Uncertainties organized by Theme, Subtheme

Criticality level indicated at left as low, medium, high, priority.
Those not given a criticality level indicated at left as '–'.

Theme: Climate change
  Subtheme: Effects - general
How will the long-term climate trends predicted for the Columbia River Basin and the northeast Pacific Ocean affect fish and wildlife in the region? (Primary)
Some modeling has been done, but future research will be an ongoing process of fine-tuning climate models and applying those models to hydrology, habitat phenology, and biota. This question provides a broad base under which researchers and others can define more specific topics. The ISAB and ISRP believe that the sub-uncertainties associated with this broad question are among the most critical climate change uncertainties. For the Program to be successful over the long term, special attention needs to be paid to two primary aspects of water: (1) maintaining reliable quantities and (2) consistent high quality. It is important to note that quality encompasses a broad variety of issues.
How could integrated ecological monitoring be used to determine how climate change affects fish and wildlife and the freshwater, estuarine, ocean, and terrestrial habitats and ecosystems that sustain them?
What are indices of climate change? How could indices of climate change be used to better understand and predict interannual and interdecadal changes in production, abundance, diversity, and distribution of Columbia Basin fish and wildlife?
Theme: Climate change
  Subtheme: Effects - food web
What food web effects are associated with long-term climate trends predicted for the Columbia River Basin? (Primary)
Theme: Climate change
  Subtheme: Effects - biological
What are the impacts of possible climate change scenarios on salmon and steelhead (stock specific)?
What are the impacts of climate change on sturgeon? Can white sturgeon condition and spawn timing be possible responses to, and a potential bellwether for, systemic changes of Columbia River reaches due to global climate change? What are the effects of water temperature increases, changes in the seasonality of the freshet and low elevation runoff, and possible changes in salt-wedge intrusion on white sturgeon spawning success and population dynamics in Columbia River waters? What are the effects of the above mentioned climate changes on white sturgeon food resources in Columbia River reaches, including the Columbia River mainstem, estuarine, and marine waters?
How are climate change, ocean acidification, salinity, estuary turbidity maximum (ETM), and localized hypoxia likely to affect forage fish, including eulachon, in the coming decades?
What are the potential effects of climate change on lampreys, including the effects of increasing water temperatures and changing runoff regimes, on lamprey energetics and performance?
How might climate change affect the success of salmonid reintroductions, supplementation or recovery efforts, particularly since warmer waters may favor other species, especially non-natives?
Theme: Climate change
  Subtheme: Effects - physical/hydrological
What are the potential effects of climate change on river hydraulics, temperature, and sediment movement in tributaries and mainstem reaches of the Columbia River Basin?
What are climate change impacts on wetted area of the floodplain and sea-level rise?
Theme: Climate change
  Subtheme: Effects - restoration
How will climate change and associated extreme climate events decrease the effectiveness of, or even negate, the region's fish and wildlife restoration efforts? (Primary)
Theme: Climate change
  Subtheme: Mitigating actions
What strategic actions, alone or in combination and at what spatial and temporal scales, could help ameliorate increased water temperatures, decreased summer river flows, changes in upland plant communities, and other ecosystem changes due to climate changes that will impact fish and wildlife? (Primary)
This was identified as a top priority in the climate change theme. A moderate amount of progress has been made addressing climate-associated effects on temperature and flow, but there has been little progress in modeling ecosystem changes. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #33, for a discussion of progress made toward addressing this uncertainty. In the summer of 2015, fish kills in the Basin due to increased, water temperatures in streams made the national news. Given predictions of a changing climate, with increased temperatures and generally reduced snow packs and summer stream flows and increasing levels of land development and resource use, the extent and severity of fish kills are likely to increase. Additional attention is needed to better document and quantify this issue. This will allow a determination whether specific response strategies are needed as part of the Program and/or whether additional research is necessary. Managers will require this information to develop strategies for adapting to climate change. For example, when selecting areas for habitat restoration, managers might first consider areas likely to provide thermal refuges for aquatic species.
Where are cool water refugia, have these areas been mapped, and how do salmonids use these areas?
How can a decision analysis framework be used to address climate change on natural and cultural resources in the Yakima and Methow river basins?
Theme: Contaminants
  Subtheme: Assessment (distribution and concentration)
What are the distributions, uses, and concentrations of toxics, including emerging contaminants, in the Columbia River Basin, and what are their trends over time? (Primary)
This is the fundamental uncertainty for this theme. Although it may be difficult to obtain data at sufficient temporal and spatial scales to fully resolve the uncertainty in the near term, it forms a foundation for understanding the magnitude of the threat and formulating approaches for tackling other contaminant-related uncertainties. Contaminants are not easily detected, so managers may unknowingly try to restore habitat in need of substantial clean-up. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #34, for a discussion of progress made toward addressing this uncertainty. The proliferation of artificial chemicals in the Basin was recently identified by the ISAB as one of the highest priorities for resolution (ISAB 2011-1, ISAB 2013-1). The most recent tally of pesticide use (average for 1999-2004) lists 182 chemicals, with an aggregate application rate of ~46,000 metric tons (~50,000 US tons) of active ingredients annually; these are concentrated mostly in agricultural lands along water courses (See Programmatic Comment 2; Figure 1; ISAB 2001-1). In the 2013 ISAB report, specific recommendations were made for addressing chemicals and contaminants: (1) Actively investigate the impact of chemicals on restoration activities by fully implementing a water quality program. This initiative will require working partnerships between federal and state agencies as well as initiating modeling of how climate and temperature affects contaminant toxicity for all parts of the Basin. (2) Work diligently with other regional agencies to implement the interagency Columbia River Basin Toxics Reduction Action Plan (US EPA 2010). (3) Update the plan regularly, so that current and future chemical inputs to the system can be addressed in a timely fashion, before they become even more serious problems. The nature of the issue dictates that this will be a large, ongoing, and collective regional effort. A new, interactive mapping tool shows predicted concentrations for 108 pesticides in streams and rivers across the United States and identifies which streams are most likely to exceed water-quality guidelines for human health or aquatic life. It also provides information on probabilities of exceeding established benchmarks. It is based on Watershed Regression for Pesticides (WARP) models as part of the National Water-Quality Assessment (NAWQA) Program. A complete description of the development and performance of the WARP models is provided in Stone et al. (2013); additional information is available at http://cida.usgs.gov/warp/home/. This mapping tool should be a useful resource in watershed assessments and in the identification and planning of restoration strategies and individual project treatments.
Why are mercury and PBDEs (polybrominated diphenyl ethers) increasing in osprey?
What are the levels of mercury and variation in bio-indicator taxa across reservoirs in the Columbia River Basin?
What are the main factors controlling mercury methylation in the region? How is mercury cycling influenced by lake stratification, dissolved oxygen, primary production, seasonal drawdown, flood-up patterns and bioaccumulation in Columbia River Basin reservoirs?
Theme: Contaminants
  Subtheme: Assessment (distribution and concentration) - contribution (point source/NPS)
How should abandoned vessels be inventoried and mapped? What are the potential impacts of contamination on aquatic species from abandoned vessels?
Can contaminants be tracked to determine constituents and sources of contaminants, nutrients and organic matter, spatially and temporally?
Do salmon carcasses provide a pathway for pollutants and artificial chemicals on spawning grounds?
Theme: Contaminants
  Subtheme: Impacts
How do toxic substances, alone and in combination, affect fish and wildlife distribution and abundance, survival and fitness, and productivity in the Columbia River Basin? (Primary)
Addressing this uncertainty will require knowledge of the distribution of contaminants and their effects on biological resources in the Basin. If unchecked, the harmful effects of toxic substances could potentially negate mitigation and restoration efforts. Addressing this uncertainty will require a high level of integration and collaboration with state and federal agencies. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #35, for a discussion of progress made toward addressing this uncertainty.
How do food web transfer, sediment transport, and biological effects of emerging and legacy organic contaminants under current management regimes affect key Columbia River species, the success of restoration projects within the Basin, and human health (i.e., the success of harvest mitigation)?
What is the role of contamination on Pacific lamprey declines relative to the threat from hydropower operations, such as dam passage?
What are the biochemical, behavioral, and reproductive effects of mercury in fishes and aquatic dependent wildlife in Columbia River Basin reservoirs?
What are the appropriate standards and criteria for fish, wildlife, and humans from toxics, especially from emerging contaminants?
What levels of chemicals of emerging concern (CECs) impact the health of focal species including Pacific lamprey, white sturgeon, and salmonids?
What are the effects on salmonids, sturgeon, and lamprey of endocrine-disrupting pharmaceuticals and chemicals in personal care products?
How are environmental toxicants impacting the reproductive fitness of fish that are impounded behind dams?
How do hydroelectric projects affect toxic contaminants in the Columbia River Basin?
What are appropriate biological markers (sensitivity and diagnostic indicators) to measure the health impacts of contaminants on Columbia River Basin fish and shellfish, particularly salmon?
Are accumulations of mercury and other contaminants in river sediments affecting lamprey recruitment and suitability for human consumption at the adult stage?
Theme: Contaminants
  Subtheme: Impacts - direct biological
What are levels of contaminant exposure and accumulation among Columbia Basin fishes, including ESA-listed stocks? (Primary)
Does accumulation of contaminants in pools above Bonneville Dam negatively affect the sturgeon and their ability to reproduce?
What are the effects of contaminants and possible additional biological threats, e.g., predation and species composition, on Kootenai River white sturgeon and their habitats?
What are the effects of metals and organochlorine pesticides in substrates on the mortality, growth, development, and deformity rates for sturgeon sac-fry reared under simulated river conditions?
What tools are available or can be developed to predict the cumulative and interrelated impacts of toxic terrestrial runoff on salmon population viability?
Are contaminants affecting the abundance of mink and otter populations in the Basin?
What are the effects of contaminants on lamprey biology, physiology, and performance, and what are the implications on lamprey restoration and human health?
Do specific toxins and contaminants affect white sturgeon survival and spawning success? Specifically, what are the baseline contaminant levels in white sturgeon and gonads of adult broodstock?
Theme: Contaminants
  Subtheme: Impacts - indirect food web
What are the impacts of chemical loads on organisms and the structure, resilience, and productivity of aquatic food webs? (Primary)
What are the effects of transfer, accumulation, and persistence of CECs (chemicals of emerging concern) in estuarine, coastal ocean, and riverine food webs?
What are the potential impacts of trace element contamination of upper Columbia River sediments on the quality of critical white sturgeon habitat throughout the upper Columbia River from Lake Roosevelt upstream to the International Border?
What are the effects of mercury exposure on forage fish (littoral and pelagic feeders) and species assemblages, and how do these effects drive mercury bioaccumulation pathways in Columbia River Basin reservoirs?
What are the cumulative and/or synergistic effects of multiple toxic contaminants, particularly pesticides, on riparian insects and other organisms that impact the carrying capacity of the Columbia River ecosystem (including estuarine, coastal ocean and riverine habitats), as well as interactions between these chemicals and non-chemical stressors?
Theme: Contaminants
  Subtheme: Mitigating actions
What strategic actions, alone or in combination, and at what spatial and temporal scale, could help ameliorate the effects of toxic contaminants? (Primary)
Does reduction of chemical runoff in to key breeding ponds decrease mortality of frogs?
What are sub-organismal toxicity levels that can be related to the population-scale?
Theme: Contaminants
  Subtheme: Management/operational effects on fate and transport
What are the impacts of different hydrologic scenarios and management actions (e.g., dam operations and flow management) on contaminant distributions and transfer of contaminants to food webs? (Primary)
What are the interactions between chemical and non-chemical habitat stressors?
Theme: Fish propagation
  Subtheme: Basinwide demographic effects
What is the relationship between basinwide hatchery production and the survival, fitness, and growth of naturally produced fish in freshwater, estuarine, and ocean habitats? (Primary)
Greater knowledge of the various ways in which hatchery fish interact, both directly and indirectly, with natural origin fish is needed to evaluate the cumulative effects of fish releases from the Basin’s hatcheries. Prospective management actions designed to lessen the cumulative impacts of hatchery fish become possible once the locations, life stages, types of impacts and their potential consequences have been identified. For example, the goals and size of supplementation programs could be regulated by estimating juvenile and adult carrying capacities in the subbasins where hatchery fish occur. It is unclear, however, if density-dependent considerations have been used or will be used to guide supplementation efforts in the Basin. Uncertainties also exist about the ability of segregated or integrated hatchery programs to meet adult production and harvest goals. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #6, for a discussion of progress made toward addressing this uncertainty.
Theme: Fish propagation
  Subtheme: Basinwide demographic effects - estuary
What are the effects of hatchery releases on the estuarine ecosystem? Experimental releases may be necessary to interpret ecosystem responses to hatchery programs.
Theme: Fish propagation
  Subtheme: Basinwide demographic effects - ocean
How do ocean productivity and river conditions affect smolt-to-adult survival rates? Is it possible to alter hatchery release numbers during years with predicted poor ocean or river conditions? What role does density dependence play in marine survival? How important are smolt size and growth rates in determining survival during the smolt out-migration period and throughout the ocean rearing period?
Theme: Fish propagation
  Subtheme: Ecosystem effects
What effect does fish propagation have on other species and the freshwater and estuarine habitats where they are released? (Primary)
What are the trophic consequences of adding hatchery fish to the system as well as the imported foods used to grow them and the waste products produced during rearing?
What are the food web consequences of imported foods to raise hatchery fish and hatchery effluent (e.g., nutrient load)?
Theme: Fish propagation
  Subtheme: Interactions/wild and hatchery
What is the cost, by life stage, to natural populations from competition, predation (direct and indirect), and disease caused by interactions with hatchery-origin juveniles and from harvest in fisheries targeting hatchery-origin adults? (Primary)
How should stocking practices for non-native species differ, in the context of the regional concern for production and conservation of native biota?
Does the overstocking of kokanee fry cause density dependent effects, leading to intraspecific competition, zooplankton overgrazing, and population declines?
How can potential density dependent impacts of hatchery releases on listed species be addressed?
Theme: Fish propagation
  Subtheme: Interactions/wild and hatchery - straying
What is the influence of out-of-basin stray hatchery fish on productivity of natural fish?
Theme: Fish propagation
  Subtheme: Interactions/wild and hatchery - food
Under what circumstances do hatchery fish displace or otherwise cause wild juveniles to move downstream (food limitations, space, and such), and what are the implications?
What are the ecological interactions between hatchery- and naturally-produced salmon within selected estuarine habitats, including, for example, effects on salmon feeding behavior and foraging success?
Theme: Fish propagation
  Subtheme: Interactions/wild and hatchery - predation
What are the impacts of hatchery releases on predator abundance and distribution, and what are the impacts on natural fish? Do releases of hatchery fish buffer natural fish from predators? Alternatively, does the number of predators and predation on natural fish increase because hatchery fish provide a forage base for predators, including sea lions?
Do hatchery programs increase the incidence of predation on naturally produced steelhead?
Theme: Fish propagation
  Subtheme: Interactions/wild and hatchery - pathogens
Do wild and hatchery origin fish have different susceptibilities to Renibacterim salmoninarum (bacterial kidney disease), Certomyxa shasta, and other pathogens? What are the mechanisms influencing Renibacterim salmoninarum infections and its effects on different species of salmonids and stock groups?
What is the potential for transmission of diseases and parasites from hatchery fish to native species, and what are the impacts?
Theme: Fish propagation
  Subtheme: Natural abundance and resilience
How can interactions between hatchery- and naturally-produced fish be reduced by spatial and temporal partitioning of natural and artificial production to achieve sustainable long-term productivity and resilience in wild populations at the subbasin, province, basin or regional scale? (Primary)
Theme: Fish propagation
  Subtheme: Natural abundance and resilience - harvest
Is Snake River steelhead management impacted by imprecise estimates of hatchery and wild adult fish harvested in the mainstem Snake River and Columbia River sport, tribal, and commercial fisheries?
Theme: Fish propagation
  Subtheme: Natural populations/demographics
What is the magnitude of any demographic benefit to the production of natural origin juveniles and adults from natural spawning of hatchery origin supplementation adults? (Primary)
It is not yet clear if hatchery supplementation provides a lasting demographic benefit to wild populations. Such appraisals require pre- and post-project reference streams, infrastructure to sample juveniles and adults, and genetic analyses to ascertain the pedigree of natural origin fish. Additionally, a suite of factors—including density-dependent effects, location of hatchery releases, habitat conditions, age and size of hatchery adults, spawning locations of hatchery fish, and genetic alterations to hatchery fish caused by domestication—can influence whether a hatchery program will provide a lasting demographic benefit to a natural population. Research is needed to unravel the relative importance of these factors in areas where supplementation has occurred. Results from these studies would help determine the level of supplementation that is appropriate for a subbasin on a species-specific basis. Additionally, in several subbasins hatchery supplementation is being used to reintroduce salmonids into areas where original populations were extirpated. Monitoring and evaluation programs are needed to track the abundance, local adaptation, and straying rates of the reintroduced fish as well as their potential impacts on local biota. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #3, for a discussion of progress made toward addressing this uncertainty.
