridge and immediately upstream. During the May detection period, before the implementation of summer flow augmentation, temperatures in the Clearwater River and Snake River arms of Lower Granite Reservoir and the downstream boundary of the confluence ranged from 8 to 17 C. During the June-August detection periods, however, temperatures in the Clearwater River arm ranged from 10-16 C down to 7 m and the Snake River arm was above 20 C down to a depth of 9 m. Incomplete mixing between the two water sources resulted in significant vertical temperature variation at the downstream boundary of the confluence during a large portion of the June-August detection periods. This variation diminished during the September and October detection periods when temperatures once again fell to 17 C and lower and eventually became uniformly distributed throughout the water column in the confluence

A field evaluation of the growth and survival of age-0 Oncorhynchus mykiss tagged with 8-mm passive integrated transponder (PIT) tags

Abstract Background In fish tagging studies, tag size limits the size of fish that can be tagged, the fraction of a population that can be represented, and ultimately inferences that can be made about the study population, particularly when juvenile fish are the subject of interest. Introduction of an 8-mm passive integrated transponder (PIT) reduced the minimum taggable size of fish, but it has not been evaluated in field trials. We evaluated the growth and survival of age-0 Oncorhynchus mykiss tagged with 8-mm PIT tags in four streams in southwest Washington, USA. Results A total of 351 PIT tagged fish and 340 control fish (marked with pelvic fin clips) were released, but recapture rates were low, particularly for control fish. Growth in length and mass did not differ between small (42–54 mm) and large (55–64 mm) PIT tagged fish. There was a slightly positive, but weak, relation between tag burden and growth in mass; however, there was considerable variability in this relation (R 2 = 0.115). Summer to autumn joint probability of fish surviving and remaining in the study area estimated with a Bayesian mark-recapture model ranged from 0.228 to 0.478 in study streams. We found no significant relation between tag burden and survival, suggesting neither tag burden nor fish size at tagging affected survival. Conclusions Although this study was limited in scope, it provided insight into how age-0 O. mykiss tagged with 8-mm PIT tags grew and survived under natural conditions. We showed that fish as small as 42 mm could be tagged without detrimental effects, which should allow researchers to represent a larger portion of study populations through PIT tagging