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Seasonal and decadal-scale channel evolution on the dammed Elwha River, Washington

More than 75,000 dams exist in the continental United States to provide water storage, flood control, and hydropower generation (Graf, 1999). Many of these were built during the early twentieth century and are due for relicensing consideration now and in the near future. The cost of repairing aging dams, together with growing understanding of the ecologic effects of river regulation (Williams and Wolman, 1984; Dynesius and Nilsson, 1994; Graf, 1999, 2003; Yang et al., 2007), in some places have prompted dam removal, facilitating restoration of riparian habitat to a more natural state. In the Pacific Northwest region of the U.S., river-restoration efforts are commonly targeted to improve habitat quality for native salmonid fish species, many runs of which have declined precipitiously from their historical conditions (owing, in part, to overfishing and habitat loss and degradation) and are now endangered (e.g., Nehlsen, 1997; Larsen et al., 2004; Pess et al., 2008). Removal of dams that block the upstream migration of anadromous fish is considered an important step toward any potential recovery of Pacific Northwest salmon and steelhead populations.

Washington↗

Genetic differences in growth, migration, and survival between hatchery and wild steelhead and Chinook salmon: Introduction and executive summary

This report presents results of studies testing for genetically based differences in performance (growth, migration, and survival) between hatchery and wild populations of steelhead and Chinook salmon (Project Number 90-052). The report is organized into 10 chapters with a general study introduction preceding the first chapter. A growing body of data shows that domestication and a resulting loss of fitness for natural rearing occur in hatchery populations of anadromous salmonids; however, the magnitude of domestication will vary among species and hatchery programs. Better information on domestication is needed to accurately predict the consequences when hatchery and wild fish interbreed. The intent of hatchery supplementation is to increase natural production through introduction of hatchery fish into natural production areas. The goal of this study was to provide managers with information on the genetic risks of hatchery supplementation to wild populations of Columbia River Basin summer steelhead and spring Chinook salmon.

Book chapter↗

Development of a bioenergetics model for age-0 American Shad

Bioenergetics modeling can be used as a tool to investigate the impact of non-native age-0 American shad (Alosa sapidissima) on reservoir and estuary food webs. The model can increase our understanding of how these fish influence lower trophic levels as well as predatory fish populations that feed on juvenile salmonids. Bioenergetics modeling can be used to investigate ecological processes, evaluate alternative research hypotheses, provide decision support, and quantitative prediction. Bioenergetics modeling has proven to be extremely useful in fisheries research (Ney et al. 1993,Chips and Wahl 2008, Petersen et al. 2008). If growth and diet parameters are known, the bioenergetics model can be used to quantify the relative amount of zooplankton or insects consumed by age-0 American shad. When linked with spatial and temporal information on fish abundance, model output can guide inferential hypothesis development to demonstrate where the greatest impacts of age-0 American shad might occur.

Report↗

Guidelines for conducting Smolt survival studies in the Columbia River

For more than a decade, investigators from different research groups in the Pacific Northwest have been using electronic tags to estimate survival of salmonid smolts as they migrate seaward past hydroelectric dams and through impoundments on the Snake and Columbia Rivers. Over the years, they have refined both analytical and field methods associated with such studies. In this collaborative paper, they synthesize years of experience to formulate a set of guidelines that may assist others with the design and execution of survival studies involving smolts during their migratory phase.

Report↗

Genetic differences between hatchery and wild steelhead for growth and survival in the hatchery and seaward migration after release (Study sites: Dworshak Hatchery and Clearwater Hatchery; Stocks: Dworshak hatchery and Selway River wild; Year classes: 1994 and 1995)

Various studies suggest that sea ranching of anadromous salmonids can result in domestication (increased fitness in the hatchery program) and a loss of fitness for natural production; however, the mechanism has not been characterized adequately. We artificially spawned hatchery and wild steelhead Oncorhynchus mykiss from the Clearwater River, Idaho, reared the resulting genetically marked (at the PEPA allozyme locus) progeny (HxH, HxW from hatchery females and wild males, and WxW) in hatcheries, and tested for differences in survival, growth, early maturation, downstream migration, and adult returns. Rearing treatments were mixed (crosses reared together) and separate (crosses reared separately from each other) at the hatchery of origin for the hatchery population where smolts are produced in one year, and at a nearby hatchery employing lower rations, lower winter temperatures, and two years of rearing to more closely mimic the natural life history (natural smolt age = 2-4 years). The hatchery population had been artificially propagated for six generations at the onset of our study. We found little or no difference in survival in the hatchery but substantially higher rates of growth and subsequent downstream migration for HxH than for WxW fish. Faster growth for HxH fish resulted in greater size at release which contributed to their higher migration rate, but other as yet uncharacterized traits also affected migration since the migration difference between crosses was apparent even within size classes. Growth of WxW fish was slower in the mixed than in the separate treatment indicating that WxW fish were competitively inferior to HxH fish in the hatchery environment. Incidence of precocious males was higher for WxW than for HxH fish in the separate but not in the mixed treatment. Incidence of HxH precocious males was similar between treatments. Apparently, the presence of HxH fish suppressed high incidence of early maturation by WxW males. A direct effect beyond the suppression of WxW growth by HxH fish was involved because the effect persisted within size categories. In-hatchery survival and growth of WxW relative to HxH fish may have been better with two-year rearing than in the standard one-year program (differences were consistent but small and non-significant); however, performance remained substantially worse for progeny of wild fish. Greater downstream migration for HxH than for WxW fish was primarily due to greater residualization for WxW than for HxH fish near the smolt release site rather than to immediate differential mortality. By August the residuals had lost condition compared to their condition in the hatchery the previous March, a month before release, and the residuals produced almost no smolts the following spring. Adult return rate was higher for HxH than for WxW fish for one year-class, consistent with the difference in downstream migration; only three adults (all WxW) returned from the other. Intermediate performance by HxW fish on growth, early maturation, downstream migration, and adult returns corroborated the genetic basis of the stock differences. Natural selection after release from the hatchery favored fish that performed well in the hatchery (grew fast, didn’t mature early, and excelled in other as yet uncharacterized traits) and genetically changed (domesticated) the wild population to resemble the hatchery population.