What are the consequences of stopping a supplementation hatchery? Given the consequences, what is the best time to stop?
Are hatchery trout analogs of natural origin trout? Could they reduce carrying capacity, depending on characteristics of the hatchery fish (e.g., degree of domestication), as well as when, where, and how many are stocked? Are growth or survival impacted in the Columbia River Basin?
Theme: Fish propagation
  Subtheme: Natural populations/demographics - habitat
What are the impacts/effectiveness of artificially propagated populations in areas of restoration?
Theme: Fish propagation
  Subtheme: Natural populations/demographics - rebuild
What is the potential role of lamprey propagation and translocation as a way to mitigate for lost lamprey production when passage and habitat improvements alone are insufficient to restore lamprey populations? Specifically, can artificial propagation be used to supplement and restore depressed populations of Pacific lamprey? (Primary)
Artificial culture is being explored as a possible option to restore Pacific lamprey abundance and distribution. Many questions remain about the methods that should be used to artificially produce juvenile Pacific lamprey, particularly during the post-hatching and early rearing periods. Translocation or the capture of adult Pacific lamprey at lower river sites and subsequent release into up-river locations is also being investigated as a recovery strategy. Research, is needed to refine adult release locations and to determine the habitat features and environmental conditions necessary to make translocation a successful strategy. Some investigators have hypothesized that Pacific lamprey may not always home to natal river basins, such as the Columbia River. Thus, a fundamental uncertainty associated with translocation and artificial culture is whether these recovery strategies will have any effect on the number of adult Pacific lamprey returning to the Columbia River. Additionally, outbreeding caused by translocation could threaten local adaptations that are not yet recognized. Genetic analyses and sampling at sites such as Bonneville Dam may help answer these questions.
Can salmon and steelhead gametes be collected, preserved, and used to rebuild a population?
What is the freshwater survival and performance of hatchery fed fry, direct planted eyed eggs, and natural production following reintroduction of chum salmon into targeted subbasins?
Theme: Fish propagation
  Subtheme: Natural populations/demographics - safety nets
What effect do safety-net and conservation hatchery programs have on the viability and recovery of the targeted populations of salmon and steelhead?
Theme: Fish propagation
  Subtheme: Conservation/metapopulations
How might artificial production and supplementation impact or facilitate the maintenance or restoration of an ecologically functional metapopulation structure? (Primary)
Are hatchery origin adult outplants effective at producing adult offspring?
What are the adaptive consequences of genetic introgression of Snake River steelhead (from increased straying of transported fish) into Middle Columbia stocks of steelhead, some of which are listed under the Endangered Species Act (ESA)?
Is there an increase in the natural spawning population abundance and age composition diversity in succeeding generations following spawning by reconditioned kelts?
What is the feasibility and effectiveness of steelhead kelt reconditioning?
What is the effect of translocation on lamprey abundance and distribution?
What are the potential impacts on wild sturgeon from mixing of genetic stocks as part of broodstock and larval fish rearing mitigation efforts?
Five population units of white sturgeon are distinguished in the Columbia River: Lower Columbia, Mid-Columbia, Snake, Upper Columbia, and Kootenai. The Upper Columbia, Kootenai, and Snake population units are at risk because natural recruitment is sporadic and inadequate. These three population units span the areas where supplementation and translocation will take place. Typically just a few white sturgeon are used as broodstock in hatchery programs because of difficulties in capturing and maintaining maturing broodstock and achieving synchronous maturation. These constraints, along with low or non-existent natural recruitment, mean that genes from hatchery fish are likely to be disproportionately represented in future generations. Translocation of adults may also reduce genetic diversity if the population units they are introduced into have small natural spawning populations. The capture and subsequent rearing of naturally produced larvae is a promising new approach to white sturgeon conservation. Analyses have shown that naturally produced larvae originate from multiple parents and are genetically diverse. This is a new method, so refinements in where, when, and how to collect larvae plus how best to rear and release them are needed. Among hatchery propagation, translocation, and capture of naturally produced larvae, the latter appears to be the best strategy for maintaining genetic diversity. Uncertainties, however, about the genetic consequences of all of these approaches on wild sturgeon populations exist. To resolve them, it will be important to periodically monitor the genetic diversity of the white sturgeon population units where sturgeon recovery efforts have taken place.
Theme: Fish propagation
  Subtheme: Conservation/carrying capacity
How can information on the carrying capacity of freshwater habitat be used to establish the goals and limitations of supplementation programs within subbasins? (Primary)
Theme: Fish propagation
  Subtheme: Conservation/genetic effects
What are the range, magnitude, and rates of change of natural spawning fitness of integrated (supplemented) populations, and how are these related to management rules, including the proportion of hatchery fish permitted on the spawning grounds, the broodstock mining rate, and the proportion of natural origin adults in the hatchery broodstock? (Primary)
Because supplementation of salmonid populations is a widely used management strategy its effects on natural populations need to be understood. Important questions remain about how deleterious genetic changes may occur in cultured populations. Are genetic changes produced by low founder sizes (i.e., too few individuals contributing genes to the population) inadvertent domestication, variable family survival rates, by a combination of these elements or by other factors? Can management strategies be implemented to reduce the likelihood of genetic changes when fish are placed into hatcheries? Additionally, once genetic changes occur, what impact do they have on the fitness of natural populations that interbreed with hatchery fish? Studies within the Basin have examined how spawning fitness in natural populations of steelhead and spring Chinook has changed due to supplementation, and more studies are underway. Results from these investigations have improved our knowledge of how supplementation programs impact natural populations. Another component of this uncertainty is an assessment of the efficacy of the management guidelines that regulate (1) the proportion of hatchery fish allowed to spawn in nature and (2) the proportion of hatchery fish used as broodstock. These management guidelines are based on evolutionary theory and are logical. Additional empirical assessments, however, are needed to verify assumed effects. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #4, for a discussion of progress made toward addressing this uncertainty.
What factors create genetic differences between hatchery and natural origin fish? Are they largely caused by genetic drift (small founder populations) or by different selection pressures in hatchery and natural environments? Are some species more susceptible to genetic change than others?
What is the fitness of hatchery origin fall Chinook salmon from Snake River hatchery programs relative to natural origin Snake River fall Chinook?
What are the fall Chinook hatchery program effects on the productivity of the fall Chinook salmon ESU (evolutionarily significant unit)?
Theme: Fish propagation
  Subtheme: Conservation/genetic effects - pHOS
What are the impacts of releasing unmarked hatchery fish on achieving spawning escapement objectives for naturally spawning populations?
How can the number and distribution of hatchery origin fish spawning in streams at the MPG (major population group) or population scales be accurately determined in different areas and situations throughout the basin so pHOS (percentage hatchery origin spawners) and PNI (proportionate natural influence) can be estimated?
How many steelhead annually return to the Tucannon River, how many of them are hatchery fish, and what proportion of the naturally spawning population is made up of hatchery adults, i.e., pHOS (percentage hatchery origin spanwers)? Can a Generalized Random Tessellation Stratified (GRTS) sampling design be employed in the Tucannon River to address these questions?
Should the number of hatchery origin jacks allowed to spawn naturally be regulated and if so what rules should be applied?
Theme: Fish propagation
  Subtheme: Conservation/genetic effects - hatchery reform
At what level of supplementation do genetic and/or ecological risks outweigh demographic benefits, such that hatchery supplementation should be scaled back? (Primary)
What are the effects of implemented hatchery reform actions on the recovery of targeted salmon and steelhead populations?
Theme: Fish propagation
  Subtheme: Harvest/wild fish protection
Can hatchery production programs meet adult production and harvest goals (integrated and segregated) while protecting naturally spawning populations? (Primary)
Can integrated hatchery production programs meet adult production and harvest goals while protecting naturally spawning populations?
Can segregated hatchery production programs meet adult production and harvest goals while protecting naturally spawning populations?
Theme: Fish propagation
  Subtheme: Life history expression
What effect does artificial propagation have on life history expression in salmonids, and do these effects have implications for the performance of natural populations (e.g., shift in age composition, precocious development, migratory patterns, and fitness/genetic and ecological consequences)?
Theme: Fish propagation
  Subtheme: Life history expression - ocean
Do hatchery practices affect oceanic migratory patterns and the potential marine survival of salmon?
Theme: Fish propagation
  Subtheme: Hatchery fish as surrogates
Can hatchery-origin fish be used to research demographic and genetic processes in natural environments? (Primary)
Can experimental hatchery releases of white sturgeon along with monitoring be used to assess the factors limiting population productivity?
Theme: Fish propagation
  Subtheme: Propagation methods
Can new or improved artificial propagation methods at fertilization, during rearing, and at release be developed? (Primary)
What permanent tagging or marking technologies or techniques can be used to identify hatchery origin larval, fingerling, and YOY (young-of-year) white sturgeon to allow for early release? 
Can burbot be successfully cultured?
Theme: Fish propagation
  Subtheme: Propagation methods - adults
What can be learned regarding burbot genetics, burbot culture, and recruitment?
Can cryopreservation techniques be used to preserve viable sperm in Kootenai sturgeon?
Theme: Fish propagation
  Subtheme: Propagation methods - marking
Can Parentage-Based Tagging (PBT) be implemented at salmonid hatcheries to monitor smolt-to-adult survival, straying, and contribution to fisheries? What methods should be used to validate PBT based parental assignments?
Theme: Fish propagation
  Subtheme: Propagation methods - juveniles
As the numbers and densities of young pre-recruited white sturgeon increase in rivers, do hatchery-reared fish released at a longer fork length survive better than smaller fish?
What fish cultural methods should be employed to increase the survival of newly hatched white sturgeon to the vigorously feeding stage?
What procedures should be used in sturgeon culture to prevent mortality due to unequal growth rates during the early rearing period?
What is the best method to collect larval sturgeon for artificial propagation?
What methods can be employed at salmonid hatcheries to reduce the occurrence of precocious maturation and residualism? For example, does an integrated hatchery approach lead to greater production of mini-jacks?
What fish release strategies can be employed at salmonid hatcheries to reduce residualism, expedite out-migration rates, and increase post-release survival?
Can two-year-old steelhead juveniles be successfully reared at production hatcheries?
Is the high growth rate experienced by 1-yr-old hatchery steelhead smolts contributing to maladaptive behavioral traits or physiological deficits that lead to reduced post-release survival and genetic fitness? Second, can hatchery reforms be instituted to develop local steelhead broodstocks that can be released as 2-yr-old smolts and meet expected conservation and harvest objectives ?
How can hatchery practices be modified to improve survival, age at maturation, and contributions to fisheries?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Estuary assessment - estimation
What is survival of focal species (anadromous salmonids, white sturgeon, pacific lamprey, eulachon) in the estuary? (Primary)
Can we predict responses of salmonids (density, growth, survival) to actions that restore habitat conditions in the estuary (e.g., tidal channel geometry, vegetation, salinity, etc.)?
What conditions in the plume lead to improved salmonid survival that can be measured and used to adjust actions taken in freshwater (e.g., transportation, hatchery release timing, flow timing, and volume)?
How can we accurately assess fish habitat and levels of connectivity between restoration sites in the tidal freshwater and estuary?
How much do specific factors impact growth, fish condition, residence time, age at maturation and survival of focal fish species (anadromous salmonids, white sturgeon, Pacific lamprey, eulachon) in the estuary, plume, and ocean?
Quantifying the impact of specific factors on focal fish species in the estuary, plume, and ocean will lead to more efficient and effective management and restoration actions throughout the Basin. The impacts of some factors (i.e., avian predation on Chinook and steelhead smolts in the estuary) are relatively well researched, whereas little is known about the impacts of other factors (i.e., climate change, hypoxia, acidification, fish propagation, contaminants, disease, and invasive species). It is important to understand these impacts across the continuum of habitats used by each species. For example, factors impacting growth in the estuary may also affect subsequent growth and survival in the plume and ocean. Monitoring estuary and ocean survival is difficult, but other biological indicators such as fish growth, condition, residence time, and age at maturation may be more feasible to monitor. Research addressing this critical uncertainty would continue to build upon a growing body of scientific information on factors impacting estuary and early marine survival of juvenile salmonids. The uncertainty is relevant to all focal species, and the results would be useful for further development of predictive (run forecasting) and life-history models. This critical uncertainty is modified from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #19, for a discussion of progress made toward addressing this uncertainty.
To what extent can predictive models be used to evaluate the potential impacts of hydrosystem projects on estuary, plume, and coastal marine habitats and their biota?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Estuary assessment - relevance
What tidal freshwater, estuary, and plume habitats and their biota are most important to focal species (anadromous salmonids, white sturgeon, Pacific lamprey, eulachon)? (Primary)
To what extent do juvenile salmonids use the tidally influenced reach (river mile 40 to Bonneville Dam) compared with the reach downstream of this area, e.g., size of fish, residence time, foraging?
What are the status and trends of the ecosystem processes in the lower Columbia River and estuary?
What are spawning and rearing life history attributes of forage fish (including eulachon) in the estuary?
How do larval, juvenile, and adult sturgeon use areas downriver of Bonneville Dam, i.e., estuarine, tidally influenced freshwater, off-channel shallow water habitat and nearshore (to 600 feet) marine habitats?
Do salmonid life history, habitat use, and performance vary by stock?
How long do salmonids reside in the estuary and plume? How much do they grow, what is their overall health before migration, and what are specific migration patterns through the estuary and plume? How does all of this influence overall marine survival?
What is the role of riparian vegetation for juvenile salmonids along tidal channel margins?
What tidal freshwater and estuarine habitats and their biota are most important to focal species (anadromous salmonids, eulachon, sturgeon, and Pacific lamprey)?
What is the role of floodplain lakes/ponds for juvenile salmonids?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Estuary impacts
What are the impacts of mainstem dams and river flow regulation on estuarine habitats and their biota (e.g., sediment transport, circulation, natural nutrient-rich runoff, salinity intrusion, water temperature, dissolved oxygen, water quality, contaminants, biological productivity, community structure, evolutionary adaptation, invasive species, etc.)? (Primary)
Has there been a change in the diets of juvenile Chinook salmon in the estuary which might have influenced their growth (compared with past 1980's data)?
How do salinity, estuary turbidity maximum (ETM), and hypoxia affect forage fish that are consumed by salmonids?
What is the ecological role of large woody debris in: a) tidal marshes, b) river floodplains, and c) floodplain lakes and ponds on salmonids?
What is the ecological role and impact of pilings on salmonids? Do they need to be removed?
What are the ecological role and impact of dredging and dredge-spoil islands on salmonids?
What are the effects of wetting and drying of the floodplain habitats caused by complex hydrodynamic interactions of tides, mainstem and tributary flows, and the effect of the FCRPS (Federal Columbia River Power System) on river conditions?
What are the effects of climate cycles and global warming on salmonid performance in the estuary?
How is the timing of ocean entry and growth in the estuary related to subsequent stock-specific survival of salmonids?
How large are density dependence effects for salmonids in the estuary and ocean, including the influence of hatchery fish and/or invasive species (e.g., American shad juveniles)?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Estuary management and restoration
How do we determine how much habitat restoration needs to be done in the estuary?
How do restoration projects in the estuary contribute to reproductive success and rearing of forage fish (including eulachon)?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Estuary management and restoration - interactions
How can we efficiently and effectively manage and restore estuarine habitat to increase the carrying capacity of the estuary for salmonids and other focal species (anadromous salmonids, white sturgeon, Pacific lamprey, and eulachon)? (Primary)
This uncertainty is the bottom-line issue for this theme because results will assist the Council in working with partners in the estuary to establish clear biological objectives and indicators that prioritize future management and restoration actions. This uncertainty focuses specifically on carrying capacity, which is defined in the Program as "The number of individuals of one species that the resources of a habitat can support. That is, the upper limit on the steady-state population size that an environment can support. Carrying capacity is a function of both the populations and their environments." At present, we lack empirical evidence that management and restoration efforts in the Columbia River estuary have increased the carrying capacity of salmonid populations. The conceptual approach currently used by partners to evaluate the overall effectiveness of restoration efforts in the estuary does not directly involve measures of fish population dynamics (e.g., carrying capacity) that are used elsewhere in the Basin (ISAB 2012-6, 2014-1). This broad question addresses core goals of the Program to restore ecosystem function, enhance conditions for salmonids, and improve and expand habitat function, structure, and complexity in the estuary. Addressing this question will also contribute to the wild fish strategy in the Program, which states as a general measure that the Council will consider the needs of wild fish in all facets of its fish and wildlife program, including carrying capacity and habitat actions. Many sub-questions can be derived from this overarching question.
What are the responses of focal species (anadromous salmonids, white sturgeon, Pacific lamprey, and eulachon), life history types, and populations to alternative restoration actions and locations in the estuary, mainstem, and tributaries that will best inform management decisions?
