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Research about Idaho, Oregon, Washington

Source-linked reports with geographic coverage including Idaho, Oregon, Washington.

At least 19 recordsLinked to original sources

Cave records reveal recent origin of North America’s deepest canyon

We explore how and when Hells Canyon, North America’s deepest river gorge (~2,400 m deep), formed, addressing these fundamental questions first posed by W. Lindgren [ The Gold Belt of the Blue Mountains of Oregon (1901)]. Existing hypotheses about the canyon’s formation and timing of incision remain speculative due to a lack of direct constraints and geomorphic analysis in the canyon. Herein, we combine cosmogenic nuclide dating of cave-bound river deposits, river profile analysis, and numerical modeling to provide the first direct age constraints and systematic analysis of incision processes at work in Hells Canyon. Our study reveals a significant drainage capture triggered rapid incision at ~2.1 ± 1.0 Ma, establishing the Snake River’s modern route into the Columbia River system. The increased drainage area and subsequent increase in stream power resulted in the rapid incision of Hells Canyon and the formation of tributary knickpoints (KPs) that decrease in elevation away from the capture location. Cosmogenic dating of cave deposits indicates incision rates increased from ~0.01 to ~0.16 mm y −1 . Numerical modeling of the stream capture supports these observations, demonstrating how abrupt drainage area increase drives rapid river incision. Our findings from Hells Canyon provide a well-constrained example of how drainage capture can dramatically shape the evolution of a major river gorge.

Idaho, Oregon, Washington↗

The mountains are calling, but will visitors go? Modeling the effect of weather and air quality on visitation to Pacific Northwest parks and protected areas using mobile device data

We investigated how visitors to federal, state, and local parks and protected areas (PPAs) respond to weather and air quality conditions in the Pacific Northwest (PNW), United States. Specifically, we modeled the relationship between weekly visitation and mean weekly minimum and maximum temperature, precipitation, Air Quality Index (AQI), and particulate matter 2.5 concentration (PM2.5, often used as an indicator of wildfire smoke) during an extended peak visitation season from 2017 to 2021 in 91 PNW PPAs. We used mobile device data from StreetLight Data Inc. to estimate weekly vehicular visitation. Our findings indicate that increasing precipitation corresponded with decreased weekly visitation to all three types of PPAs and rising minimum temperatures corresponded with increased visitation. We found that rising maximum temperatures corresponded with increased visitation in federal and local PPAs, but corresponded with decreased visitation in local PPAs once temperatures reach a maximum threshold. We did not observe a maximum threshold effect in federal or state settings. Further, we found that the effect of air quality and smoke on visitation varies based on the metric used: increased PM2.5 concentrations (possibly indicating the presence of wildfire smoke) in federal and local PPAs corresponded with decreased visitation, while increased AQI in federal PPAs corresponded with increased visitation. These findings indicate that visitors may respond differently to different types of air pollution. Our results have implications for adapting peak- and shoulder- season visitor use management to current and future climate change within and beyond PPAs of the PNW.

Idaho, Oregon, Washington↗

Integrating Sr isotopes, microchemistry, and genetics to reconstruct Salmonidae species and life history

Recent approaches to fisheries research emphasize the importance of the coproduction of knowledge in building resilient and culturally mindful fisheries management frameworks. Despite widespread recognition of the need for Indigenous knowledge and historical reference points as baseline data, archaeological data are rarely included in conservation biology research designs. Here we propose a novel multiproxy method to learn from former fisheries stewards by generating archaeological data on past salmonid population parameters. We used a newly developed, high throughput qPCR (HT-qPCR) chip, originally designed for environmental DNA (eDNA), for species identification of archaeological salmonid vertebrae. We combine this with the laser ablation split-stream (LASS) approach to identify ocean-migration versus freshwater residency. We test this multidisciplinary approach using both contemporary and archaeological salmonid samples and new radiocarbon dates from the Tronsdal Site on the Skagit River, Washington State, USA. This is a useful approach for extracting information about Salmonidae species and life history diversity from archaeological remains to reconstruct historic baselines for several population parameters in anadromous species with long periods of freshwater residency. The approach outlined in this paper may be particularly useful for research investigating past fisheries dynamics, offering hundreds to thousands of years of temporal depth for modern fisheries management, harvest policies, restoration ecology, and conservation biology.