Idaho↗

Influence of a low intensity electric sea lion deterrence system on the migratory behavior of fishes in the upstream migrant tunnel (UMT) at Bonneville Dam.

Predation by pinnipeds, such as California sea lions (Zalophus alifornianus), Pacific harbor seals (Phoca vitulina), and Stellar sea lions (Eumetopias jubatus) on returning adult Pacific salmon (Oncorhynchus spp.) in the Columbia River basin has become an increasing concern for fishery managers trying to conserve and restore threatened and endangered runs of salmonids. As a result, Smith-Root Incorporated (SRI; Vancouver, Washington) proposed a demonstration project to evaluate the potential of an electrical array to deter marine mammals (SRI 2007). The objective of their work was to develop, deploy, and evaluate a passive, integrated electric and sonar array that selectively inhibits upstream marine mammal movements and predation, without injuring pinnipeds or affecting anadromous fish migrations. However, before such a device could be placed in the field, concerns by regional fishery managers about the potential effects of such a device on the migratory behavior of or injury to Pacific salmon, steelhead (O. mykiss), Pacific lampreys (Entoshpenus tridentata), and white sturgeon (Acipenser transmontanus) needed to be addressed.

Oregon, Washington↗

Snake River fall Chinook salmon life history investigations: Annual report 2011 (April 2011 - March 2012)

Executive Summary Chapter One &ndash; This chapter was published in the Transactions of the American Fisheries Society in 2012. We conducted a three-year radiotelemetry study in the lower Snake River to answer the questions: do fall Chinook salmon juveniles pass dams during winter when bypass systems and structures designed to prevent mortality are not operated; does downstream movement rate vary annually, seasonally, and from reservoir to reservoir; and, what are some of the factors that contribute to annual, seasonal, and spatial variation in downstream movement rate? Fall Chinook salmon juveniles moved downstream up to 169 km and fast enough (7.5 km/d) such that large percentages (up to 93%) of the fish passed one or more dams during winter. Mean downstream movement rate varied annually (9.2-11.3 km/d), increased from winter (7.5 km/d) to spring (16.4 km/d), and increased (6.9-16.8 km/d) as fish moved downstream from reservoir to reservoir. Fish condition factor at tagging explained some of the annual variation ( P &le; 0.01) in downstream movement rate, whereas water particle velocity ( P &le;0.0001) and temperature ( P &le;0.0001) explained portions of the seasonal variation. An increase in migrational disposition as fish moved downstream helped explain the spatial variation ( P =0.05-0.07). The potential cost of winter movement might be reduced survival due to turbine passage when the bypass systems and spillway passage structures are not operated. Efforts to understand and increase passage survival of winter migrants in large impoundments might help to rehabilitate some imperiled anadromous salmonid populations. Chapter Two &ndash; Natural juvenile fall Chinook salmon in the Snake and Clearwater rivers exhibit two life history strategies. &ldquo;Ocean-type&rdquo; fish migrate out to the ocean in their first summer of life as subyearlings, but &ldquo;reservoir-type&rdquo; fish delay seaward migration during the summer, and some overwinter in reservoirs before continuing their migration the following spring as yearlings. Earlier emerging fish produced in the Snake River tend to adopt the ocean-type life history whereas many of the later emerging fish from the Clearwater River tend to adopt the reservoirtype life history. The underlying cause of the reservoir-type life history is poorly understood, but we believe there may be link to physiological development. We used traditional markers of the parr-smolt transformation (smoltification), including gill Na + /K + -ATPase activity and thyroid hormone levels, along with gene expression microarrays to assess the development of ocean-type juvenile fall Chinook salmon and then compared it to that of juvenile fall Chinook salmon from the Clearwater River. We showed that parr in the Snake River are physiologically distinct from actively-migrating smolts but smolts migrating early and late in the summer and fall are physiologically similar. Juvenile fall Chinook salmon collected from the Clearwater River were similar in size to early-migrating smolts in the Snake River but were most physiologically similar to Snake River parr. Genes differentially expressed between Snake River parr and smolts and between fish from the Clearwater River and smolts from the Snake River were involved in the cell cycle, steroid metabolism and other metabolic pathways, and DNA repair and packaging. Many of the genes differentially expressed in these comparisons had expression patterns that correlated with gill Na + /K + -ATPase activity, suggesting that they were related to smoltification and migration status. Chapter Three &ndash; Natural subyearlings produced in the Clearwater River are exposed to cool (~10-12&deg;C) temperatures when water is released from Dworshak Reservoir for summer flow augmentation. Total dissolved gas (TDG) levels range from 100-110% in the lower Clearwater iv River. When fish move into the Snake River, they encounter temperatures up to 24&deg;C at the surface which have the potential to incur gas bubble disease (GBD) in fish as dissolved gases in their bodies expand under warmer temperatures. This may result in both direct and indirect mortality, but this situation has been little studied. We conducted laboratory experiments to examine subyearling mortality rates and incidence and severity of GBD in fish that were moved between waters that varied in TDG and temperature. Fish experienced significant mortality only at temperatures of 25&deg;C, which increased with exposure time. However there was no significance difference in mortality between fish acclimated to 100% TDG and 110% TDG. Fish that died did show signs of GBD. Generally, signs of GBD such as bubbles in the lateral line and unpaired fins were higher in fish acclimated at 110% TDG than in fish acclimated at 100% TDG, but there were few trends related to exposure temperature. Field measurements of TDG showed that TDG ranged from about 100% to 122.5% at some locations. Generally, TDG fluctuated daily, up to 8% during August and early September, and was highest late in the afternoon and lowest in the early morning. Laboratory results and field monitoring demonstrated that emigrating juvenile salmon can potentially be at risk from elevated temperatures, TDG, and GBD albeit to an unknown extent, which may increase their vulnerability to predation. Chapter Four &ndash; We conducted monthly beam trawling in Lower Granite and Little Goose reservoirs to describe the seasonal abundance of benthic epifauna that are potentially important as prey to juvenile fall Chinook salmon. The predominant taxa collected were Siberian prawns, the opossum shrimp Neomysis mercedis , and the amphipod Corophium sp. Prawns were relatively abundant at shallow sites in both reservoirs in June, but were more abundant at deep sites in lower and middle reservoir reaches in autumn. Prawn densities were commonly <0.2/m2. Prawn length-frequency data indicated that there were at least two size classes. Juvenile prawns present in shallow water more often than adult prawns, which were generally only found in deep water by autumn. Ovigerous prawns had an average of 171 eggs, which represented about 11.5% of their body weight. Limited diet analyses suggested that prawns consumed Corophium , Neomysis , and aquatic insects. Neomysis dominated all catches both in terms of abundance and biomass, and they were more abundant in Lower Granite compared to Little Goose reservoir. Neomysis were more abundant at shallow sites than at deep sites. Corophium were present in our collections but were never abundant, probably because our trawl was not effective at capturing them. The caloric content of prawns (4,782 Kcal), Neomysis (4,962 Kcal), and Corophium (4,926 Kcal) indicates that these prey would be energetically profitable for juvenile salmon. Subyearling fall Chinook salmon prey heavily on Neomysis and Corophium at times, but the importance of prawns as prey is uncertain.