The lack of information on responses of focal species, life history types, and populations to alternative restoration actions and locations throughout the Basin is a major information gap. Answers to this question will have direct application to guide future protection and restoration work. The scale of data collection is presently insufficient throughout the Basin to address relative benefits of restoration by life stage and habitat type. This uncertainty is relevant to all focal species, and the results would be useful for further development of predictive capabilities (e.g., run forecasting) and life-history models. This critical uncertainty is modified from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #17, for a discussion of progress made toward addressing this uncertainty.
Theme: Habitat estuary, plume, and ocean
  Subtheme: Estuary management and restoration - physical processes
How do the physical processes of tidal wetlands respond to different types of restoration actions (e.g., culvert replacement, number of dike breaches, self-regulating tide gates, channel creation)?
What is the amount of increased juvenile salmonid survival in the estuary that could reasonably be expected if all 23 management actions in the module were implemented, and what is the proportion of that increased survival that could be attributed to each action?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Ocean assessment - estimation
What is salmonid smolt survival in the ocean? (Primary)
Can early ocean data on Chinook salmonid smolt condition be used to predict jack rates?
How do factors limiting salmonid survival during their first weeks/months at sea relate to the causes of interdecadal fluctuations in salmonid production?
What is the significance of plume and nearshore ocean conditions on eulachon survival? Can we develop an ocean ecosystem indicators model of marine survival of eulachon?
What is salmonid survival in the plume and nearshore ocean (early survival)?
What is salmonid survival in the high seas?
What is overall survival at sea of each salmonid ESU (evolutionarily significant unit)/population?
What ocean factors can be used as indicators for forecasting of salmonid returns?
What is the ecological importance of the tidal freshwater and estuary, plume, and nearshore ocean environments to the viability and recovery of eulachon in the Columbia River Basin (ocean/plume or estuary)?
To what extent does mortality after the initial few months at sea affect overall salmonid survival and production trends?
Can SAR data (including survival estimates after smolts leave Bonneville Dam) be associated with estuarine and oceanographic conditions and salmonid life history diversity such as ocean entry timing, to further evaluate factors affecting salmonid survival and abundance?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Ocean assessment - relevance
What ocean habitats and their biota are most important to survival of each focal species (anadromous salmonids, white sturgeon, Pacific lamprey and eulachon)? (Primary)
What role do forage fish (including eulachon) have in survival of juvenile Chinook salmon, coho, and steelhead in the plume and ocean, such as by providing alternative prey to avian predators and sea lions?
What are the biological factors such as predators and prey affecting survival of focal fish species (anadromous salmonids, white sturgeon, Pacific lamprey, eulachon) in the plume and ocean?
What are the roles of the estuary and ocean in maintaining the sturgeon stock below Bonneville Dam?
What is the survival of subyearling Chinook salmon in ocean sandy beach surf zone habitat relative to estuary habitat and ocean pelagic habitat?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Ocean impacts
What are the mechanisms and relative magnitude of mortality by salmonid life stage that occur in the ocean compared with freshwater and the estuary? (Primary)
Do ecological interactions between natural and hatchery juvenile salmonids affect early marine survival of natural populations?
Do Columbia River salmonid smolts experience density dependent mortality in the ocean during years of low ocean productivity?
How variable is winter ocean mortality of juvenile salmonids among years, and what are the mechanisms that are involved with winter mortality?
What are the causal mechanisms and migration/behavior characteristics affecting survival of larval eulachon during their first weeks in the Columbia River estuary, plume, and ocean environments?
Do management actions in freshwater impact ocean ecology and survival of anadromous fish?
What are the effects of ocean conditions on lamprey?
What ocean conditions affect salmonid survival?
What are the causal mechanisms and migration/behavior characteristics affecting survival of larval eulachon during their first weeks in the ocean?
How does estuarine habitat degradation affect abundance, survival, and production of focal fish (anadromous salmnids, white sturgeon, Pacific lamprey, eulachon) and wildlife, and what are the legacies of past effects?
Do factors such as diversity in timing and size at ocean entry (both between and within stocks) affect the resilience of salmonid populations to increasingly variable ocean conditions?
What are the impacts of mainstem dams and flow regulation on plume and ocean habitats and their biota (e.g., coastal erosion, decrease natural nutrient rich runoff, increase salinity due to reduced freshwater flow)?
How do climate change, hypoxia, and ocean acidification affect survival of focal fish species (anadromous salmonids, white sturgeon, Pacific lamprey, eulachon) in the estuary, plume, and ocean?
What is the combined effect of the warm water mass that emerged off the Pacific Northwest coast in 2013 (the “blob”) and El Nino and La Nina conditions?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Ocean management and restoration
Is there information we can learn from ocean research that might help how we manage in the river (e.g., flows, hatcheries, habitat)? (Primary)
Can monitoring of ocean conditions and abundance of salmon and steelhead during their first weeks or months at sea improve our ability to predict interannual fluctuation in the production of Columbia Basin evolutionarily significant units (ESUs) or populations to enable appropriate changes to harvest levels?
Theme: Habitat estuary, plume, and ocean
  Subtheme: Ocean management and restoration - interactions
How can interannual and interdecadal changes in ocean conditions be incorporated into management decisions relating to hydrosystem operations, the numbers and timing of hatchery releases, and harvest levels to enhance survival rates, diversity, and viability of ESA-listed salmonids?
How can interannual and interdecadal changes in ocean conditions, including hypoxia and acidification be incorporated into management decisions relating to hydrosystem operations, the numbers and timing of hatchery releases, and harvest levels to enhance survival rates, diversity, and viability of ESA-listed salmonids?
Theme: Habitat mainstem
  Subtheme: Assessment
How much spawning and rearing habitat is available to white sturgeon above and below Bonneville Dam under a range of actual operational conditions? How do these conditions differentially affect spawning success and juvenile growth and survival to the recruitment stage and their entire lifespan?
Nearly all white sturgeon habitat in the Basin is in mainstem reaches of the Columbia and Snake rivers and major tributaries. As a result, every life stage of this species is impacted by conditions in the mainstem. This is an especially critical uncertainty above Bonneville Dam where environmental conditions have led to a lack of recruitment. Managers’ actions to propagate, translocate, or otherwise increase the number of white sturgeon will not be successful if there is inadequate mainstem habitat—and connectivity between habitats—in which they can grow and mature. Also see the Population Structure and Diversity section of this report for other uncertainties related to white sturgeon.
Theme: Habitat mainstem
  Subtheme: Assessment - relevance
Where, when, and at what frequency under different conditions do salmonids and other native species use coldwater thermal refuges in the lower Columbia and Snake rivers? (Primary)
The need to identify locations of thermal refuge and how to enhance them will be increasingly critical to the preservation and enhancement of salmon in mainstem habitats under increased temperature regimes projected with climate change. For example, high water temperatures are thought to be a major contributor to the high mortality in returning sockeye salmon in 2015. The effects of climate change are already being experienced and are likely to escalate in a relative short period of time.
What should the magnitude and timing be for restored flows and temperature regimes for the free-flowing segments (Hanford Reach) of the river?
What are the substrate and hydraulic conditions associated with successful white sturgeon incubation?
To what extent are riparian and off-channel shallow water habitats used by white sturgeon early life history stages in the Ives and Pierce Island complex downstream of Bonneville Dam? What are the effects of daily and hourly flow variations associated with power peaking on survival of early life history stages in riparian and off-channel shallow water habitats?
What are slough characteristics that provide benefits to white sturgeon survival during early life history stages and recruitment? Are there potential slough restoration sites that would provide benefits to white sturgeon?
What are the optimal temperature and water quality regimes for fish survival in mainstem reaches affected by dams, and are there options for hydrosystem operations that would enable these optimal water quality characteristics to be achieved?
Based on feeding ecology, what is the relative importance of non-native prey items such as American shad and Asian clams to white sturgeon? What are the effects on white sturgeon of a diet consisting of various combinations of native and non-native prey items Does foraging on thiaminase-rich American shad have a negative effect on white sturgeon? Are food resources sufficient for all life stages of sturgeon throughout the river and in various segments? What is the carrying capacity, especially in pools? How may various management actions affect food resources for white sturgeon (e.g. shad, reestablishing lamprey, shellfish). How can bioenergetics modeling and food web analysis contribute to our understanding of carrying capacity and conditions affecting growth, survival and recruitment? How does reservoir productivity affect carrying capacity?
Theme: Habitat mainstem
  Subtheme: Assessment - Remote sensing
How do sedimentation and sediment transport changes resulting from operations positively or negatively affect white sturgeon spawning site selection and success? How do changes in sediment transport as it affects turbidity affect juvenile sturgeon growth and survival to the recruitment stage?
Theme: Habitat mainstem
  Subtheme: Assessment - Estimation
What are the appropriate metrics for assessing fitness of migrant salmonids and other species as they move past dams, through reservoirs, and through habitats with differing food webs?
Can an effective and validated white sturgeon habitat model be developed for the Upper Columbia River throughout the year in conjunction with mainstem hydrosystem operations?
Where are the remaining locations and conditions where inriver gas supersaturation continues to significantly reduce salmonid survival, and how can conditions in these locations be ameliorated?
Theme: Habitat mainstem
  Subtheme: Impacts of hydro operations and other factors
How does habitat degradation affect abundance, survival, and production of fish and wildlife in the mainstem and what are the legacies of past effects? (Primary)
Theme: Habitat mainstem
  Subtheme: Impacts - inriver
What are the effects of shoreline modifications along reservoirs (rip-rap, erosion, and permanent sloughs) on sub-yearling Chinook salmon, compared to the normative river condition?
Are fine sediments stored on the bottom of mainstem reservoirs problematic for restoration of drowned flood plains owing to extreme turbidity resulting from flushing of fines downstream after drawdown?
How does dredging and in-water work contribute to operational related mortality of white sturgeon at different life stages?
How does dredging and in-water work contribute to operational related mortality of lamprey at different life stages?
How does the productivity of mainstem habitat for white sturgeon recruitment to adulthood differ by reach and reservoir, and how can any differences best be estimated and measured?
What is the impact of past spawning and rearing habitat losses on white sturgeon population dynamics?
What are the effects of channel modifications (e.g., channelization, diking, piles, and gravel extraction) on habitat and white sturgeon recruitment (including dispersal rates of larvae and sub-yearling white sturgeon)?
What role do changes to the historical mainstem habitat (prior to dam construction) have in changing the density-dependent responses of salmon, sturgeon, and other species (anadromous and resident)?
Understanding the carrying capacity of the current mainstem habitats for focal species is critical in assessing density-dependent responses to fish stocking and other management actions. For example, are current stocking levels exceeding current carrying capacity? This uncertainty has basinwide consequences and is applicable as long as there are dams in the river system. Furthermore, habitats may have been irreversibly changed after dam construction (See Programmatic Comment 6). If current capacity is far below historical levels, can it be increased?
How do habitat changes resulting from operational decisions regarding flow and spill affect rearing and passage conditions for salmon, sturgeon, lamprey, and other species?
How is mainstem habitat quantity and quality for different species affected by water quality (temperature, dissolved gas, and other parameters)?
What are the effects of different levels of turbidity on juvenile white sturgeon survival as it affects recruitment?
What is the effect of the proposed construction (e.g. spill training wall) in the tailrace of The Dalles Dam on white sturgeon spawning habitat quantity, quality, and distribution?
Theme: Habitat mainstem
  Subtheme: Impacts - Food webs
How do nutrient concentrations, primary production and secondary production affect sturgeon recruitment to harvest fisheries? How does predation from higher trophic levels in these food webs affect sturgeon recruitment to harvest fisheries?
Theme: Habitat mainstem
  Subtheme: Restoration
How might operational decisions and other mainstem habitat actions maintain and improve focal populations of anadromous fish, resident fish, and wildlife? (Primary)
This is an important uncertainty because much effort and money has been and likely will continue to be spent on efforts to restore habitat for focal species in mainstem habitats. Can these efforts be enhanced by operational changes? Are there operational changes that negate the benefit of habitat improvements? Are there operational changes that are more effective under different climate regimes (e.g., La Niña)? Resolving this uncertainty will be particularly important under projected impacts of climate change.
What are the impacts of hydrosystem operations on mainstem habitats, including the freshwater tidal realm from Bonneville Dam to the salt wedge? How might hydrosystem operations be altered to recover mainstem habitats?
Theme: Habitat mainstem
  Subtheme: Restoration - Physical processes that create habitat
How would sturgeon respond to reestablishment of riparian floodplains and riverine-floodplain food webs?
For white sturgeon, what are the merits of creating spawning habitat and early rearing habitat in selected tailrace areas? For example, how does the use of artificial substrates and instream structures improve white sturgeon egg and larval survival and relocate sturgeon spawning?
Theme: Habitat mainstem
  Subtheme: Restoration - Interactions
How can sturgeon reproductive success be improved by creating a more normal hydrograph and thermograph? Can sturgeon reproductive success be improved by attracting fish to more suitable substrates?
How do water temperature fluctuations and seasonal changes resulting from Columbia River hydrosystem operations affect growth, survival, and habitat use of white sturgeon?
What would be the effects of operational changes for optimizing water temperatures and water quality for fish in shoreline and riparian habitats, as well as for wildlife in these habitats?
What should be the magnitude and timing of restored flows, ramping rates, and temperature regimes for the free-flowing segments of the river?
What is the relationship between recruitment failure and habitat conditions for white sturgeon? Can natural recruitment of white sturgeon be improved by operational changes in water management?
Theme: Habitat tributary
  Subtheme: Assessment
How do fish populations respond to change in habitat conditions? (Primary)
What is the extent and distribution of cold water refugia in the Columbia Basin?
What is the spatial distribution of low dissolved oxygen? What are the effects on behavior and physiology?
What is the role of density dependence in Pacific lamprey population decline?
How do changes in biological productivity affect white sturgeon and their habitats?
Theme: Habitat tributary
  Subtheme: Assessment - relevance
Is current habitat carrying capacity sufficient to support sustainable populations of both native and hatchery fish? (Primary)
What are the time and data resources needed to detect the effects of a habitat restoration action, or collection of actions, on target populations?
What are the limiting factors for riparian avian productivity in target species?
What are the limiting factors for productivity of small populations of grassland/sage target species?
Are projects and watershed level assessments of habitat, habitat restoration and fish productivity beneficial? (For example, in the RPA pilot subbasins: Wenatchee, Methow and John Day Rivers.)
What are the critical habitat variables to measure, and are they being measured at the right scale to assess what fish use and need at each life stage (spawning, rearing, migration)?
What are the stream habitat and landscape-level characteristics and conditions at fish sampling sites?
What are the incidence and benefits of sage grouse re-using abandoned leks? How does this inform acquisition and restoration actions and prioritization?
Theme: Habitat tributary
  Subtheme: Assessment - Remote sensing
Can remote sensing (drones, aircraft, satellites, etc.) replace on-the-ground measurements? (Primary)
Theme: Habitat tributary
  Subtheme: Assessment - Estimation
Of the marine-derived nutrients recruited to streams naturally (and through nutrient supplementation), how much is exported from watersheds through smolt emigration, insect emergence, and in suspended material?
What is the quality of fish habitat on private lands throughout the basin? How significant are dewatering of streams, elevated stream temperatures? What is the status of riparian habitat and overall habitat integrity?
What are juvenile and adult lamprey mainstem and tributary habitat capacities? (e.g., rearing, spawning, migration), and requirements (i.e., passage, screen impingement, entrainment, etc.)
Theme: Habitat tributary
  Subtheme: Impacts - instream
How have past impacts to stream channels and riparian areas (water diversion, channelization, dredging, large wood removal (snagging), gravel mining, mining for precious metals, etc.) affected past and current abundance, survival, and production of fish and wildlife? (Primary)
What are limiting factors and improved methods for monitoring and evaluating the status and distribution of lamprey, lamprey habitat, and lamprey passage?
How will water quality improvements enhance aquatic community diversity, abundance, and prey quality?
Have fewer pieces of large wood reduced low velocity habitat needed for overwintering, fry colonization and active rearing?
Are fine sediments a limiting factor for bull trout abundance and recovery, and if so, where?
Theme: Habitat tributary
  Subtheme: Impacts - riparian
How have grazing, logging, mining, agriculture and other riparian habitat degradation affected fish and wildlife, past and present? (Primary)
Does the decrease in shading from reduced and degraded riparian zones lead to 1) an ecologically significant increase in maximum water temperatures and 2) an increase in winter icing conditions?
Theme: Habitat tributary
  Subtheme: Impacts - upslope watershed
How have resource management practices and land uses in the watersheds upslope from riparian zones affected fish and wildlife, past and present? (Primary)
Theme: Habitat tributary
  Subtheme: Impacts - Movement and migration barriers
How has the reduction in stream connectivity caused by development (road-stream crossings, water diversions, large dams, etc.) affected fish and wildlife populations? (Primary)
What is the impact on adult lamprey when they must pass over multiple diversion dams to reach putative spawning areas?
Does the type of screening present on a diversion dam influence larval entrainment?