Idaho, Oregon, Washington↗

Wildfires influence mercury transport, methylation, and bioaccumulation in headwater streams of the Pacific Northwest

The increasing frequency and severity of wildfires are among the most visible impacts of climate change. However, the effects of wildfires on mercury (Hg) transformations and bioaccumulation in stream ecosystems are poorly understood. We sampled soils, water, sediment, in-stream leaf litter, periphyton, and aquatic invertebrates in 36 burned (one-year post fire) and 21 reference headwater streams across the northwestern U.S. to evaluate the effects of wildfire occurrence and severity on total Hg (THg) and methylmercury (MeHg) transport and bioaccumulation. Suspended particulate THg and MeHg concentrations were 89 and 178% greater in burned watersheds compared to unburned watersheds and increased with burn severity, likely associated with increased soil erosion. Concentrations of filter-passing THg were similar in burned and unburned watersheds, but filter-passing MeHg was 51% greater in burned watersheds, and suspended particles in burned watersheds were enriched in MeHg but not THg, suggesting higher MeHg production in burned watersheds. Among invertebrates, MeHg in grazers, filter-feeders, and collectors was 33, 48, and 251% greater in burned watersheds, respectively, but did not differ in shredders or predators. Thus, increasing wildfire frequency and severity may yield increased MeHg production, mobilization, and bioaccumulation in headwaters and increased transport of particulate THg and MeHg to downstream environments.

Idaho, Oregon, Washington↗

Encounter rates and catch-and-release mortality of steelhead in the Snake River basin

Objective The potential influence (i.e., impact rate) of catch-and-release fisheries on wild steelhead Oncorhynchus mykiss is poorly understood and is a function of the abundance of wild fish, how many fish are encountered by anglers (i.e., encounter rate), and the mortality of fish that are caught and released. In Idaho, estimates of wild steelhead encounter rates have been derived using the number of wild and hatchery steelhead passing Lower Granite Dam, the number of hatchery steelhead harvested, and the number of hatchery steelhead caught and released. The method includes assumptions that hatchery and wild steelhead have equal encounter rates and catch-and-release mortality is 5% for wild steelhead. Here, we investigated wild and hatchery steelhead encounter rates by anglers, estimated catch-and-release mortality, and concatenated both aspects to examine how existing recreational steelhead fisheries influence wild steelhead mortality. Methods We sampled, tagged, and released 1,251 spawn-year 2020 (SY2020) and 1,956 spawn-year 2021 (SY2021) adult steelhead at Lower Granite Dam with T-bar anchor tags and passive integrated transponder (PIT) tags to estimate steelhead encounter rates and catch-and-release mortality. Differences in survival of caught steelhead and those not reported as caught were evaluated using detections at various locations (e.g., PIT arrays, weirs). Result Estimated encounter rates were 43.7% (95% credible interval; 28.2%, 100.0%) for wild fish and 46.7% (29.6%, 100.0%) for adipose-clipped fish in SY2020. In SY2021, encounter rates were 47.2% (32.4%, 100.0%) for wild fish and 52.3% (37.1%, 100.0%) for adipose-clipped fish. Based on detections of caught fish and those not reported as caught, catch-and-release mortality of wild steelhead was estimated to be 1.6% (0.0%, 5.2%). Wild steelhead impact rates were 0.7% (0.0%, 2.7%) in SY2020 and 0.7% (0.0%, 2.8%) in SY2021. Conclusion Estimated rates of impact on wild steelhead were consistent and low across years despite major differences in the structure of the fisheries. Our results suggest assuming that encounter rates are equal between hatchery and wild steelhead, and that steelhead catch-and-release mortality is 5%, will likely lead to a conservative estimate of the wild steelhead impact occurring from catch-and-release fisheries.

Idaho, Oregon, Washington↗

Back from the brink: Estimating daily and annual abundance of natural-origin salmon smolts from 30-years of mixed-origin capture-recapture data

Evaluating the status and trends of natural-origin anadromous fish populations over time requires robust estimates of out-migrating juvenile abundance. Information on abundance is typically acquired by capturing actively migrating fish as they pass stationary monitoring platforms. Challenges to estimation include protracted migration timing, temporally varying capture probabilities and the contemporaneous presence of unmarked hatchery-origin fish. The confounding effects of unmarked hatchery fish are especially pernicious in systems hosting multiple hatchery programs with variable mark-rates among releases. Here, we address this problem for a regionally and culturally important population of Chinook salmon ( Oncorhynchus tshawytscha ) supported by a hatchery-supplementation program implemented in response to the listing of this population under the U.S. Endangered Species Act. We developed a model to estimate daily and annual abundance of naturally produced age-0 fall Chinook salmon passing Lower Granite Dam (Snake River, USA) for each of the last 30 years. We accounted for variable hatchery marking rates by integrating two related data sources: 1) release-recapture data of fish with individually identifiable tags and 2) counts of marked and unmarked sample of fish captured each day. We fit joint parameters for daily fish arrival and capture probabilities to these data to estimate the daily abundance of hatchery- and natural-origin fish. Our results show that from 1992 to 2021, the annual abundance of juvenile natural-origin Snake River fall Chinook salmon increased by two orders of magnitude. These results are the first comprehensive evaluation of multi-decadal trends in abundance and run-timing for this population. Our approach can be adapted to other runs and locations within the Columbia River basin or similar systems where out-migrating fish are monitored at fixed locations.