Oregon, Washington↗

Associations between iron concentration and productivity in montane streams of the Black Hills, South Dakota

Iron is an important micronutrient found in aquatic systems that can influence nutrient availability (e.g., phosphorus) and primary productivity. In streams, high iron concentrations often are associated with low pH as a result of acid mine drainage, which is known to affect fish and invertebrate communities. Streams in the Black Hills of South Dakota are generally circumneutral in pH, yet select streams exhibit high iron concentrations associated with natural iron deposits. In this study, we examined relationships among iron concentration, priphyton biomass, macroinvertebrate abundance, and fish assemblages in four Black Hills streams. The stream with the highest iron concentration (~5 mg Fe/L) had reduced periphyton biomass, invertebrate abundance, and fish biomass compared to the three streams with lower iron levels (0.1 to 0.6 mg Fe/L). Reduced stream productivity was attributed to indirect effects of ferric iron Fe +++ ), owing to iron-hydroxide precipitation that influenced habitat quality (i.e., substrate and turbidity) and food availability (periphyton and invertebrates) for higher trophic levels (e.g., fish). Additionally, reduced primary and secondary production was associated with reduced standing stocks of salmonid fishes. Our findings suggested that naturally occurring iron deposits may constrain macroinvertebrate and fish production.

South Dakota↗

Proceedings of a workshop on American Eel passage technologies

Recent concerns regarding a decline in recruitment of American eels ( Anguilla rostrata ) have prompted efforts to restore this species to historic habitats by providing passage for both upstream migrant juveniles and downstream migrant adults at riverine barriers, including low-head and hydroelectric dams (Castonguay et al. 1994, Haro et al. 2000). These efforts include development of management plans and stock assessment reviews in both the US and Canada (COSEWIC 2006, Canadian Eel Working Group 2009, DFO 2010, MacGregor et al. 2010, ASMFC 2000, ASMFC 2006, ASMFC 2008, Williams and Threader 2007), which target improvement of upstream and downstream passage for eels, as well as identification and prioritization of research needs for development of new and more effective passage technologies for American eels. Traditional upstream fish passage structures, such as fishways and fish lifts, are often ineffective passing juvenile eels, and specialized passage structures for this species are needed. Although designs for such passage structures are available and diverse (Knights and White 1998, Porcher 2002, FAO/DVWK 2002, Solomon and Beach 2004a,b, Environment Agency UK 2011), many biologists, managers, and engineers are unfamiliar with eel pass design and operation, or unaware of the technical options available for upstream eel passage, Better coordination is needed to account for eel passage requirements during restoration efforts for other diadromous fish species. Also, appropriately siting eel passes at hydropower projects is critical, and siting can be difficult and complex due to physical restrictions in access to points of natural concentrations of eels, dynamic hydraulics of tailrace areas, and presence of significant competing flows from turbine outfalls or spill. As a result, some constructed eel passes are sited poorly and may pass only a fraction of the number of eels attempting to pass the barrier. When sited and constructed appropriately, however, eel passes can effectively pass thousands of individuals in a season (Appendix D). technologies for preventing impingement and entrainment mortality and injury of downstream migrant eels at hydropower projects are not well developed. Traditional downstream fish passage mitigative techniques originally developed for salmonids and other species are frequently ineffective passing eels (Richkus and Dixon 2003, EPRI 2001, Bruijs and Durif 2009). Large hydropower projects, with high project flows or intake openings that cannot be fitted with racks or screens with openings small enough to exclude eels, pose significant passage problems for this species, and turbine impingement and entrainment mortality of eels can be as high as 100%. Spill mortality and injury may also be significant for eels, given their tendency to move during high flow events when projects typically spill large amounts of flow. Delays in migration of eels that have difficulty locating and utilizing bypass entrances can also be significant. Therefore, downstream passage technologies are at a much more nebulous state of development than upstream passage technologies, and require further evaluation and improvement before rigorous design guidelines can be established. There have been few studies conducted to evaluate effectiveness of current mitigative measures for both upstream and downstream passage of eels. Research is needed to determine eel migratory timing, behavior, and appropriate mitigation technologies for specific sites and eel life history stages. Both upstream and downstream eel passage structures can be difficult to evaluate in terms of performance, and examples of how evaluation and monitoring can be accomplished were reviewed at the workshop.