When do larval lamprey enter irrigation canals? Does it occur at the time an irrigation gate is raised in the spring or do they steadily enter throughout the irrigation season?
What is the fate of lamprey juveniles that enter a diversion canal?
How can fine sediment be controlled in diversion canals so that larval lamprey will not find them attractive rearing areas?
Theme: Habitat tributary
  Subtheme: Impacts - Food webs
How has degradation of instream, riparian and upslope habitats affected food webs that support resident and anadromous fish species past and present, and what are the legacies of past effects? (Primary)
What are the sustainable food web structures for various habitat types? For each broad type of habitat, how do sustainable food web structures compare with degraded food web structures? And which habitat types should be protected or restored? (Primary)
What are the trophic consequences of adding hatchery fish to the Columbia River system, the foods imported used to grow them, and the waste products generated during rearing?
What are appropriate planning goals for biota and food webs under climate, land use, and other changes?
How can we more accurately, thoroughly, and efficiently measure food webs and their interactions with their environments?
Where are rapidly changing habitats that are matched with stable reference sites? How do biotic components and abiotic parameters differ between them? [translate those differences into “real time” and “real world” sensitivity analyses, by characterizing the changes that occur in the food webs, and extrapolate from these empirical comparisons to wider predictions, and from there to policy choices.]
How accurate are predictions about the most effective food webs to sustain and enhance species of interest?
What are the relationships between river discharge, floodplain inundation, food webs and fish production? How does large scale and seasonally appropriate floodplain inundation affect the food web?
What are the fluxes of nutrient organic matter, water and thermal energy in natural and altered systems, and what are the consequences of such alterations to fish?
How can we more accurately, thoroughly, and efficiently measure food webs and their interactions with their environments?
What are the links between river discharge, floodplain inundation and fish production, and what are the food web effects of large scale and seasonally appropriate floodplain inundation?
What is the ability of the system to produce foods to support proposed or anticipated numbers of both wild and hatchery reared fishes at a level promoting adequate growth and/or successful migration?
What is known about biotic and abiotic factors, as well as processes, governing food web structure and function?
What are the responses of fish communities to the transition from oligotrophic to mesotrophic to eutrophic states in various environments?
What is the relationship between nutrient and prey fluxes in wetlands and their surrounding environments and what processes control nutrient cycling in these areas?
Theme: Habitat tributary
  Subtheme: Restoration
Do increases in pool quantity, quality and complexity increase survival of steelhead in the following life stages: a) incubation; b) subyearling rearing; c) overwintering; d) yearling rearing?
Does a decrease in summer temperatures increase survival of steelhead in the following life stages: a) subyearling rearing; b) yearling rearing?
Does a decrease in bedscour increase survival of steelhead in the following life stages: a) incubation; b) overwintering. Spring Chinook survival will increase in the following life stages: a) incubation; b) overwintering; c) fry?
Does an increase in summer flows increase survival of spring Chinook and steelhead in the following life stages? a) subyearling rearing; b) yearling rearing?
What is the effectiveness of water transactions in improving the survival of fish and other aquatic organisms?
Can social engagement and economic incentives be used to increase water flow in salmon-bearing rivers?
Is it feasible to purchase enough water, or change timing or location sufficiently, to improve ecological functions?
Many water purchases are short term, and may only be for one year, or a short period. Are these short periods sufficient to create a meaningful impact?
Can acquired or contracted water be accurately measured for delivery to streams and rivers to benefit fish and wildlife?
Does restoration of riparian vegetation increase input of terrestrial invertebrates, which can increase growth and abundance and decrease emigration of natural-origin trout?
What are the effects of individual habitat restoration actions at project sites and what are post-restoration trajectories based on project-specific goals and objectives?
What are the cumulative effects of habitat conservation and restoration projects in terms of cause-and- effect relationships between ecosystem controlling factors, structures, and processes affecting salmon habitats and performance?
Does managed grazing decrease spread of non-native understory plant species and help reestablish a native plant community?
Does increasing beaver presence restore hydrological function (groundwater recharge and discharge, riparian vegetation, etc.) to floodplains?
Do silvicultural practices that retain large tracts of intact late seral forests decrease temporary fragmentation of focal species?
Does removing reed canary grass (decreasing monotypic stands) increase presence of native species, and increase habitat quality for wildlife?
How can habitat restoration activities or hydrosystem operations modify groundwater-surface water interactions and floodplain habitats to provide refuges during extreme events and improve overall survival, productivity, distribution, and abundance of anadromous and resident native fish populations?
How do riparian revegetation efforts affect changes in fish and wildlife species composition inhabiting those areas?
What are the causes and impacts of increased presence of didymo in some parts of the Basin? And what are the methods to control it?
Can habitat restoration, removing barriers, and transporting fish above barriers sufficiently increase carrying capacity to recover native wild fish populations in the face of introduced hatchery fish and non-native invasive species that also compete for the same resources?
The goal of restoring habitat in tributaries, and removing barriers or transporting fish above them, is to increase carrying capacity in tributaries where habitat has been degraded or lost to barriers like dams and culverts. However, a critical uncertainty is whether restoring or reconnecting this habitat is sufficient by itself to recover native fish and wildlife populations, and whether hatchery or non-native invasive species will usurp these resources and prevent benefits to native populations. If the uncertainty is not addressed, then it could be that restored habitat often will be dominated by hatchery fish or non-native species and, therefore, be of little benefit for recovering native wild fish. Addressing whether or not transporting anadromous and resident fish around barriers will aid in recovering populations will help determine the cost-effectiveness of this approach.
Theme: Habitat tributary
  Subtheme: Restoration - dam removal and reintroductions above dams
How much does eliminating barriers (removing dams and culverts, or transporting migrating fish above dams) increase carrying capacity and contribute to recovering important fish populations? (Primary)
Does dam removal lead to an increase in recreational activity associated with poaching of adult salmon and steelhead and harassment of adults prior to and during spawning?
How will spawning be affected by the changes in habitat associated with the modification or removal of a dam?
Theme: Habitat tributary
  Subtheme: Restoration - mitigation via restored tributary habitat
How much can restoring habitats (e.g., for spawning, rearing, and refuges) in tributaries mitigate for degraded conditions throughout the rest of the Basin (e.g., mainstem habitat lost to dams, degraded estuary habitat, and unfavorable ocean conditions)? (Primary)
This is the most critical question of the Tributary Habitat theme, and it must be addressed at the largest scale and throughout entire fish life cycles. The main issue is that the benefits of restoring tributary habitat interact with mainstem, estuary, and ocean habitat conditions, with fish passage through the hydrosystem, and with other stressors such as non-native species and toxic chemicals. These interactions are not well understood. By addressing this uncertainty managers will know whether restoring tributary habitat to mitigate for degraded habitat elsewhere is effective, and the use of available resources will be improved. This critical uncertainty was modified from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #13, for a discussion of progress made toward addressing this uncertainty.
Is the region’s investment in an evolving suite of habitat actions contributing significantly to the recovery and rebuilding of fish species important to the region?
Theme: Habitat tributary
  Subtheme: Restoration - physical processes that create habitat
What physical processes must be restored or maintained at what spatial and temporal scales to create and maintain the habitats needed by fish and wildlife? (Primary)
What are the options and effectiveness of actions to reduce water temperature for steelhead?
What is the need and magnitude of adding nutrients as part of an ESU (evolutionarily significant unit)-wide plan to determine where, how, and how much nutrient supplementation is beneficial?
Is placement of fish carcasses by field crews at least as effective as carcasses placed through natural spawning processes?
What are the public perceptions of controlled nutrient additions as pollution, especially if nutrients are sourced from treated wastes?
Does reduction in sediment (turbidity, percent fines and embeddedness) increase survival of steelhead in the following life stages: a) incubation; b) subyearling rearing; c) overwintering; d) yearling rearing? Spring Chinook survival in the following life stages: a) incubation; b) yearling rearing; c) fry?
Does an increase in LWD densities increase survival of steelhead in the following life stages: a) incubation; b) subyearling rearing; c) overwintering; d) yearling rearing? Spring Chinook survival will increase in the following life stages: a) overwintering; b) yearling rearing; c) pre-spawning?
Does an increase in riparian function and a decrease in confinement increase survival of steelhead in the following life stages: a) incubation; b) subyearling rearing; c) overwintering; d) yearling rearing? Spring Chinook survival will increase in the following life stages: a) overwintering; b) yearling rearing; c) fry d) pre-spawning?
Does managed grazing in riparian areas help reduce the damage to riparian understory vegetation, and in turn avoid the narrowing of stream channels and reverse increases in water temperature?
Does avoiding road-building activities, restoring habitat on abandoned roads or railroads, and relocating problematic roads decrease stream bank erosion, decrease sediment loads to rivers, and decrease disturbance to nesting species?
Does increasing floodplain area in selected reaches allow for hydrologic reconnection into wetland habitats?
Does reintroducing fire into used and potentially used squirrel habitat increase the quality of the habitat and result in greater numbers of western gray squirrels?
Does increasing the number of larger, late seral ponderosa pine and Oregon white oak trees within Lewis’ woodpecker range increase available nesting trees and forage and thus increase in presence and numbers of Lewis’ woodpecker?
Does restoring stream channels in selected reaches allow for hydrologic reconnection into wetland habitats?
Does relocating wetland meadow roads, reducing or improving stream crossings, and locating motorized recreation to more appropriate sites improve hydrologic conditions, reduce fragmentation, and decreases disturbance to sensitive wildlife?
Does limiting silvicultural practices above meadows and enforcing a buffer around meadows decrease sediment release in meadow hydrology and increase water quality for fish and wildlife needs?
Does decreasing the loss of wetlands stabilize populations of important fish and amphibian species?
Does increasing water quality in important breeding ponds increase survivorship of tadpoles?
Does reestablishing corridors of movement enable beaver to reestablish themselves in historical locations?
Does restoration of riparian vegetation increase food availability and quality for beaver, increasing survivorship and establishment efforts?
What is the effectiveness of present stormwater best management practices at both site-specific and watershed scales?
How successful are best management practices (e.g., re-regulation of flows, forest and riparian grazing prescriptions, pollution abatement, crop rotation) in reducing habitat degradation?
What is the relationship between sediment sources in a catchment and instream effects on the habitat of important fish species?
Does reestablishing a long term natural fire regime benefit target species?
How effective are aspen regeneration management methods in different fire and grazing/browsing regimes?
Are treatments to improve channel complexity and fish productivity in the Entiat River Basin effective?
Are treatments to reduce entrainment and provide better fish passage flow conditions in the Lemhi River Basin effective?
Are treatments of channel incision and its effects on passage, channel complexity and fish productivity in Bridge Creek (John Day River basin) effective?
Does reintroduction of an ecologically-based fire regime decrease encroachment of conifers into montane wet meadows, increasing the water table and reestablishing proper hydrological function?
What are the specific downstream ecosystem impacts, in terms of biological community changes, of nutrient addition projects?
How do streamflow, sediment, and large woody debris interact under current management regimes? How do those geomorphic processes sustain the success of aquatic and floodplain restoration projects for biological benefits?
Which nutrients have the greatest effect on the productivity of food webs, and are existing concentrations limiting or enhancing productivity?
What land use actions can be implemented to result in improved water quality?
Theme: Habitat tributary
  Subtheme: Restoration - interactions
Will any increase in carrying capacity be usurped by non-native invasive species, preventing recovery of native fish and wildlife populations? (Primary)
What watershed and landscape-scale configurations and combinations of protected and restored habitats (aquatic, riparian and upland) are most effective at meeting the life cycle needs and sustaining populations of fish and wildlife in tributaries? (Primary)
Does management of livestock grazing in wetland areas minimize damage to native meadow and streamside vegetation, reduce damage to stream banks, and reduce pollution in streams and ponds?
Do new habitats, appropriate for specific populations, have a negative impact on other populations? Do proposed mitigation actions cause problems for other wildlife or ecosystem attributes?
Does in-stream habitat restoration increase carrying capacity for resident trout and increase density (by increasing survival and decreasing emigration rather than affecting growth, fecundity or immigration)?
What pattern and amount of habitat protection and restoration is needed to ensure long term viability of fish and wildlife populations in the face of natural environmental variation as well as likely human impacts on habitat in the future?
How effective are nutrient additions and what techniques of nutrient addition are most beneficial (cumulative effects, how many sites are needed in a watershed, how much is too much, what forms are the most cost-effective, etc)? In other words, will adding nutrients, carcass analogs or carcasses lead to increases in ecosystem-scale productivity and food web pathways that result in more fish of interest to the program, or will the nutrient additions lead to other food web pathways?
Theme: Habitat tributary
  Subtheme: Restoration - role of variability
Is the protection and restoration of watersheds and riparian/aquatic habitats sufficient to sustain fish populations during periods of unprecedented climate that cause extreme events (e.g., droughts or floods) and in watersheds declining in overall condition? (Primary)
Extreme climate events are becoming more frequent (e.g., Salathé et al. 2010) and causing extreme and unfavorable habitat conditions for fish and wildlife. A highly critical question is whether restoration can provide resilience to buffer against these extremes sufficiently to sustain and recover native species of interest.
Theme: Habitat tributary
  Subtheme: Restoration - socio-political processes
What governance structures and stakeholder engagement processes allow achieving restoration at the scale needed to sustain focal fish populations? (Primary)
Theme: Harvest
  Subtheme: Assessment ocean, catch and bycatch
What is the catch and bycatch in the ocean by species, stock (including evolutionarily significant units [ESUs]) and hatchery/wild origin? (Primary)
Can hatchery harvest rates be a reasonable surrogate for wild chinook harvest rates in the ocean?
How many hatchery versus natural salmon are captured in the ocean?
Is uncertainty about ocean harvest a source of bias in SAR (smolt-to-adult return ratio) estimates?
Theme: Harvest
  Subtheme: Assessment ocean, catch and bycatch - new techniques
What new techniques can be used for stock identification?
Theme: Harvest
  Subtheme: Assessment inriver, catch and bycatch
What is the catch and bycatch and escapement in freshwater by species? (Primary)
Theme: Harvest
  Subtheme: Assessment inriver, catch and bycatch - species, stock, hatchery/wild origin
To what extent does inconsistent sampling of commercially caught steelhead underestimate the interception of non ad-clipped endemic hatchery steelhead downriver?
Can hatchery harvest rates be a reasonable surrogate for wild chinook harvest rates in freshwater?
How many hatchery versus natural salmon are captured inriver?
Theme: Harvest
  Subtheme: Target reference points
What is the spawning escapement or harvest rate (range), accounting for hatchery and natural fish and nutrient return, needed to sustain productive fish populations and fish harvests in the future? What is the biological goal for spawning escapement? (Primary)
This knowledge is needed to understand if escapements are sufficient to achieve the Fish and Wildlife Program's Appendix D Goal 13: "Achieve full mitigation for anadromous fish, native resident fish, and wildlife losses by restoring healthy, self-sustaining, and harvestable, natural-origin anadromous fish….and resident fish." A biologically based spawning escapement goal is the number of spawners required to potentially maximize the average harvest or return for a specific population in the foreseeable future. Knowledge and application of biologically based spawning escapement goals are fundamental to sound harvest and hatchery management. Where possible, biological escapement goals should be based on stock recruitment curves (i.e., the relationship between parent spawning escapement and the abundance of their progeny). These goals, which consider productivity and carrying capacity of the population (See Programmatic Comment 6; ISAB 2015-1), can be used to evaluate effects of harvests on fish populations (or stock management units) and to identify when observed spawning escapements are too low, adequate, or too high. The biological goals should also consider (1) pHOS guidelines developed by the Hatchery Scientific Review Group (HSRG) and (2) if spawner abundances in excess of carrying capacity are needed to support ecosystem function. Some biologically based goals already exist in the Basin, but many more could be developed.
What are the long-term harvest requirements of tribal and non-tribal fisheries, and what is progress towards these long-term goals?
What are the harvest goals for each hatchery as recommended by the Hatchery Science Review Group?
In view of burbot's decline in many locations, how plausible is it to develop and promote fisheries for them?
Theme: Harvest
  Subtheme: Impacts
What are the impacts of directed (intentional) and incidental (unintentional) harvests on population-specific characteristics and productivity of Columbia River Basin fishes? (Primary)
Theme: Harvest
  Subtheme: Impacts - catch and release mortality
What is the catch-and-release mortality by species and stock, and in relation to environmental variables in the ocean, estuary and freshwater?
Theme: Harvest
  Subtheme: Impacts - new strategies, techniques (such as selective fisheries)
What new harvest and escapement strategies (including selective harvest) can be employed to improve harvest opportunities and ecological benefits within the Columbia River Basin while minimizing negative effects on ESUs (evolutionarily significant units) or populations of concern?