Report↗

Guidelines for monitoring and adaptively managing restoration of Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) on the Elwha River

As of January, 2014, the removal of the Elwha and Glines Canyon dams on the Elwha River, Washington, represents the largest dam decommissioning to date in the United States. Dam removal is the single largest step in meeting the goals of the Elwha River Ecosystem and Fisheries Restoration Act of 1992 (The Elwha Act) &mdash; full restoration of the Elwha River ecosystem and its native anadromous fisheries (Section 3(a)). However, there is uncertainty about project outcomes with regards to salmon populations, as well as what the &lsquo;best&rsquo; management strategy is to fully restore each salmon stock. This uncertainty is due to the magnitude of the action, the large volumes of sediment expected to be released during dam removal, and the duration of the sediment impact period following dam removal. Our task is further complicated by the depleted state of the native salmonid populations remaining in the Elwha, including four federally listed species. This situation lends itself to a monitoring and adaptive management approach to resource management, which allows for flexibility in decision-making processes in the face of uncertain outcomes. The Elwha Monitoring and Adaptive Management (EMAM) guidelines presented in this document provide a framework for developing goals that define project success and for monitoring project implementation and responses, focused upon two federally listed salmon species &mdash; Puget Sound Chinook salmon (Oncorhynchus tshawytscha) and Puget Sound steelhead (O. mykiss). The framework also should serve as a guide to help managers adaptively manage fish restoration actions during and following dam removal. The document is organized into seven sections, including an introduction (Section 1), a description of the adaptive management approach (Section 2), suggested modifications to the existing restoration strategy developed in previous Elwha River restoration documents (section 3), specific descriptions of an adaptive management framework, including establishment of goals, performance indicators, and potential adaptive management responses to monitoring information (section 4), monitoring tools and methods for use in evaluating performance and project outcomes (section 5), and brief sections on data record keeping and reporting (Section 6) and an estimated budget (section 7). The purpose of the EMAM guidelines is to propose (1) refinement of existing goals established in previous documents (e.g., Ward et al. (2008), U.S. Department of the Interior, Department of Commerce, and Lower Elwha S&rsquo;Klallam Tribe (1994)); (2) an adaptive management framework, (3) specific trigger values for relevant performance indicators that guide the adaptive management approach, (4) a specific monitoring strategy for evaluating outcomes of restoration activities; (5) a data management strategy, (6) information needed for adjusting goals when observations indicate conditions are different from anticipated. When taken together, our proposed adaptive management guidelines rely upon setting goals and objectives for each species of interest, which are monitored by relevant performance indicators and measurable trigger values that define success within each phase of the project. The guidelines themselves are arranged in a hierarchy for each species of interest. The levels of this hierarchy are goals, objectives, performance indicators, decision rules, triggers, and decisions (i.e., management/policy response). The monitoring and adaptive management approach provided is based on monitoring several categories of performance indicators, each containing associated &lsquo;trigger&rsquo; values which, when met, alters restoration activities (e.g., hatchery releases and/or strategies) through four successive restoration phases. Performance indicators proposed in these EMAM guidelines are based upon Viable Salmon Population (VSP) metrics, including abundance, productivity, distribution, and diversity (McElhany et al. 2000). Trigger values for each performance indicator are developed for four different restoration phases: Preservation, Recolonization, Local Adaptation, and Viable Natural Population. These biologically-based phases each have a set of objectives that are based on resource management scenarios, including the dam removal project itself, which change largely based on the level of active management required and the degree, if any, of resource utilization. Thus, details of prescribed management actions for each phase are based upon different needs specific to that phase. The creation of biologically-based phases is one of the major differences between our proposed EMAM guidelines and previously presented plans for Elwha River Restoration Project management. Changed largely in response to the recommendations of the most recent of three Hatchery Scientific Review Group project reviews (HSRG 2012), the goal-oriented phases replaced the previous system of temporal changes centered around the decommissioning of the dams (i.e., before, during, and after dam removal). By focusing on outcomes associated with rebuilding salmon populations instead of an engineering schedule, the guidelines are more amenable to an adaptive management framework and the ability for management actions to influence outcomes, particularly in the periods during and following dam removal. Trigger values for each performance indicator were generally developed using existing data from the Elwha River watershed, the Puget Sound region, or other Pacific Northwest rivers (i.e., elsewhere in Washington State, Oregon, British Columbia) modified to be relevant for Chinook salmon and steelhead recovery in the Elwha River. By meeting all of the trigger value levels for all performance indicators for a set amount of time within a management phase, the guidelines call for moving to the next phase. This next phase has a new set of trigger values for the same performance indicators. For example, upon moving from the Preservation phase to the Recolonization phase, the trigger value for intrinsic potential increases. Intrinsic potential is a pre-defined estimate of the total extent of available habitat within a watershed for adult and juvenile fish, specific to the target species and is therefore a performance indicator of spatial distribution. By the final Viable Natural Population phase, the entire intrinsic potential of the watershed is being occupied by the species of interest. For those cases when a performance indicator is not exceeding the target value for a particular phase after a certain time period, the trigger values provided in this document, as well as a series of exogenous variables, are explored that may help explain why the performance indicator is not being met. These exogenous variables include variables that are not part of the suite of performance indicators, such as hatchery production, harvest, habitat, and ecosystem indicators. In these cases where the program is stuck in a particular recovery phase, the situation could be caused by the selection of inappropriate trigger values or unforeseen environmental conditions. If the former, adaptive management would call for existing monitoring data to be used for modifying trigger values to an appropriate level. If one of the exogenous variables is found to be preventing the program moving to the next phase, then appropriate changes to management would be advised. For each performance indicator and many of the exogenous variables, a set of monitoring tools were proposed. Data standards were also proposed for data generated by each monitoring tool. Data management, record keeping, and reporting of monitoring and adaptive management activities and results are also outlined. Management of data from the focused monitoring program and documenting the outcomes of trigger value evaluations and associated decisions from the adaptive management approach are key components of the EMAM guidelines. Without a clear history of data generated and adaptive management decisions taken by managers, the ability to learn through adaptive management breaks down. In addition to the long time period involved, another complication is the fact that the data will likely be collected by different federal and state agencies, tribal staff, and others. Having a system of reporting developed should help alleviate potential problems. The restoration of the migration route to spawning and rearing habitats upstream of the former Glines Canyon Dam represents a great opportunity for salmon on the Olympic Peninsula. By removing two aging structures, it will be possible for all 5 species of salmon and steelhead to return to wild stretches of the Elwha River and major floodplain habitat characterized by multiple channels, as well as significant portions of numerous tributaries. Measuring the progress of restoration, from the perspective of both salmon populations and the ecosystem upon which they depend, is a great test for a collaborative team of scientists. The normally challenging conditions of working in a steep gradient, high velocity wilderness river are exacerbated by the release of millions of cubic yards of sediment that had accumulated in the reservoirs. After the first two years of the dam decommissioning process, this release has changed the ecology of the river, estuary, and nearshore habitats downstream of the dams. Our goal in developing the guidelines described is to provide a roadmap for tracking what hopefully will become a successful outcome. If successfully implemented, this information should prove useful as others begin planning for the removal, alteration, or reconstruction of dams throughout North America and elsewhere, an inevitable outcome of an aging dam infrastructure.

Washington↗

Wind River subbasin restoration: U.S. Geological Survey annual report November 2012 through December 2013

Executive Summary The Wind River subbasin in southwest Washington State provides habitat for a population of wild Lower Columbia River steelhead Oncorhynchus mykiss . There have been no hatchery steelhead planted in the Wind River subbasin since 1994, and hatchery adults are estimated to be less than one percent of adults in any year (pers comm. Thomas Buehrens, Washington Department of Fish and Wilflife). We used Passive Integrated Transponder (PIT)-tagging and a series of instream PIT-tag interrogation systems (PTIS) to investigate life-histories, populations, and efficacy of habitat restoration actions for these steelhead. Data from our study, and companion work by Washington Department of Fish and Wildlife (WDFW), will contribute to Bonneville Power Administration&rsquo;s (BPA) Research Monitoring and Evaluation (RM&E) Program Strategy of Fish Population Status Monitoring ( www.cbfish.org/ProgramStrategy.mvc/ViewProgramStrategySummary/1 ), specifically the sub-strategies of: 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and to uncertainties research regarding differing life histories of a wild steelhead population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer 2013, we PIT-tagged parr steelhead in headwater areas of the Wind River subbasin to investigate variable life-histories, specifically to compare fate of those juvenile steelhead that move downstream prior to smolting with those that remain in their natal areas until smolting. A series of instream PTISs monitored movement of these fish. Detections at the instream PTISs showed trends of parr emigration during summer and fall, in addition to the expected movement of parr and smolts in spring. Long-term monitoring of PIT-tagged fish over multiple years will provide information on contribution of various life-history strategies to smolt production and adult returns, as well as helping to identify factors influencing parr movement. Movements of PIT-tagged adult steelhead were tracked with our instream PTISs. These data have provided information on timing of adult movements to various parts of the watershed, which is allowing us to assess adult returns to tributary watersheds within the Wind River subbasin. Determination of adult use of tributary watersheds has provided data that will contribute to evaluating the efficacy of the removal of Hemlock Dam from Trout Creek. Hemlock Dam, located at rkm 2.0 of Trout Creek was removed in summer 2009 and had contributed to hydrologic impairment of Trout Creek. Evaluating restoration efforts is of interest to many managers and agencies so that funding and time are allocated for best results. The evaluation of various life-histories of Lower Columbia River steelhead within the Wind River subbasin will provide information to better track populations, and to direct habitat restoration and water allocation planning. Increasingly detailed Viable Salmonid Population information, such as that provided by PIT-tagging and instream PTISs networks like those we are building and operating in the Wind River subbasin, will provide data to inform policy and management, as life-history strategies and production bottlenecks are identified and understood.