This question is fundamental to Fish and Wildlife Program’s Appendix D Goal 18: "Enhance harvest of anadromous fish….." and the legal requirement to mitigate for lost fishing opportunities. Harvesting surplus hatchery fish could benefit both people and natural origin populations; opportunities to do so exist when the total spawning escapement exceeds carrying capacity. Some strategies exist for targeting surplus hatchery fish, but further development is needed to address challenges such as catch and release mortality and opposition to marking fish visually and releasing fish that have been captured. Concerns that efficient use of surplus hatchery fish might lead to reduced efforts to restore habitat and improve production of natural populations must be addressed. This critical uncertainty is from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #25, for a discussion of progress made toward addressing this uncertainty.
Theme: Harvest
  Subtheme: Impacts - ecological
How can the multiple ecological benefits that salmon provide to the watersheds where they spawn (e.g., provision of a food resource for wildlife and a nutrient source for streams and riparian areas) be incorporated effectively into procedures for establishing escapement goals? (Primary)
Theme: Harvest
  Subtheme: Impacts - population structure, productivity, size/timing selected harvest
What are the impacts of different harvest regulations on population structure and characteristics (e.g., size selective harvest, early run vs. late run, etc.)? (Primary)
Can stock-specific data on ocean abundance, distribution, density-dependent growth and survival, and migration of salmonids, both hatchery and wild, be used to evaluate and adjust marine fishery interceptions, harvest, and hatchery production in order to optimize harvests and ecological benefits within the Columbia River Basin?
Does harvest impact adult productivity?
What are the impacts of a variety of fishing techniques and harvest strategies, including estimated illegal harvest and post-release mortality from commercial and recreational fishing, on white sturgeon population productivity?
How can fishery interceptions and harvests of ESUs or populations, both hatchery and wild, best be managed to minimize the effects of harvest on the abundance, productivity, and viability of those ESUs and populations?
Most fisheries in the ocean and in the Columbia River mainstem harvest salmonids from a variety of populations and hatcheries. Better information is needed on the stock composition of fish in mixed-stock fisheries both within and outside the Basin to manage and evaluate harvest impacts on natural-origin populations. Newly emerging tools could improve the accuracy and the cost effectiveness of stock identification. The information can be used adaptively by managers to achieve harvest rates (range) needed to sustain productive fish populations and fish harvests in the future (see Biological Goal above for identification of sustainable harvest rates). This critical uncertainty is derived from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #24, for a discussion of progress made toward addressing this uncertainty.
Theme: Human development
  Subtheme: Impacts
How might the projected changes in society’s use of land and other resources, as well as protection and restoration efforts under different future scenarios, affect environmental quality, habitats, and fish and wildlife populations? What changes in human population levels and their distribution, per capita income, and economic activity are expected over the next 20 years?
There is uncertainty about changes in the human system and in society's support for restoration efforts, including how changing preferences will affect collective actions. The human and natural systems of the Pacific Northwest are not static, and changes such as population growth, land development, and technological innovation will influence the effectiveness of restoration efforts. Most models of projected salmon and steelhead populations in the Basin do not incorporate future change in the human system. Fortunately, growth in population and associated changes in land use can be predicted, indicating areas where landscape and riverscape changes are most likely to occur (e.g., due to urban expansion). Other changes that will impact environmental quality, water scarcity, and resource depletion may be more uncertain. Effects of future changes in human systems on natural resources can be projected and evaluated with a range of model types representing coupled human-natural systems. This critical uncertainty combines two critical uncertainties from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, Critical Uncertainties (CUs) #39 and 40, for the ISAB/ISRP discussion of progress made toward addressing this uncertainty.
Theme: Hydrosystem flow and passage operations
  Subtheme: Hydrosystem effects on survival
How do hydrosystem operations affect fish survival (including salmonids, eulachon, sturgeon, lamprey, and other focal species)? (Primary)
Information is needed to assess project compliance with mandated targets, understand impacts of management actions on fish, and understand where and when the largest sources of mortality are occurring so that corrective actions can be taken. For example, the Federal Columbia River Power System Juvenile Dam Passage Performance Standards and Metrics (NOAA Fisheries, FCRPS Supplemental Biological Opinion, section 3.3.3.2) requires an “average across Snake River and Lower Columbia River dams of 96% average dam passage survival for spring Chinook and steelhead and 93% average across all dams for Snake River subyearling Chinook.” This is currently being monitored by PIT-tagging (and JSATs tagging in the US Army Corps of Engineers-funded projects) juvenile salmon. Some tagged fish are detected during their downstream migration and then as returning adults, and statistical methods are used to estimate survival probabilities, straying rates, etc. The Comparative Survival Study reports (CSS 2015) examine how juvenile survival and smolt-to-adult returns (SARs) change in response to changes in flow and spill. A life cycle model is being constructed by the CSS that models survival from eggs to spawners so that impacts on changes in survival due to management actions such as changing spill can be predicted. Without such knowledge, the consequences of management actions will be unknown and potentially ruinous for stocks.
How should nutrient additions be conducted in relation to flow conditions and operations (stable flow) in the Kootenai River subbasin?
What are the effects of water withdrawals, transfers, and exchanges on flows and migration?
What are the operational effects of a new Columbia River Treaty?
How close to normative are current water volume, temperature and flow timing?
What are the effects of the normative hydrograph on riparian function, and thus how can this inform riparian rehabilitation efforts in the Kootenai River subbasin?
How does the existing hydrograph affect reproductive and recruitment success for sturgeon and burbot and thus conservation aquaculture operation decisions in the Kootenai River subbasin?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - juveniles
What factors and operations affect the durations and intervals of movement and holding, for resting and feeding for Chinook salmon, particularly sub-yearling Chinook?
What is the relationship between speed of migration (travel time) and reservoir mortality?
What is the relationship between levels of flow and spill and survival of juvenile fish through the Columbia Basin hydrosystem?
What are the effects on subyearling chinook salmon of changes in river flows designed to aid yearling migrants, principally spring chinook salmon and steelhead? What are the effects of augmented flows and/or reservoir drawdowns on nearshore habitats (because actions that aid yearlings are probably detrimental to subyearlings)?
Can existing project data on the effects of water height, flow, velocity, and temperature on chum and fall Chinook salmon be used in a computer model to regulate hydrosystem operations to ensure that suitable spawning, incubation, and juvenile rearing conditions exist for these species below Bonneville Dam?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - juveniles - pulsed flows
How does the hydrosystem affect fish survival when pulse flows are used? (Primary)
What hydrodynamic features are effective in moving fish (emigration) with less water?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - juveniles - life history diversity
How do hydrosystem operations affect salmon survival differently by life history type and stock (e.g., Snake River fall Chinook) thereby indicating the need for different hydrosystem operations? (Primary)
Maintaining life history diversity promotes resilience. Thus, hydrosystem operations that adversely affect some life histories (e.g., yearling versus subyearling migrants) may threaten resiliency. This uncertainty will become even more critical when effects of climate change and a revised Columbia River Treaty are superimposed.
What is the survival of over-wintering reservoir-type Chinook salmon?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - adults
What are the consequences of changing the spill regime for upriver movements of adult salmon and steelhead, and any other species for which changes in summer spill timing and volume are relevant?
What are factors (migration timing, spatial distribution, etc.) that might explain the differential conversion rates (Bonneville Dam to McNary Dam) observed for upper Columbia River steelhead and spring Chinook salmon compared to Snake River steelhead and spring/summer Chinook salmon?
What are the effects of the adult passage experience in the Federal Columbia River Power System on pre-spawning mortality?
What is the relationship between levels of flow/spill and the survival on adult fish through the Columbia Basin hydrosystem?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - plume characteristics
How does the hydrosystem affect plume characteristics, and what are the effects on survival? (Primary)
What are the conditions below Bonneville Dam (including estuary & ocean) that are important to white sturgeon movements, reproduction, feeding and growth?
What are in-river migration conditions that maximize survival in light of river travel time and annual conditions in the estuary and ocean?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - non-salmonids, resident fish
What are the ecological effects of hydrosystem operations on downstream mainstem and estuarine habitats and on populations of resident fish and wildlife?
How do specific hydrosystem operations (e.g., flow stabilization, flow characteristics, and channel features) affect resident fish species?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - Bull trout
What is the significance of protecting or improving the critical mainstem habitat for recovering bull trout population?
How do reservoir conditions and hydrosystem operations effect foraging, overwintering, and migrating bull trout?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - Sturgeon
How does the hydrosystem affect sturgeon? (Primary)
What are the limitations for white sturgeon in the pools above Bonneville Dam compared to the river below Bonneville Dam, with the ultimate outcome of providing scientific information on recruitment relevant to dam operations and impacts?
What are the effects of power peaking operations and load following on white sturgeon spawning behavior and success?
What are the theoretical water velocities and downstream dispersal rates of larvae and sub-yearling white sturgeon for the Columbia River upstream to Celilo Falls under pre-impoundment and pre-channelization conditions? What is the likelihood of early-aged sturgeon washing to the estuary from historic spawning sites upstream of where Bonneville Dam is located?
How do the range of spring/summer flows affect the rate and extent of downstream dispersal of white sturgeon larvae and sub-yearlings in the lower Columbia River, including drift to brackish and saltwater portions of the estuary where fish of these life-stages would not survive?
What are spawning and rearing conditions and available habitat for sturgeon created from water releases at mainstem dams?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - Eulachon
How do hydrosystem operations affect reproductive success, growth, survival, productivity, and recovery potential of eulachon? (Primary)
How do changes in the Columbia River hydrograph affect survival, productivity, and recovery potential of eulachon?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - Lamprey
How do hydrosystem operations affect lamprey? (Primary)
What are the migration routes and survival rates for juvenile lamprey through the mainstem hydrosystem and estuary?
What are the lamprey passage efficiency, direct mortality, and/or other metrics that relate to loss of fitness (i.e., stresses or injuries that reduce ability to survive throughout migration and early-ocean periods)?
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - wildlife
How does the hydrosystem affect wildlife? (Primary)
Theme: Hydrosystem flow and passage operations
  Subtheme: Effects on survival - non-natives
How does the hydrosystem affect non-native species (walleye, bass, etc.)? (Primary)
Are non-native species effectively suppressed where habitats are maintained by natural flow and temperature variation?
Theme: Hydrosystem flow and passage operations
  Subtheme: In-river versus transportation
What are the effects of specific transportation operations on adult fish migration behavior, straying, pre-spawning mortality, and smolt-to-adult return ratios (SARs)? (Primary)
How does multiple dam passage versus transportation affect juvenile-to-adult survival rates for each species? (Primary)
Recent studies (e.g., CSS reports) have shown that transportation benefits appear to be marginal for some stock, under certain flows at different times of the year. But other research studies indicate a potential problem with non-random sampling of fish for the transportation studies. Delayed mortality (D) is the ratio of ocean survival of Snake River fish that were transported to the ocean survival of similar fish migrating in-river. The CSS concluded that “Estimated D values for subyearling Snake River fall Chinook were below 1, for nearly all groups in the years 2006 to 2012. That was similar to patterns seen in yearling Chinook and steelhead (hatchery and wild groups) in the same years. A longer time series for subyearling Chinook would be helpful to determine if D estimates would have been higher prior to 2005 (the beginning of court-ordered summer spill) similar to the pattern seen for hatchery and wild steelhead groups that had D values that were well above 1 for several years prior to 2006.” Smith et al. (2013) found that with some exceptions, the estimated benefit of transportation was usually nearly constant throughout the season or steadily increasing for both wild and hatchery Chinook salmon. Estimated benefits of transportation for wild steelhead were relatively constant throughout the season for 8 of the 10 migration years. Hatchery steelhead exhibited more variation in patterns of transportation benefits than did wild steelhead. The reasons for the variation in results are unknown. However, Hostetter et al. (2015) indicated that juvenile bypass systems tend to select smaller fish in poorer condition compared to fish that use the spillway or turbine systems. Because the juvenile bypass system is used to select fish for transport, this may explain the negative findings of the effect of transport. Further studies on this question would benefit from incorporating multiple populations and collection locations plus multiple years to address these additional complexities.
What is the influence of transport operations on the number of in-river fish and how does it affect fish survival due to predation?
Is management of transport and spill likely to increase or decrease genetic and life history diversity?
Is there significant delayed mortality due to passage through the hydrosystem in the estuary or in the ocean?
How can the number of out-of-basin strays due to transportation be reduced in Lower Columbia tributaries?
How does juvenile passage through multiple dams versus transportation affect adult fish migration behavior, straying, and pre-spawn mortality, and juvenile-to-adult survival rates?
How does juvenile passage through multiple dams versus transportation affect adult fish pre-spawn mortality?
How does juvenile passage through multiple dams versus transportation affect adult fish migration behavior, including straying rates?
If juvenile bypass systems tend to select fish in poorer condition compared to fish that use the spillway/turbine, and the juvenile bypass system is used to select fish for transport, does this explain the negative findings of the effect of transport?
Theme: Hydrosystem flow and passage operations
  Subtheme: In-river versus transportation - delayed mortality
Under what conditions is delayed mortality (e.g., multiple dam passages) related to downstream migration through the hydrosystem, and what is the magnitude of that delayed mortality? (Primary)
Theme: Hydrosystem flow and passage operations
  Subtheme: Spill operation effects
What are the effects of spill operations on returning adults that subsequently affect adult fish migration behavior, straying, pre-spawning mortality, and smolt-to-adult return ratios (SARs)? (Primary)
What are the effects of total dissolved gasses on white sturgeon survival?
What are the effects of spill operations on juveniles that subsequently affect adult fish migration behavior including straying?
What are the effects of spill operations on juvenile salmonids and the subsequent effect on pre-spawn mortality?
What are the effects of spill operations on juvenile-to-adult survival rates?
Theme: Hydrosystem flow and passage operations
  Subtheme: Spill operation effects - total dissolved gas impacts
What are the total dissolved gas impacts of spill on fish mortality?
How do complex in-river mixing of supersaturated water from spill and water from turbines and tributaries not enriched with gases interact?
Theme: Hydrosystem flow and passage operations
  Subtheme: Dam passage effects - existing dams
What are the effects of water temperature at mainstem dams and reservoirs on fish passage (both juvenile and adults)? (Primary)
Climate change is projected to increase water temperatures, which will impact the migration and health of fish through the Basin. What are the projected impacts and can they be alleviated by changes in operations (e.g., by providing thermal refuges for fish during periods of warm water to increase survival of returning adults)?
How effective are new surface passage technologies such as removable spillway weirs?
Will mainstem passage problems be resolved to enable sufficient numbers of adult lamprey to migrate into tributaries?
What are the relationships between descaling, disease resistance, osmoregulation capability, and survival (See Zydlewski et al.)?
What are lamprey passage efficiency, direct mortality, and/or other metrics relating to migratory success of lamprey?
What factors contribute to differences in dam counts of lamprey between Bonneville and The Dalles dams and other critical index points in the hydrosystem?
What are the movement, behavioral, and recruitment characteristics of white sturgeon that could have implications for passage?
Do surface flow outlets during the winter months provide a safer fallback route for over-wintering steelhead and kelts?
What are the energetics of adult lamprey during migration and the relationship between energetics and passage?
What is the feasibility of developing PIT tag detectors for spillways and turbines?
What are larval and juvenile sturgeon downstream passage and mortality, and what are the tradeoffs between upstream and downstream subpopulations?
What actions could be taken to minimize downstream passage mortality for white sturgeon at mainstem dams?
What are the effects of energetics, water management operations, TDG (total dissolved gas), swimming performance, turbines, screens, predation and other obstacles to juvenile lamprey passage?
What levels of flow and spill provide the maximum effectiveness of surface-flow passage devices for juvenile lamprey?
What are the specific structures or operations that delay, obstruct, or kill migrating adult lamprey?
To what extent are mainstem dam fishways, especially entrances, useful for lamprey passage?
What are the effects of turbine operations on smolt survival and condition?
What are the effects of gas bubble disease at the bypasses of dams?
How well do gas abatement measures at the dams work?
Are the surface ice and trash sluiceways effective as a passage route for juvenile salmonids?
What structural and hydraulic conditions result in optimal passage routes at specific dams for various species in the Columbia River? For example, how can fish passage design and fish behavior be factored into design and operations?
What are the juvenile fish survival rates assignable specifically to turbines, surface weirs, bypasses, spillways, tailraces, and forebays?
What is the incidence of fish diseases at adult and juvenile passage and collection facilities?
Theme: Hydrosystem flow and passage operations
  Subtheme: Restored passage/reintroduction
Can an enhanced life cycle model be developed for evaluation of the short-term, transitional, and long-term biological effects of dam breaching? (RPA)
What is the feasibility of reintroducing self-sustaining anadromous fish at each federal and non-federal project that currently blocks anadromous fish from historic habitat? Specifically, what is the feasibility of implementing adult and juvenile passage at dams that currently do not have passage?