Washington↗

Snake River fall Chinook salmon life history investigations, 1/1/2013 – 12/31/2013

Smallmouth bass predation on subyearling fall Chinook salmon was examined in the upper portion of Lower Granite Reservoir during 2013. During the time subyearlings were present in the reservoir, smallmouth bass were collected, their stomach contents removed for diet analysis, and their abundance estimated with mark-recapture techniques. In 2013, the greatest consumption of subyearlings by smallmouth bass occurred in late May and early June&mdash;as much as 50% of their diet by weight. Sand rollers were the most common non-salmonid fish consumed by smallmouth bass. In the section of the reservoir above the confluence with the Clearwater River, the abundance of bass was higher in non-riprap habitat than in riprap, but the opposite was true in the section below the confluence. We estimated that over 168,000 subyearlings were lost to smallmouth bass predation in 2013. Given the predominance of sand rollers in the diet of smallmouth bass, we believe this species reduces predation on subyearling fall Chinook salmon. A complete report of our findings is provided in the Appendix.

Washington↗

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2014 through December 2014

Executive Summary The Wind River subbasin in southwest Washington State provides habitat for a population of wild Lower Columbia River steelhead Oncorhynchus mykiss , which are listed as threatened under the Endangered Species Act. No hatchery steelhead have been planted in the Wind River subbasin since 1994, and hatchery adults are estimated to be less than one percent of adults in any year (Thomas Buehrens, Washington Department of Fish and Wildlife, personal communication). Numerous restoration actions have been implemented in the subbasin, including the removal of Hemlock Dam on Trout Creek in 2009. We used Passive Integrated Transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTIS) to investigate life-histories, populations, and efficacy of habitat restoration actions for these steelhead. Data from our study, and companion work by Washington Department of Fish and Wildlife (WDFW), will contribute to Bonneville Power Administration&rsquo;s (BPA) Research Monitoring and Evaluation (RM&E) Program Strategy of Fish Population Status Monitoring ( www.cbfish.org/ProgramStrategy.mvc/ViewProgramStrategySummary/1 ), specifically the sub-strategies of: 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and to Uncertainties Research regarding differing life histories of a wild steelhead population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer 2014, we PIT-tagged steelhead parr in headwater areas of the Wind River subbasin to investigate life-history diversity, specifically to compare fate of those juvenile steelhead that move downstream prior to smolting with those that remain in their natal areas until smolting. A series of instream PTISs monitored movement of these fish. We added a new multi-antenna PTIS on Trout Creek and made improvements to two of our smaller tributary PTISs during 2014. Detections at the instream PTISs showed trends of parr emigration during summer and fall, in addition to the expected movement of parr and smolts in spring. Long-term monitoring of PIT-tagged fish will provide information on contribution of various life-history strategies to smolt production and adult returns, as well as helping to identify factors influencing parr movement. Movements of PIT-tagged adult steelhead were tracked with our instream PTISs. These data will contribute to a better understanding of timing and distribution of spawning by this population of wild steelhead within the Wind River subbasin. Additionally, these data have provided information on timing of adult movements to various parts of the watershed, which is allowing us to assess adult use of tributary watersheds within the Wind River subbasin. These data are contributing to evaluating steelhead response to the removal of Hemlock Dam from Trout Creek. Hemlock Dam, which was located at rkm 2.0 of Trout Creek, was removed in summer 2009 and had contributed to hydrologic impairment of Trout Creek and potentially caused some deterrent to upstream adult steelhead migration. Evaluating restoration efforts is of interest to many managers and agencies so that funding and time are allocated for best results. The evaluation of various life-histories of Lower Columbia River steelhead within the Wind River subbasin provides information to better track populations, and more effectively direct habitat restoration and water allocation planning. Increasingly detailed Viable Salmonid Population information (Crawford and Rumsey 2009), such as that provided by PIT-tagging and instream PTISs networks like those we build and operate in the Wind River subbasin, provide data to better inform policy and management, as life-history strategies and production bottlenecks are identified and understood.

Washington↗

Mycobacterial infections in adult salmon and steelhead trout returning to the Columbia River Basin and other areas in 1957

The degree of incidence of acid -fast bacillus infections in adult salmonid fishes was determined. The disease was shown to be widely distributed in the area examined. It is believed the primary source of infection is derived from the hatchery practice of feeding infected salmon products to juvenile fish. One group of marked adults that had been hatchery reared for 370 days showed a 62 percent incidence of infection. A statistical analysis indicated that length of fish is independent of infection

California, Oregon, Washington↗

Benthic prey fish assessment, Lake Ontario 2013

The 2013 benthic fish assessment was delayed and shortened as a result of the U.S. Government shutdown, however the assessment collected 51 of the 62 planned bottom trawls. Over the past 34 years, Slimy Sculpin abundance in Lake Ontario has fluctuated, but ultimately decreased by two orders of magnitude, with a substantial decline occurring in the past 10 years. The 2013 Slimy Sculpin mean bottom trawl catch density (0.001 ind.·m-2, s.d.= 0.0017, n = 52) and mean biomass density (0.015 g·m-2 , s.d.= 0.038, n = 52) were the lowest recorded in the 27 years of sampling using the original bottom trawl design. From 2011-2013, the Slimy Sculpin density and biomass density has decreased by approximately 50% each year. Spring bottom trawl catches illustrate Slimy Sculpin and Round Goby Neogobius melanostoma winter habitat overlaps for as much as 7 months out of a year, providing opportunities for competition and predation. Invasive species, salmonid piscivory, and declines in native benthic invertebrates are likely all important drivers of Slimy Sculpin population dynamics in Lake Ontario. Deepwater Sculpin Myoxocephalus thompsonii, considered rare or absent from Lake Ontario for 30 years, have generally increased over the past eight years. For the first time since they were caught in this assessment, Deepwater Sculpin density and biomass density estimates declined from the previous year. The 2013 abundance and density estimates for trawls covering the standard depths from 60m to 150m was 0.0001 fish per square meter and 0.0028 grams per square meter. In 2013, very few small (< 80 mm) Deepwater Sculpin were caught and most sculpin were at sites of 150 meters or greater, which is in contrast to previous years when juvenile fish were caught around 80-100 meters. The reduced effort and late seasonal timing of the 2013 assessment make it difficult to have high confidence in declines observed in 2013, however observed Alewife Alosa psuedoharengus abundance increases and reduced juvenile Deepwater Sculpin catches are consistent with the hypothesis that Alewife negatively influence Deepwater Sculpin recruitment. Nonnative Round Gobies were first detected in the USGS/NYSDEC Lake Ontario spring Alewife assessment in 2002. Since that assessment, observations indicate their population has expanded and they are now found along the entire south shore of Lake Ontario, with the highest densities in U.S. waters just east of the Niagara River confluence. In the 2013 spring-based assessment, both the abundance and weight indices increased slightly as compared to 2012. The number index value of 16.6 was 30% of the maximum number observed in 2008 when the number index was 95.2. Round Goby density estimates from the 2013 fall benthic prey fish survey were 33 times greater than fall Slimy Sculpin density, indicating Round Goby are now the dominant Lake Ontario benthic prey fish.

Lake Ontario↗

Status and trends of the Lake Huron deepwater demersal fish ommunity, 2008

The U.S.Geological Survey Great Lakes Science Center has conducted trawl surveys to assess annual changes in the deepwater demersal fish community of Lake Huron since 1973. Since 1992, surveys have been carried out using a 21 m wing trawl towed on-contour at depths ranging from 9 to 110 m on fixed transects. Sample sites include five ports in U.S. waters with less frequent sampling near Goderich, Ontario. The 2008 fall bottom trawl survey was carried out between October 24 and November 20, 2008 and sampled only the three northern U.S. ports at DeTour, Hammond Bay, and Alpena due to mechanical problems with the research vessel and prolonged periods of bad weather. Therefore, all data presented for 2008 are based on samples collected from these ports. Compared to previous years, alewife populations in Lake Huron remain at low levels after collapsing in 2004. Age-0 alewife density and biomass appears to have increased slightly but overall levels remain near the nadir observed in 2004. Density and biomass of adult and juvenile rainbow smelt showed a decrease from 2007 despite record-high abundance of juveniles observed in 2005, suggesting recruitment was low. Numbers of adult and juvenile bloater were low despite recent high year-classes. Abundances for most other prey species were similar to the low levels observed in 2005 - 2007. We captured one wild juvenile lake trout in 2008 representing the fifth consecutive year that wild lake trout were captured in the survey. Based on pairwise graphical comparisons and nonparametric correlation analyses, dynamics of prey abundance at the three northern ports followed lakewide trends since 1992. Density of benthic macroinvertebrates was at an all-time low in 2008 since sampling began in 2001. The decline in abundance was due to decreases in all taxonomic groups and a large reduction in recruitment of quagga mussels. Density of Diporeia at northern ports in 2008 was the lowest observed. Diporeia were found only at 73-m sites of three ports sampled in northern Lake Huron. While no lakewide estimate of prey biomass was calculated due to the limited spatial scope of the 2008 survey, existing data suggest prey biomass remains depressed. Prey available to salmonids during 2009 will likely be small alewives, small rainbow smelt and small bloaters. Predators in Lake Huron will continue to face potential prey shortages.