There are wide-ranging discussions in the Basin about the feasibility of reintroducing anadromous salmon and other fishes extirpated by the development of the hydrosystem. While this may be a laudable goal, there are numerous uncertainties associated with the endeavor. The extirpation of the original fish community took place many decades ago and novel biotic communities have assembled in response to new biophysical conditions. These communities are substantially different from those historically encountered and, in essence, they may be occupying nearly all the available niche space. Additionally, successful re-introduction of anadromous fishes into upper Basin areas will require adequate survival of migrating juveniles and adults through multiple dams and reservoirs in addition to potentially unfavorable conditions in the ocean. Before embarking on an endeavor to reintroduce native fishes above artificial barriers it will be necessary to evaluate the feasibility of establishing productive and resilient populations. The key question is whether a self-sustaining population can be established above the high-head dams in the upper Basin. Trap-and-haul and other technologies can move fish, but will this support a viable population? Resolving this question has a broad spatial scope and over time could have a large impact on abundance, productivity, and diversity of anadromous fishes. Prior to dam development the upper Basin supported sustainable populations, but whether it is possible to reestablish them in the currently modified system is less clear. Although passage technologies may be transferable, the hydraulic conditions at every dam are different. Studies to address this uncertainty are planned above Chief Joseph Dam and in some Willamette and lower Columbia River tributaries.
What infrastructure changes at Albeni Falls Dam and habitat enhancements would benefit resident and migratory fish in areas impacted by the dam? How can lessons learned from the Thompson Falls (Montana) fish ladder be used in designing fish passage at Albeni Falls Dam?
What is the feasibility of upstream and downstream passage options for salmon and steelhead in the upper Columbia (above Chief Joseph and Grand Coulee dams)?
Theme: Monitoring and evaluation methods
  Subtheme: Fish survival tagging
Fish survival is currently estimated using capture-recapture methods. How can advances in genetic stock identification, reductions in sizes of tags, new tag technologies, and other emerging methods be used to improve estimates of survival (better precision and less bias) and/or reduce costs? (Primary)
Fish survival is one of the primary metrics of performance. Better estimates will allow more reliable detection of finer differences in survival rates among stocks, under different hydrosystem operations, or for different life stages thereby providing opportunities to develop management actions to help stocks with low productivity. Monitoring and evaluation of fish population status is a critical task that should occur every year as a means to inform decisions involving harvests, hatchery production, and efforts to restore fish populations (See Programmatic Comment 7). Some fish monitoring, including tagging, is funded by the Program, but much of it is conducted outside the Program by government agencies. A common strategy by the Program and outside agencies, along with cooperation and integration of efforts, is needed to effectively and efficiently achieve the goals for monitoring and evaluation in the Basin. A limitation of tagging methods is the requirement to physically handle fish and apply tags. If handling fish or the physical tag affects subsequent behavior (including survival), estimates of performance may be biased. Tagging methods also require substantial numbers of fish to be tagged to compensate for subsequent mortality and imperfect detection—this may be costly and logistically difficult to do and may not be feasible for species with low abundance. Parent-based genetic tagging appears promising based on the pace of development to date. Smaller and injectable acoustic tags would make it possible to tag smaller juvenile salmon and also juvenile lamprey to assess survival over dams. The increased use and establishment of PIT tag arrays in subbasins would provide information on straying and spawning.
Can PIT tags and novel tag detection technologies be used for generating survival estimates based on year to year recaptures of white sturgeon?
How are life cycle parameters for low abundance salmon and steelhead stocks estimated?
To what degree do coded-wire tagged fish represent associated natural salmon?
Can a new survival model be developed to effectively incorporate data collected from instream PIT tag monitoring sites, given the problem of a lack of independence in detections of a fish between multiple PIT tag-arrays on the same stream?
What are the acute and chronic effects of various tag types on fish survival, for example PIT-tag effects on juvenile salmonids?
Theme: Monitoring and evaluation methods
  Subtheme: Fish survival tagging - juvenile
Can survival of juvenile salmonids from spawning to estuary be best monitored using PIT tags, acoustic tags, genetic or other tags? (Primary)
Are there enough tagged fish in the system to meet precision requirements?
How do smolts use the estuary during their migration, and what is the estimated survival rate downstream of Bonneville Dam and into the estuary?
What are PIT tag effects on chronic mortality of juvenile fish?
What are PIT tag effects on shedding rates of juvenile fish?
Can tagged fish be used to monitor for untagged juvenile fish, since size limitations for tagging juveniles precludes tagging fry size?
Are juvenile fish tagged at the right locations to meet precision requirements?
Can mortality be effectively partitioned for juvenile fish?
Theme: Monitoring and evaluation methods
  Subtheme: Fish survival tagging - adult survival
What is a cost effective adult PIT tag detection system design, and will installation of PIT tag detectors improve detection of adults migrating upriver at dams and in tributaries?
How effectively can the origin of adults be monitored by tagging juveniles?
Are there alternatives to increasing the tagging of juveniles in order to monitor adults?
Are there effective methods for alternatives to using PIT tags for survival estimation based on easily measured external covariates?
Can Genetic Stock Identification combined with PIT tagging juveniles be an effective method of monitoring adults?
Can mortality be effectively partitioned for adult fish swimming upstream?
For adult salmon monitoring, given the very large sample sizes needed for PIT-tagged juveniles, perhaps other methods can be considered such as genetic stock identification of some returning adults with new tags added at the adult stage rather than at the juvenile stage?
Theme: Monitoring and evaluation methods
  Subtheme: Fish survival tagging - detection improvements
What improvements in the detection of tagged fish are known/predicted? (Primary)
What is the feasibility of detecting tagged fish in natal streams and tributaries, or other locations as appropriate to support more comprehensive and integrated All-H monitoring designs and assessments of stray rates?
What detection rates at bypass facilities are needed to improve estimates of survival and travel time through the hydrosystem?
What improvements in the development of spillway detectors for juveniles are known/predicted?
What improvements in the development of in-stream arrays for juveniles and adults are known/predicted?
What improvements in the development of estuary (and beyond) detections for juveniles and adults are known/predicted?
What improvements to the calibration of detectors independent of other detections are known/predicted?
What improvements to fish ladder detectors and calibration are known/predicted?
Theme: Monitoring and evaluation methods
  Subtheme: Fish abundance and harvest
How do we best estimate the number of juvenile-recruits per spawner given tradeoffs between costs, precision, and accuracy?
Can we estimate PIT tag fish removals (harvest, straying) in the mainstem to refine estimates of in-river harvest rates, upstream survival rates, and straying rates?
Are there effective methods for estimating the total number of smolts from the entire river system reaching the estuary?
Are there effective methods for expanding fish ladder counts for returning adults to account for downtimes, etc.?
Are there effective methods for determining expansion factors applied to tagged recoveries for abundance of small stocks based on combining PIT tags and other methods?
Are there effective CWT (coded wire tag) methods for estimating harvest in the ocean?
Are there effective GSI (genetic stock identification) methods for estimating harvest in the ocean?
Are there effective methods for estimating SAR (smolt-to-adult return ratio) using alternatives to PIT-tagged fish?
Are there effective methods for estimating SAR (smolt-to-adult return ratio) at finer resolutions combining PIT tags and other methods?
Are there effective methods for estimating density at an appropriate scale (i.e., to account for fish movement)?
Are there effective methods for differentiating between Ricker and Beverton-Holt models for density dependence?
Are there effective methods for estimating harvest in the river?
Theme: Monitoring and evaluation methods
  Subtheme: Fish abundance and harvest - fish-in/out monitoring
Are there effective methods for fish-in and fish-out monitoring for measuring effects of habitat restoration and other changes? (Primary)
Ideally the number of fish entering a restored habitat (fish-in, e.g. spawning adults for spawning habitat restoration; juvenile fish for rearing habitat restoration) and the number of fish leaving a restored habitat (fish-out, e.g. juveniles produced or juvenile fish moving to other habitats) can be enumerated. The difficulty is that the habitat areas often cannot be closed off and fish are difficult to detect. Costly methods (e.g., fences and rotary screw traps) are often used, but these methods are not suited for high water conditions when fish are actively moving. Resolving this uncertainty will lead to more rapid learning and propagation of effective restoration actions to other parts of the Basin. Reducing uncertainties in fish-in and fish-out monitoring by reducing bias and increasing precision could lead to better evaluation of the effects of habitat restoration for all species of fish.
Are there effective methods for estimating outmigration using a rotary screw trap and using fish-independent alternatives for calibration?
Are there effective alternatives to rotary screw traps for estimating outmigration?
Are there effective methods for estimating adult returns using fences and weirs and using tagged fish for efficiency calibration?
Are there effective methods for estimating adult returns using fences and weirs and using fish-independent alternatives for calibration?
Are there effective alternatives to fences and weirs for estimating adult returns?
Are there effective methods for estimating outmigration using a rotary screw trap and using tagged fish for efficiency calibration?
Theme: Monitoring and evaluation methods
  Subtheme: Stock identification
How can natural origin fish stocks be identified and studied in freshwater, estuarine, and ocean habitats of the Columbia River Basin? (Primary)
Theme: Monitoring and evaluation methods
  Subtheme: Stock identification - batch marking methods
Are there effective methods for using batch marking to identify fish stocks? (Primary)
How can returning adult fish populations be partitioned with finer resolution to determine their origin and final destination?
Can natural origin salmon stocks be identified and studied in freshwater, estuarine, and ocean habitats of the Columbia River Basin?
Can geochemical signatures in fish scales be used more effectively?
Can coded wire tags be used more effectively?
Are there effective methods for using otolith to identify fish stocks?
Are there effective methods for using parasites to identify fish stocks?
Theme: Monitoring and evaluation methods
  Subtheme: Stock identification - genetic tagging
Are there effective methods for using genetic tagging to identify fish stocks? (Primary)
Can genetic baselines be developed for effectively using genetic tagging to identify fish stocks?
Can stocks be differentiated with sufficient resolution in order to effectively using genetic tagging to identify fish stocks?
Can full parental genotyping effectively be used for genetic tagging to identify fish stocks?
Theme: Monitoring and evaluation methods
  Subtheme: Habitat monitoring
Can a common probabilistic (statistical) site selection procedure for population and habitat status and trend monitoring be developed cooperatively? (Primary)
What are the most effective methods for quantitative estimates of changes to abundance, survival, movement, and production in response to habitat restoration, and how can these estimates be integrated across a range of spatial scales from individual restoration treatments to whole watersheds, and temporal scales from individual seasons to entire life cycles? (Primary)
Effective methods are available to quantitatively estimate abundance, survival, movement, production and habitat capacity over reach scales (or between two reaches). However, the methodology for integrating these estimates to assess effects of human activities and restoration across watershed scales and through several generations of fish or wildlife has not been sufficiently studied. Because of these large scales, relatively little is known about whether current methods are accurate. As well, there are many smaller habitat restoration projects implemented, each of which may contribute only a small amount to a stock’s overall performance and whose benefits are difficult to detect. By understanding the cumulative effects, the benefit of restoration activities can be quantified to see if they are cost effective compared to other actions.
Can a scientifically credible trend monitoring procedure for habitat assessments be developed using remote sensing and similar methods?
How effectively can EDT (ecosystem diagnosis and treatment) and QHA (qualitative habitat assessment) be used to prioritize restoration actions while accommodating the various types of artificial production programs in the Basin (mitigation hatcheries, supplementation programs, captive brood, etc.)?
How do projects affect local or site scale attributes such as changes in habitat and use by fish?
Are habitat actions substantially increasing abundance of focal species? Are models used to predict habitat benefits of actions prior to implementing actions accurate and useful in order to prioritize actions and assess cost/benefit ratios?
Can various habitat attributes be measured using on the ground measurements?
Are the right habitat attributes being monitored at the right times?
Do the current methods for detecting effects of many small, incremental habitat improvements on fish populations provide answers with sufficient precision and accuracy to evaluate the success of these programs?
How can we assess the quality of mainstem habitat that is optimal for viable fish populations?
What relationships exist between habitat conditions and fish productivity (limiting factors)? To what extent has this been addressed by work in the following study subbasins: Wenatchee, Methow and Entiat river basins in the Upper Columbia River, the Lemhi and South Fork Salmon river basins, and the John Day River Basin?
Theme: Monitoring and evaluation methods
  Subtheme: Statistical methodology
What statistical methodologies are available for estimating the number of fish (1) entering and then leaving habitat areas or for (2) entering and the number of progeny leaving the habitat area? And how effective are the statistical methodologies for different habitat types? (Primary)
How effective is combining multiple small studies using Bayesian methods for estimating the number of fish?
How effective is combining GSI (genetic stock identification) and tagging data for estimating the number of fish?
When can environmental correlates and empirical (e.g., regression) models be used for predicting habitat quality and abundance or presence-absence of focal species?
Theme: Monitoring and evaluation methods
  Subtheme: Lamprey
What methods can be used to estimate the survival and abundance of lamprey? (Primary)
What methods could be used to delineate populations of lamprey?
What are appropriate aging techniques for lamprey?
Can juvenile lamprey be captured and tagged?
Can adult lamprey be captured and tagged?
Theme: Monitoring and evaluation methods
  Subtheme: Wildlife
How can the impacts of restoration activities on wildlife populations (other than fish) be effectively monitored? (Primary)
Wildlife monitoring is a critical component in the landscape-scale approach to assessing ecosystem health. Monitoring of impacts on wildlife populations provide a critical and more enhanced view of the overall effects of restoration actions. Interactions between species (e.g., bears transporting nutrients to forests via salmon) need to be understood to evaluate impacts of management actions. Currently, there is often little systematic monitoring of non-fish species.
Can impacts to small localized wildlife populations (e.g., bears) be effectively monitored?
Can impacts to transient wildlife populations (e.g., waterfowl) be effectively monitored?
Theme: Monitoring and evaluation methods
  Subtheme: Monitoring ecosystem health
Can overall ecosystem health be monitored? (Primary)
What are appropriate indicators/measures of success that could be used in evaluating the health of the ecosystem?
Can specific indicators of overall ecosystem health be monitored?
Can multiple indicators of overall ecosystem health be combined?
Theme: Non-native species
  Subtheme: Abundance and distribution
What is the current distribution and abundance of non-native species (e.g., the baseline condition), and how is this distribution related to existing habitat conditions (e.g., flow and temperature regimes, human development, restoration actions)? (Primary)
Theme: Non-native species
  Subtheme: Impacts
To what extent is the viability or abundance of native fish and wildlife species in the Columbia River Basin jeopardized by non-native species? (Primary)
This overarching question reflects advice in both the Program and the ISAB non-native report (ISAB 2008-4).Both documents emphasize that the increasing presence of non-native species, potentially exacerbated by continued legal and illegal introductions and climate change, is imperiling native species recovery efforts. Detrimental effects on native species are resulting from predation, competition for food, interbreeding, disease transmission, food web disruption, and physical habitat alterations. Non-native species change biotic interactions, create novel ecosystems, and have the potential to undermine otherwise successful habitat restoration efforts. Effects of non-natives on the native fauna are seldom well understood, are typically difficult to predict accurately, and may be recognized only after the native species are in steep and sometimes irreversible declines in abundance and recruitment. Once non-native species are established, efforts to remove them are typically unsuccessful. A key principle outlined in the Program is to “prevent, monitor, control, and stop or minimize the spread of non-native and invasive species where these pose a threat... to native fish, or to wildlife species.” In many cases, habitat conditions that originally favored native species no longer exist. Managers, thus, may have a difficult choice between attempting to manage for the native species poorly suited to the new conditions or compromising and providing fisheries with popular non-natives that are better suited to available habitat. In systems containing established non-native species, an important aspect of the decision-making process is determining whether the return to a previous state, dominated by native species, is feasible or whether there is a need to develop new goals and objectives to deal with the novel ecosystems. Management and policy decisions must consider not only the ecological aspects of non-native species on native species but the social issues and perceptions of stakeholders and the public. Among non-native fishes, the most problematic species in terms of policy development are those already introduced into a basin and that have perceived benefits (e.g., game fish) that militate against eradication or reduction actions (ISAB 2008-4). Managing such problematic species entails not only attempting to control their distribution, abundance and productivity, but also considering their effects on often-declining native species, the continually evolving landscape, and divergent, rapidly shifting public opinion. The current inconsistent management strategy for non-native, problematic species such as lake trout, walleye, northern pike, smallmouth bass, largemouth bass, and other panfishes (e.g., Centrarchidae) reflects how those species are perceived to be harmful to humans and other species, but also reflects ambiguous, and sometimes strongly conflicted, attitudes by the public and co-managers about the value of those species. Future research should include not only interactions among fishes, but among fish and other fauna and flora. Issues involving non-native pathogens and hosts also need to be better understood. Research also must consider effects of non-native aquatic, terrestrial and riparian species on riparian and terrestrial native species recovery efforts. Various management interventions and restoration initiatives for controlling or eradicating invasive non-native species should be implemented and monitored. This critical uncertainty is derived from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #37, for a discussion of progress made toward addressing this uncertainty.
What are the impacts of non-native plants on native grassland plant diversity and productivity?
What are the invasive potential and risks to fish, wildlife, and their habitats of using non-native bioenergy feedstock species, cultivars, and hybrids?
What is the inter-specific competition between Mysid shrimp and native amphipods?
What is the inter-specific competition between juvenile American shad and juvenile white sturgeon?
What is the inter-specific competition between Asian clams and native freshwater mussels?
What are the impacts of brook trout on bull trout recovery efforts and how can they be mitigated?
What are the potential effects of non-native species on the success of the kokanee mitigation effort in Lake Roosevelt? How can those effects be ameliorated?
Theme: Non-native species
  Subtheme: Management
What are the primary pathways of introduction of invasive and non-native species, and what management actions could limit new introductions or mitigate the impact of invasive species? (Primary)
This overarching question also comes from the Program and the ISAB’s non-native report (ISAB 2008-4). Non-native fish species introductions have resulted from both deliberate and unintentional human activity. Introductions of non-native fishes have been initiated for perceived aquaculture benefits, as well as to develop or enhance fisheries, and fill vacant niches as in blocked areas above dams. Although many historical introductions of non-native species were initially made by state and federal agencies, in recent years more have been illegal, unintentional, and not approved by agencies. There is a need for more outreach on species identification, so that non-natives may be recognized more readily in surveys and by the public. Identifying the most likely introduction pathways, both in specific situations (e.g., in a particular water body) and vectors (e.g., the pet trade, on trailers, boat hulls or in ballast) is crucial to preventing and curtailing introductions. This critical uncertainty is derived from the 2006 Research Plan; see Part 2, ISAB/ISRP 2016-1, CU #38, for a discussion of progress made toward addressing this uncertainty.
How would management actions, especially mainstem flow augmentation from headwater reservoirs to promote anadromous fish survival and productivity, reduce or increase the abundance and limit the spread of non-native species?
What management actions (i.e., habitat restoration versus non-native species control programs) most effectively reduce the impacts to native fishes in reservoirs from non-native species' competition and predation?
What management actions in subbasins are warranted to suppress or reduce the further expansion of non-natives determined to be a significant threat to bull trout?
What are the long-term management options for eradicating noxious weed invaders?
Does reduction of California ground squirrels and eastern gray squirrels increase survival of western gray squirrels?
Theme: Population structure and diversity
  Subtheme:
What is the status and viability of ESA-listed populations? (Primary)
What is an effective early warning indicator that a species is likely to have substantially reduced abundance (and productivity) in the future?
Theme: Population structure and diversity
  Subtheme: Diversity
What is the relationship between genetic diversity and ecological and evolutionary performance, and to what extent does the loss of stock diversity reduce the fitness, and hence survival rate and resilience, of remaining populations? (Primary)
Recognition that genetic diversity is critical to long-term ecological and evolutionary performance is fundamental to the landscape approach and the 2014 Program. Research and adaptive management to address this uncertainty could have long-term, basinwide benefits by identifying and averting management actions that would jeopardize genetic diversity and the resilience of focal populations. Our understanding of the long-term consequences of genetic diversity for ecological and evolutionary performance is still primarily theoretical (e.g., Fraser 2008) and more empirical research is needed.
Theme: Population structure and diversity
  Subtheme: Diversity - persistence/abundance
What is the risk of extinction relative to population size for isolated populations of bull trout and migratory fish (e.g., West Fork Bitterroot River, East Fork Bitterroot River)?
At the subbasin scale, is the long-term persistence and abundance of bull trout limited by the loss of fluvial population components and genetic interchange?
At the subbasin scale, is the long-term persistence and abundance of westslope cutthroat trout limited by genetic introgression with rainbow trout and by the loss of fluvial population components and genetic interchange, which is the direct result of lost connectivity?
Can parentage analysis (genetic sampling of progeny) be used to determine the genetically effective population size (or number of redds in a subbasin that produced offspring) for bull trout? Can this metric be used to measure population resilience?
For ESA-listed steelhead in the Imnaha River subbasin, is there sufficient information on the adults to manage and recover the population?
Theme: Population structure and diversity
  Subtheme: Diversity - life history/habitat
Which juvenile life histories in anadromous salmonids contribute to adult returns, and can restoration that accounts for different juvenile life histories benefit the resilience and recovery of tributary populations?
What is the relationship between resident and anadromous O. mykiss subpopulations, and can the expression of these life histories be affected by habitat change and degradation?
Theme: Population structure and diversity
  Subtheme: Diversity - evolutionary relationships
What is the evolutionary relationship among populations and are there differences in age structure among populations of steelhead in the basin?
What are the relationships to population viability between resident (rainbow trout) and anadromous (steelhead) O. mykiss with overlapping geographical distribution?
Theme: Population structure and diversity
  Subtheme: Life history
What life history strategies are utilized by Columbia River Basin fishes (e.g., Pacific salmon, lamprey, sturgeon, eulachon), and how do they influence survival and growth in tributaries, the mainstem above and below the dams, estuary, and ocean plume? (Primary)
Greater understanding of the life history diversity of focal species is needed to set appropriate targets for abundance, distribution, and harvest rate and to improve strategies for habitat restoration and hatchery supplementation. Potential benefits of improved management are large and long-term because life history diversity enhances the basinwide carrying capacity of the species as well as its adaptability to environmental changes in the future.
Theme: Population structure and diversity
  Subtheme: Life history - salmonids
What are the differential effects of flow augmentation, transportation, and summer spill on the diversity of life history types?
Is the expression of early life history strategies in salmonids similar or different between various reaches within the tidal freshwater area of the Lower Columbia River Estuary?
What life history strategies and corresponding egg-to-smolt survival rates are exhibited by Columbia Basin spring Chinook?
How do juvenile Chinook life histories and performance compare (i.e., growth, foraging success, survival) among genetic stocks, including less abundant stocks that are under-represented in past estuarine surveys?
What effect does summer spill have on life history expression of Snake River fall Chinook, including overwintering, reservoir-type Chinook?
Theme: Population structure and diversity
  Subtheme: Impacts - on sturgeon
What is the current total mortality level for lower Columbia River (below Bonneville Dam) for recruited white sturgeon above age 2? What components of mortality occur in the lower Columbia River?
Theme: Population structure and diversity
  Subtheme: Life history - eulachon
What are the life history characteristics of eulachon, and what actions could be aimed at rebuilding eulachon populations?
Theme: Population structure and diversity
  Subtheme: Life history - lamprey
What is the abundance, distribution and diversity of Pacific lamprey in the Columbia River Basin? (Primary)
This uncertainty is deemed critical because of serious concerns about the current abundance of Pacific lamprey in the Basin. It will be especially important to identify and protect diversity in Pacific lamprey in tandem with artificial propagation efforts. Research to address the uncertainty seems feasible with large potential benefits for improving management strategies and recovering the species. Considerable knowledge already exists about the general life history of Pacific lamprey, including adult migration, overwintering, attraction to pheromones, fecundity, early development, emergence and initial settlement as ammocoetes, sediment preferences, and factors affecting growth. However, more information is needed about trends in the abundance and distribution of both juvenile and adults, about the current population structure and range of life history diversity, and about population dynamics and factors affecting productivity and carrying capacity. This general uncertainty encompasses six other uncertainties about more specific aspects of lamprey ecology and management.
Would implementing a PIT tagging program for lampreys throughout the Columbia River Basin provide new insight into juvenile fish passage issues and also provide unprecedented information on lamprey biology and life history (e.g. growth rates, time spent in the ocean, and homing efficiency—or a lack thereof)?
Can juvenile Pacific lamprey be tagged to track juvenile lamprey in the estuary and near-ocean environment?
Are adult Pacific lamprey attracted to juvenile lamprey pheromones when they migrate to spawning locations, and might this mechanism improve survival or maintain population structure in Pacific lamprey?
What factors motivate migration of adult lamprey?
What is the ecological function of anadromous lamprey (e.g., predator/prey relationships, linkages to other aquatic and terrestrial organisms)?
What methodologies can be used for gender identification of lamprey in the field and laboratory (e.g., identify spawning sex ratios, sex related behavioral characteristics)?
What are mortality rates for lamprey by life-stage?
What are the physiological and behavioral responses of lamprey to the various environmental factors they encounter during their life-cycle?
What is the biology of over-wintering adult lamprey?
What are the life history characteristics of freshwater, estuary, and ocean-phase anadromous lamprey (e.g., age, growth, timing of metamorphosis, movement, basin-specific comparisons)?
Theme: Population structure and diversity
  Subtheme: Life history - sturgeon
What are the life history and habitat requirements for all life stages of white sturgeon?
Can methods be improved to better characterize individual white sturgeon throughout their life cycle and incorporate these into population forecasts and viability assessments?
What are the size and age distribution, growth, condition, and abundance of white sturgeon by sex?
Theme: Population structure and diversity
  Subtheme: Life history - migration connectivity
How do fish move among rearing habitats, and what is the importance of habitat connectivity and spatial distribution? (Primary)
This uncertainty has long-term and basinwide implications for the effectiveness of habitat restoration projects that are central to the Program. Understanding how fish move among habitats and how much connectivity is needed to maintain the viability of focal populations can also guide landscape planning decisions that affect the spatial distribution of efforts to restore habitat or mitigate for climate change. Knowledge varies among species and regions. Some aspects of this uncertainty may need to be resolved at relatively small scales to understand how projects interact and could complement one another. Kanno et al.’s (2014) study of brook trout movements inferred from PIT tag detections and genetic pedigree data could serve as a template for future research.
What are migration patterns of bull trout upstream of Painted Rocks Reservoir?
How do fluvial fish move in the lower Bitterroot (Lolo Creek population connectivity)?
What is the origin of migratory bull trout at Milltown Dam? What is the life history and spawning habitat of bull trout congregating below Milltown Dam?
Do the mainstem dams isolate sturgeon populations, and if so, what is the feasibility of restoring connectivity to maintain genetic diversity in the long-term?
What is the importance of the estuary and ocean in sturgeon production below Bonneville Dam?
How much interchange occurs with white sturgeon between the Columbia River and other out-of-basin rivers?
How much spawning site fidelity do bull trout actually show (in this system and in general) and what are the factors affecting the degree of fidelity?
Theme: Population structure and diversity
  Subtheme: Distribution
How are fish and wildlife populations distributed within the Columbia Basin? (Primary)
Adult chum salmon annually pass over Bonneville Dam. Are these fish straying or homing to undiscovered spawning areas above the dam?
Theme: Population structure and diversity
  Subtheme: Distribution - methods
What are methods to differentiate among lamprey species at all life stages (field-based)?
Can new genetic markers be developed to supplement existing libraries for lamprey (e.g., microsatellites, single nucleotide polymorphisms, etc.)?
Do anadromous lamprey in the Columbia River Basin represent a panmictic population (completely mixed)?
What is the feasibility of genetic stock identification monitoring techniques?
Can genetic methods be employed to identify potential microsatellite or SNP markers that could be used to help determine the genetic composition of lamprey populations?
Theme: Population structure and diversity
  Subtheme: Distribution - genetics
What is the genetic composition and ecological role of Pacific lamprey in specific subbasins? Translocation experiments need to be guided by better knowledge of tributary-specific life history characteristics.
What are the levels of genetic diversity and degree of spatial genetic differentiation among populations or aggregations of Pacific lamprey from the Columbia River Basin and rivers along the west coast of North America? Specifically, what are the genetics of anadromous and resident lamprey populations (e.g., existence of genetically distinct population structure, rate of gene flow, population/subpopulation characteristic, etc.)?
What populations and genetic diversity are present for steelhead, including the reference condition for steelhead genetic variation?
What is the genetic baseline of bull trout in tributary populations (for use in regional studies of genetic assignments, determining genetic origin, and extents of hybridization)?
Theme: Population structure and diversity
  Subtheme: Distribution - genetics/environment
What is our understanding of genetic diversity among sturgeon populations?
What is the distribution of genetically pure westslope cutthroat trout in the Columbia River Basin?
What is the current range of biological diversity (life history and genetic) of fish and wildlife populations in Columbia River Basin ecosystems, and how is that diversity in focal populations influenced by geographic location and changing environmental conditions?
This uncertainty reflects inadequate knowledge about existing biological diversity and its role in maintaining viable populations of fish and wildlife in the Basin. Human actions, including fisheries have reduced the range of life history strategies and genetic diversity in many native fish populations. Although the scope of the uncertainty is long-term and basinwide, efforts to monitor trends in diversity are needed to help understand factors responsible for changes in diversity and to guide management actions to restore habitat loss and mitigate the impacts of climate change. Maintaining diversity is considered essential to long-term sustainability, as described in the scientific principles that guide the Program. Genetic differences arising from geographical isolation among salmonid populations are well documented (e.g., Project # 2009-005-00 "Influence of environment and landscape on salmonid genetics"), but our understanding of the long-term consequences of these differences for ecological and evolutionary performance is more theoretical. Patterns of genetic diversity in widely distributed species, like cutthroat trout, offer an opportunity to assess where historical watershed connections may have existed and can help to explain the current distribution of biological diversity across a landscape (e.g., Loxterman and Keeley 2012).
What is the relationship between genetic differences and fish (species) performance (e.g., survival, growth, fecundity, phenotype) in various environmental settings (elevation, aspect, gradient, etc.)?
How do environmental conditions correlate with genetic integrity of westslope cutthroat trout in the Bitterroot Subbasin?
Does any genetic variation in lamprey microsatellites coincide with distinct migration behaviors and spawning locations within the Willamette River basin?
Theme: Population structure and diversity
  Subtheme: Distribution - abundance
What is the distribution and status of bull trout populations in the Blackfoot subbasin?
What are the abundance and distribution of adult and juvenile lamprey by population in the Columbia River Basin?
Can historical databases be used to better understand historical distributions and abundance of lamprey?
What are the impacts of weirs for adult collection on the spawning ground distribution of adult spring Chinook? Do weirs affect spawn timing and the distribution of spawning adults?
What are the factors affecting accuracy and precision of bull trout redd surveys? Can these surveys be improved, and if so, how?
Theme: Population structure and diversity
  Subtheme: Distribution - migration
What are the geographic origins and life histories of salmonids sampled in the estuary? Stock identification would benefit from higher resolution genetic baselines. Life history reconstructions would benefit from smaller tags and improved chemical methods for otolith analyses.
What is the population structure, pre-spawn mortality, distribution, and movement among spawning areas for adult spring Chinook?
Does the straying rate of chum salmon limit the natural rate of recolonization of streams from which they were extirpated?
Theme: Population structure and diversity
  Subtheme: Distribution - demographics
What is the estimated age composition at the MPG (major population group) or population scale for spring Chinook?
Theme: Population structure and diversity
  Subtheme: Distribution - wildlife
What are local population/distribution data for target wildlife species, especially in riparian, wetland, grassland, and sage habitats?
What quantity and which species of the avian target species are present in wetland habitats in each Game Management Unit in the Bitterroot Subbasin?
Theme: Population structure and diversity
  Subtheme: Status and trends
What are current trends in population status by tributary or sub-population? (Primary)
Theme: Population structure and diversity
  Subtheme: Status and trends - targets
After anticipated restoration of tributary habitats and given the range in ocean conditions and spawner densities, what level of SARs is needed for each salmon ESU in order to (1) provide for a self-sustaining population, and (2) provide harvests that meet harvest goals?
How can the abundance and diversity of salmonid populations in the Columbia River be increased and sustained over the long term given the multitude of biological, physical, and cultural constraints? In particular, what are the potential benefits and risks of re-introducing anadromous fish into blocked areas throughout the Pacific Northwest?
This uncertainty is central to the vision and goals of the Program and focuses on practical strategies that are consistent with a landscape approach needed for improving current Program activities. Current knowledge is low, potential benefits are large, and research seems feasible. Much remains to be learned about how hatcheries and environmental changes will affect the long-term sustainability of natural salmon populations. A number of projects within the Basin are examining the effects of supplementation on natural population abundance and productivity. Climate change is expected to alter the distributions of salmonids, especially bull trout and cutthroat trout, and continued monitoring and evaluation will be required. Efforts to re-introduce anadromous salmonids to blocked areas with favorable water flows and temperatures (e.g., to higher elevations or more northerly locations) may prove beneficial to the long-term viability of salmon populations in the Basin. However, specific uncertainties about the effectiveness and unintended consequences of re-introduction remain to be addressed.
What are the best approaches to maintain genetically pure, self-sustainable resident populations of native trout and char (cutthroat trout, rainbow trout, redband trout, bull trout, etc.) in the face of population fragmentation; habitat degradation; climate change; naturalized populations of non-native trout, char, and other aquatic species; and other stressors?
What is the status of lamprey in various subbasins, and can a comparison of their status inform an analysis of limiting factors?
Theme: Population structure and diversity
  Subtheme: Status and trends - assessment
How effective is genetic assessment for determining trends in population status and population diversity? (Primary)
The capability to track trends in abundance, harvest rates, and straying in steelhead and Chinook has increased dramatically with the development of Parentage Based Tagging (PBT) and Genetic Stock Identification (GSI) methods based on SNP (single nucleotide polymorphism) panels. Further technical development of SNPs and PBT looks feasible. Already these genetic assessment tools appear to hold much promise for cost-effectively monitoring trends in population status and population diversity in salmon and other species. The Pacific Salmon Commission is currently considering the use of PBT and GSI.