Lake Huron↗

The Chief Joseph Hatchery Program 2013 Annual Report

The Chief Joseph Hatchery is the fourth hatchery obligated under the Grand Coulee Dam/Dry Falls project, originating in the 1940s. Leavenworth, Entiat, and Winthrop National Fish Hatcheries were built and operated as mitigation for salmon blockage at Grand Coulee Dam, but the fourth hatchery was not built, and the obligation was nearly forgotten. After the Colville Tribes successfully collaborated with the United States to resurrect the project, planning of the hatchery began in 2001 and construction was completed in 2013. The monitoring program began in 2012 and adult Chinook Salmon were brought on station for the first time in June 2013. BPA is the primary funding source for CJH, and the Mid-Columbia PUDs (Douglas, Grant and Chelan County) have entered into cost-share agreements with the tribes and BPA in order to meet some of their mitigation obligations. The CJH production level was set at 60% in 2013 in order to train staff and test hatchery facility systems during the first year of operation. Leavenworth National Fish Hatchery (LNFH) provided 422 Spring Chinook broodstock in June, 2013; representing the official beginning of CJH operations. In July and August the CCT used a purse seine vessel to collect 814 summer/fall Chinook as broodstock that were a continuation and expansion of the previous Similkameen Pond program. In-hatchery survival for most life stages exceeded survival targets and, as of April 2014, the program was on track to exceed the 60% production target for its start-up year. The CJH monitoring project collected field data to determine Chinook population status, trend, and hatchery effectiveness centered on five major activities; 1) rotary screw traps (juvenile outmigration, natural-origin smolt PIT tagging) 2) beach seine (naturalorigin smolt PIT tagging) 3) lower Okanogan adult fish pilot weir (adult escapement, proportion of hatchery-origin spawners [pHOS], broodstock) 4) spawning ground surveys (redd and carcass surveys)(viable salmonid population [VSP] parameters) 5) eDNA collection (VSP parameter—distribution/spatial structure). Adult summer/fall Chinook spawning escapement in 2013 was estimated to be 8,193, with more than 6,227 natural-origin spawners, which exceeded the recent five year and long term averages. The values for pHOS (0.24) and proportion of natural influence (PNI) (0.79) in 2013 exceeded the objectives (0.67), but the five year averages fell short of the goals (0.39 and 0.62, respectively). An Annual Program Review (APR) was held in March, 2014 to share hatchery production and monitoring data, review the salmon forecast for the upcoming year, and develop action plans for the hatchery, selective harvest, and monitoring projects. Based on a strong pre-season forecast of 67,500 Upper Columbia summer/fall Chinook, the plan for 2014 is to operate the hatchery at full program levels of 2 million summer/fall Chinook and 900,000 spring Chinook. To maximize PNI, broodstock for the integrated program should Chief Joseph Hatchery Program 2013 Annual Report 3 be 100% natural-origin broodstock (NOB) and CCT should plan to harvest their full allocation with the selective harvest program removing as many adult hatchery Chinook as possible with the purse seine, the weir, and at the hatchery ladder.

Report↗

Evaluation of stream flow effects on smolt survival in the Yakima River Basin, Washington, 2012-2014

The influence of stream flow on survival of emigrating juvenile (smolts) Pacific salmon Oncorhynchus spp. and steelhead trout O. mykiss is of key management interest. However, few studies have quantified flow effects on smolt migration survival, and available information does not indicate a consistent flow-survival relationship within the typical range of flows under management control. It is hypothesized that smolt migration and dam passage survival are positively correlated with stream flow because higher flows increase migration rates, potentially reducing exposure to predation, and reduce delays in reservoirs. However, available empirical data are somewhat equivocal concerning the influence of flow on smolt survival and the underlying mechanisms driving this relationship. Stream flow effects on survival of emigrating anadromous salmonids in the Yakima Basin have concerned water users and fisheries managers for over 20 years, and previous studies do not provide sufficient information at the resolution necessary to inform water operations, which typically occur on a small spatiotemporal scale. Using a series of controlled flow releases from 2012-2014, combined with radio telemetry, we quantified the relationship between flow and smolt survival from Roza Dam 208 km downstream to the Yakima River mouth, as well as for specific routes of passage at Roza Dam. A novel multistate mark-recapture model accounted for weekly variation in flow conditions experienced by radio-tagged fish. Groups of fish were captured and radio-tagged at Roza Dam and released at two locations, upstream at the Big Pines Campground (river kilometer [rkm] 211) and downstream in the Roza Dam tailrace (rkm 208). A total of 904 hatchery-origin yearling Chinook salmon O. tshawytscha were captured in the Roza Dam fish bypass, radio-tagged and released upstream of Roza Dam. Two hundred thirty seven fish were released in the tailrace of Roza Dam. Fish released in the tailrace of Roza Dam were tagged concurrently with fish released upstream of the dam using identical tagging methods. Tagging and release events were conducted to target a range of flow conditions indicative of flows observed during the typical migration period (March-May) for juvenile spring Chinook salmon in the Yakima River. Three, five and four separate upstream releases were conducted in 2012, 2013, and 2014 respectively, and at least 43 fish were released alive on each occasion. The release sample sizes in 2014 were much larger (~130) compared to previous years for the purpose of increasing precision of survival estimates across the range of flows tested. Migration movements of radio-tagged spring Chinook salmon smolts were monitored with an array of telemetry receiver stations (fixed sites) that extended 208 rkm downstream from the forebay of Roza Dam to the mouth of the Yakima River. Fixed monitoring sites included the forebay of Roza Dam (rkm 208), the tailrace of Roza Dam (rkm 207.9), the mouth of Wenas Creek (rkm 199.2), the mouth of the Naches River (two sites, rkm 189.4), Sunnyside Dam (two sites, rkm 169.1), Prosser Dam (rkm 77.2), and the mouth of the Yakima River (two sites, rkm2 3). This array segregated the study area into four discrete reaches in which survival of tagged fish was estimated. Aerial and underwater antennas were also used to monitor tagged fish at Roza Dam. Aerial antennas were located in the forebay, on the East gate, on the West gate, and in the tailrace of Roza Dam. Underwater antennas were located in the fish bypass, upstream of the East gate, and upstream of the West gate to collect route-specific passage data for tagged fish. Additional years of data collection and analysis could alter or improve our understanding of the influence of flow and other environmental factors on smolt survival in the Yakima River. Nevertheless, during 2012-2014, yearling hatchery Chinook salmon smolt emigration survival was significantly associated with stream flow in the

Report↗