What is the status of white sturgeon populations in the Columbia River Basin? (Primary)
This uncertainty is deemed critical because of serious concerns about inadequate recruitment and connectivity for white sturgeon populations above Bonneville Dam. Considerable research on factors affecting recruitment is underway for some populations, and it is essential that these efforts continue. Connectivity is a concern for all migratory species in the Basin and is likely a critical issue for the long-term viability of white sturgeon. Parent Based Tagging and other genetic methods appear well suited to addressing this uncertainty, particularly given the prominent role of artificial propagation in maintaining the abundance of landlocked populations of white sturgeon. Further development of such technical capacity seems feasible and may be of value in measuring connectivity and maintaining genetic diversity. This general uncertainty encompasses 11 other more specific uncertainties related to white sturgeon.
What are the size, age and sex distribution, growth, condition, and abundance of white sturgeon, i.e., stock assessment?
Theme: Population structure and diversity
  Subtheme: Status and trends - limiting factors
What factors within and outside of the Columbia River Basin influence trends in recruitment, mortality, and abundance of Columbia River Basin fish and wildlife populations? (Primary)
Understanding how environmental and ecological factors affect vital rates and abundance of fish and wildlife populations in the Basin is critical for guiding management actions to improve population status. The uncertainty varies widely among species and is typically greatest for factors affecting migratory fish and wildlife during life stages spent outside the Basin. However, the ocean synthesis has provided considerable information on how salmon growth and abundance are influenced by food availability and other factors (Jacobson et al. 2012). The list of potential factors is long, and six more specific sub-uncertainties were each given high criticality ratings.
What are the density effects in salmon populations that spawn in the lower Basin and in coho salmon populations throughout the Basin?
How important are species interactions such as predation and competition (including interactions with non-natives) to population recruitment compared with habitat alterations?
Do egg-to-smolt survival problems related to habitat availability limit the expansion of anadromous salmonids more than other sources of mortality? Empirical information describing cause and effect relationships influencing abundance in Columbia River salmonid populations are needed.
What are the relative contributions of habitat loss, harvest, predation and mainstem passage to reduced riverine survival and production of anadromous salmonids and other fishes targeted in the Fish and Wildlife Program?
What role do forage fish have in the survival of juvenile Chinook salmon, coho, and steelhead?
What are the factors that limit burbot abundance and sustainabilit? For example, in a comparative approach among populations, what factors are allowing burbot to thrive in some areas but causing them to decline in others?
Theme: Population structure and diversity
  Subtheme: Status and trends - limiting factors - sturgeon
Is the lower productivity of impounded white sturgeon related to the reduced carrying capacity for sturgeon that were formerly anadromous but are now landlocked?
Is lower food availability manifested in density dependent responses such as smaller adult sturgeon with fewer eggs?
What factors are limiting recruitment of white sturgeon above and below Bonneville Dam?
Above Bonneville Dam: What specific factors affect recruitment of white sturgeon?
Below Bonneville Dam: What specific factors affect recruitment of white sturgeon?
How does the size of the adult population of white sturgeon relate to recruitment of the number of age-1 juveniles or to recruitment of the number of sub-adults and adults that comprise the age/size range of the recreationally and commercially harvestable portion of the population? What is the adult female population size and annual recruitment to sub-adult life stage?
Which females are the largest contributors to recruitment success? The working hypothesis is that the large, old females are the primary contributors.
What is the abundance of juvenile, sub-adult, and adult white sturgeon by age class? This abundance estimate is needed to evaluate overall recruitment success through various traditional and novel capture and/or non-capture methods.
Above Bonneville Dam: What are white sturgeon spawner contributions to juvenile multi-year cohorts? This could be estimated on a decadal basis using genetic tools.
Below Bonneville Dam: What are white sturgeon spawner contributions to juvenile multi-year cohorts?
Below Bonneville Dam: What are the annual levels of, and variation in, white sturgeon recruitment in spawning areas of the Columbia River Basin?
Above Bonneville Dam: What are the annual levels of, and variation in, white sturgeon recruitment in spawning areas of the Columbia River Basin?
Theme: Population structure and diversity
  Subtheme: Status and trends - limiting factors - lamprey
What factors contribute to inadequate energy reserves for Pacific lamprey to successfully spawn?
What are the key uncertainties regarding lamprey disease and parasitism?
What are the demographic rate parameters capable of changing the size of populations such as birth, death, immigration, and emigration rates of lamprey?
What is the rate of increase/decrease of lamprey populations in the Columbia River Basin, including abiotic and biotic factors?
Theme: Population structure and diversity
  Subtheme: Conservation
How do management actions or approaches to population recovery and habitat restoration affect meta-population structure or diversity in ways that will increase viability of fish and wildlife in the Columbia River Basin? (Primary)
Theme: Population structure and diversity
  Subtheme: Conservation - targets
Are data available to assess the quality of available spawning and rearing habitats, determine the minimum viable population size and productivity of Columbia Basin anadromous salmonid stocks? What will the role of hatchery fish be, relative to wild fish, in the long-term sustainability of anadromous salmonid fisheries?
What are the natural production SAR (smolt-to-adult return ratio) estimates at the MPG (major population group) or population scale?
Theme: Population structure and diversity
  Subtheme: Conservation - reintroduction
What is the success rate of the current efforts at re-introducing anadromous fish into blocked areas throughout the Pacific Northwest?
Can extirpated populations be recolonized by relying on out-of-basin brood stock?
Theme: Population structure and diversity
  Subtheme: Conservation - hydrosystem
What are the differential effects of flow augmentation, transportation, and summer spill on “ocean type vs. reservoir type” fall Chinook?
Theme: Population structure and diversity
  Subtheme: Conservation - management actions
How do management actions for one species, such as salmon, affect another species, such as lamprey?
Theme: Predation
  Subtheme: Abundance and food web
Has the abundance and distribution of (keystone) predators in the Columbia River changed over time, and how does the intensity of predation vary by species, life stage, and location? (Primary)
What is the temporal and spatial species composition, abundance, and foraging rates of juvenile salmonid predators at representative locations in the estuary and plume?
What is the distribution, abundance, and size composition of forage fishes available to predators as alternatives to salmonids, sturgeon, and lamprey?
Theme: Predation
  Subtheme: Abundance and food web - avian
What is the abundance and diet of sooty shearwaters and common murres collected in the plume and how does it relate to the abundance of forage fishes?
Theme: Predation
  Subtheme: Abundance and food web - pinnipeds
Can the adult fish stocks taken by sea lions be identified (and take estimated) based upon when the various stocks move through the Bonneville ladders?
Are pinnipeds (and harbor porpoises) significant predators of juvenile salmon in the ocean?
Theme: Predation
  Subtheme: Impacts
To what extent is the viability or abundance of native fish and wildlife populations in the Columbia River Basin jeopardized by predation? (Primary)
This uncertainty is highly relevant to the Fish and Wildlife Program vision regarding the abundance, diversity, and resilience of focal species. Considerable theoretical and some historical knowledge exist about the long-term dynamics of native predators and their co-evolved prey. However, predicting how predators will impact prey populations is particularly difficult when other factors affecting the abundance or vulnerability of the prey are changing beyond historical norms (see Programmatic Comment 4). The ISAB has not comprehensively reviewed the impacts of predation on Columbia River salmon, but it has summarized some existing knowledge in its reports on food webs (ISAB 2011-1) and density dependence (ISAB 2015-1).
What are the impacts of non-native predators on native salmonids and other native species at regional scales and where many species co-occur?
What level of anadromous fish mortality is caused by increased predation by cormorants and pelicans?
Theme: Predation
  Subtheme: Impacts - on salmonids
How does predation affect fish survival in the ocean?
What are the effects of predation on salmonids?
What is the abundance of avian predator populations in the Mid-Columbia River and what are their impacts on outmigrating juvenile salmonids?
What are the impacts of adult salmon feeding on juvenile salmon off the Columbia River and other coastal areas?
What is the mortality and effects on life cycle recruitment in salmon populations targeted by pinnipeds (predation on adult salmon by pinnipeds)?
What influence does juvenile salmonid loss to predators (bird and fish predators) have on the adult return rate of the various salmon stocks?
What is the total mortality of salmonids from avian predation in the plume?
Theme: Predation
  Subtheme: Impacts - on sturgeon
What are river-wide white sturgeon losses to pinniped predation?
Theme: Predation
  Subtheme: Impacts - on lamprey
What is the extent of predation on lamprey at Bonneville Dam and other upstream dams?
What are predation levels on adult and juvenile lamprey during migration?
Theme: Predation
  Subtheme: Management
How effectively can undesirable impacts of predation be ameliorated by management actions including hydrosystem operations, habitat modifications and predator population control? (Primary)
Predators respond behaviorally, ecologically, and evolutionarily to foraging opportunities, such as those created by hydroelectric dams that modify the migratory corridors of juvenile and adult salmon, and the release of large concentrations of naïve hatchery-reared smolts. Contemporary predator populations are probably supported to some degree by the relatively constant annual releases of about 140 million salmon and steelhead from hatcheries. The feasibility and cost effectiveness of predator control programs are questionable except in relatively restricted areas where prey are especially vulnerable and predator impacts are concentrated (e.g., near bird colonies and tailraces). Benefits of reducing smolt mortality due to piscivorous birds and fish might be largely lost through density dependent (i.e., non-additive) mortality at later life stages (ISAB 2015-1; see Programmatic Comment 5). Such compensatory effects are less likely later in life, and predation during upstream migration is likely to have more impact on adult abundance than an equivalent rate of predation at earlier life stages. Predator control programs can also have counter-intuitive and unintended consequences for both the target populations and other predator and prey species.
Theme: Predation
  Subtheme: Management - predator control
To what extent is any single factor such as spill, or the predator control program, a factor in lowering the rate of predation of northern pikeminnow on juvenile salmon?
What is the effectiveness of the management plans to decrease avian predation of anadromous salmonids in the estuary?
Theme: Predation
  Subtheme: Management - hydrosystem operations
Can predation rates be reduced when flows are high or when fish move past bird colonies relatively quickly? The implication is that mortalities might be accentuated when flows are low or travel times reduced. Similarly, increased mortality might also result through predation by northern pikeminnow and other fishes in Columbia and Snake River reservoirs.
Theme: Predation
  Subtheme: Management - habitat restoration
What are the impacts of birds and fish predation on juvenile salmon in restoration sites? Evaluate possible ecological engineering solutions.
Theme: Public engagement
  Subtheme:
How well does the public understand the Fish and Wildlife Program? (socioeconomic engagement)
How well does the Fish and Wildlife Program communicate with and engage the public (and its diverse social groups) associated directly or indirectly with the landscape?
Tracking and analyses of the engagement and diversity of groups involved in Program efforts are vital for long-term success. This requires analyses of engagement outcomes (their effectiveness and cost-effectiveness), communicating results of Program projects to the public and to local decision makers, and evaluating the impact of these activities on management and public support for restoration actions. New knowledge that could improve management will have no impact if it is not disseminated. But while effective dissemination may be a necessary condition, it may not be sufficient to ensure expected outcomes due to a range of factors including community perceptions, beliefs, and mental models that lead to differing reactions to scientific information. These factors often influence decisions of local governance groups, private citizens, non-governmental organizations (NGOs), restoration practitioners, and other participants in regional conservation and restoration efforts.
How well does the Fish and Wildlife Program strategy incorporate the human-related aspects of landscape ecology and resilience?
Projections of future trajectories of fish and wildlife populations are not likely to be robust unless they incorporate changing patterns of land use and land cover. Public engagement of local, state, and federal land use planners and natural resource economists could improve projections of changes in the landscape (Hulse et al. 2004). Models of socioeconomic change could also help to predict future landscape conditions and their effects on restoration efforts or the resilience of threatened salmon populations and other focal species.
How well does the Fish and Wildlife Program strategy develop organizations that support collaboration, integration, and effective governance and leadership?
The study of public engagement in environmental issues can provide guidance in understanding how scientists, working with others, can contribute to effective solutions. Promotion of more collaborative and participatory decision-making at multiple governance levels has gained attention in recent years. Adherents of this approach point to the need for more collaboration among NGOs, governments, and businesses (Newig and Fritsch 2008). The actual benefits of public engagement are difficult to evaluate, rigorous evaluation is both complicated and rare (Rowe 2005), and the evidence is mixed (Newig and Fritsch 2008). One factor important to public engagement is community homogeneity—research has shown that public engagement is lower in more-heterogeneous communities (Costa and Kahn 2003). Coordination and cooperation are costly; they incur transactions costs, i.e., expending time and effort to establish channels of communication and to decide which entities, among a multitude of potential cooperators, represent sources of information and communication that are sufficiently valuable to warrant investments and continued expenditures (see Arrow 1974). These transaction costs can be high, and the benefits of cooperation must be sufficiently large relative to those costs for each participating entity to justify their continued involvement, otherwise collective engagement is unlikely to be sustainable. Although in some cases conservation and restoration actions appear to be working at odds with each other, resolving the conflicts are not always straightforward. Adaptive problems, such as river conservation and restoration, are socially and ecologically complex, the solutions to these problems are not known, and even if they were, no single entity has the resources or authority to bring about necessary changes (Naiman 2013). Reaching effective solutions generally requires innovation, sharing new information, and learning by members of the public involved in the problems (Ostrom 1990, Lee 1994). Success can depend on the willingness of the public to change their behaviors in ways that are viewed as costly or simply contrary to habit, belief, or tradition (Ostrom 2014). International examples suggest that large-scale common pool resources (e.g., entire watersheds) can be successfully managed (Ostrom 1990). Such successes typically require coordination among governments with multiple overlapping jurisdictions and among multiple NGOs (e.g., Morton Bay, Australia; see Sarker et al. 2008 and Bunn et al. 2010). The challenges as well as successful examples have been well documented (Bromley and Cernea 1989; Ostrom 1990, 2009; Dietz et al. 2003). The challenges, which are likely to be site specific, amount to discovering the best way to engage and coordinate with government entities at various jurisdictional scales, and with NGOs, to promote public communication, consultation, and participation to further the goals of the Program. An initial step would be to support organizations that show promise for assisting with coordination, integration, and leadership toward achieving Program objectives.
How well does the Fish and Wildlife Program strategy promote adaptive capacity based on active learning through assessment, monitoring, innovation, experimentation, and modeling?
Annual variability and long-term change are inherent properties of landscapes, ecosystems, and fish and wildlife populations and are also difficult to anticipate. Attempts to manage for a specific benefit may disrupt adaptive capacity and resilience of riparian and aquatic ecosystems by simplifying the diversity of habitats, altering connectivity, and disrupting mechanisms for feedback. Damage to the adaptive capacity of the ecosystem could also significantly harm human communities that depend on salmon and other species. Many future ecosystems will have no natural or historical precedent (ISAB 2011-1) due to factors such as non-native species (ISAB 2008-4), climate change (ISAB 2007-2), and extensive land cover conversion (ISAB 2003-2, ISAB 2011-4). Adaptive management is a cornerstone of the Program because it provides a robust mechanism to learn about changing landscapes, ecosystems, and populations and to revise our actions appropriately. Another cornerstone is the concept of resilience, which argues that diversity, modularity, and feedback lead to retention of adaptive capacity. Resilience includes anticipation that change is to be expected and there is a need for alternatives and flexibility to new situations and challenges. For this reason, many organizations are working to integrate biophysical and socioeconomic science with environmental and resource management. This integration is intended to improve management decisions and also strengthen adaptive capacity and ultimately the resilience of human-natural systems faced with change. More specifically, monitoring and modeling are already major elements of the Program, but there could be greater attention to active learning in broader social and economic settings with more interactive tools.
How well does the Fish and Wildlife Program incorporate a clear process to generate new information and revise objectives, strategies, and actions in response to that information?
Adaptive management is a process for deciding better approaches when science points toward an improved policy, when knowledge is incomplete, or when there is considerable uncertainty about future conditions. For example, one option for ecosystem management may require control and homogenization of ecosystems, but such an approach can reduce the biological diversity needed for adaptive capacity. Adaptive management allows scientific knowledge from monitoring, modeling, and assessing the linkages and feedbacks of coupled human-natural systems, to be used to make predictions, set new goals, and identify mechanisms to achieve those goals. Adaptive management also benefits from innovation and comparison among groups engaged in similar activities. One of the Program’s primary goals is to improve resilience and adaptive capacity of fish and wildlife populations through an effective feedback of learning through experimentation, innovation, and sharing new knowledge. The uncertainty relates to how well the Program is incorporating adaptive management into program improvements. Evaluating the use of adaptive management requires assessment of 1) the institutional process for program management, 2) the designs of future objectives and strategies, and 3) the operational processes associated with regional decision making.