Idaho, Oregon, Washington↗

Snake River Fall Chinook Salmon research and monitoring

In Chapter 1, we report on development and application of an integrated population model (IPM) for the natural-origin fall Chinook salmon population upstream of Lower Granite Dam. This year’s efforts represent the third update to the model. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model and estimating the effects of covariates on key demographic parameters. The goals of this year’s report are to 1) describe the modifications and advances made since the previous report, 2) to annually update and report the abundance estimates and other quantities used in the model, 3) to provide annual estimates of population parameters estimated by the IPM, and 4) to outline the next year’s tasks for advancing and/or applying the model. Since our last report on the life-cycle model, we have made a number of changes including: 1) incorporating jack abundance and age-structure data into the observation model, 2) changing smolt-to-adult survival (SAR) for subyearling and yearling to partial SARs that represent the joint probability surviving and entering the ocean at a given juvenile age, 3) combining age categories for rarely observed ages, 4) using scale data from unmarked fish to estimate age structure, and 5) generating composite life-cycle demographic parameters (cumulative capacity and productivity) from stage-specific parameters. We also generated juvenile abundance estimates, extended the model to include three additional brood years (1992– 2021), and ran the model to forecast returns to Lower Granite in 2022. For posterior medians of life stage-specific parameters, we estimated a mean productivity of 438 natural-origin juvenile recruits per female spawner, a capacity of 1.36 million juveniles, and a mean smolt-to-adult survival (SAR) of 1.2%. We detected strong density-dependent regulation, with juvenile recruits per spawner declining to about 50 juvenile recruits per female spawner at high spawner abundance. Across the entire life cycle, these stage-specific parameters resulted in a median cumulative intrinsic productivity of 1.93 adult female recruits per female spawner and a median equilibrium abundance of 2,851 female spawners (7,842 total spawners). Annual juvenile productivity varied from about 250–1,000 juveniles per spawner but displayed no temporal trends or patterns. For the three most recent brood years added to the model, recruits per spawner were higher than average but well within the range of uncertainty observed over the entire time series. In contrast to juvenile recruitment variability, SAR varied considerably among years and exhibited two periods of high survival (1996–2001 and 2007–2012) when SAR ranged from 2% to 6% and cumulative productivity ranged from 2 to 8 recruits per spawner. Partial SARs revealed that yearling outmigrants contributed substantially to the high SARs in the first high-survival period, but the second period was dominated by subyearlings. Yearlings contributed >30% to SAR in most years prior to 2007, and <30% since 2007. Our two-stage IPM provides a wealth of information about population dynamics affecting two key life-stage transitions (spawner to juvenile, and juvenile to spawner) centered on passage at Lower Granite Dam. By summarizing these stage-specific demographic parameters across the entire life cycle, this information will be useful for informing the recovery status of this threatened population. Whereas previous versions introduced hydrosystem and ocean covariates into the model, this phase of model development focused on solidifying the underlying model structure by introducing the concept of partial SARs and developing composite productivity and capacity as a function of underlying stage-specific parameters. Given this advancement, our next steps are to re-incorporate covariates into the model, specifically to understand how different factors affect partial SARs of subyearling and yearlings. Longer term model developments include:1) incorporating hatchery fish to explicitly estimate their survival as an alternative method for estimating natural-origin age composition, 2) expanding the model’s structure to include the three major spawning aggregates, 3) more explicitly modeling hydrosystem effects including transportation, and 4) using the model to assess retrospective and prospective management actions. In 2022, the U.S. Geological Survey (USGS) focused adult salmon survey efforts in the Snake River on deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses. We use used a boat-mounted underwater video camera to count 99 deepwater redds at 16 of the 29 sites surveyed. Redd depths averaged 4.4 m. In conjunction with the Idaho Power Company, we collected genetic samples from 318 live fall Chinook salmon (Oncorhynchus tshawytscha) and 19 carcasses at 40 unique geographic locations that spanned 91 river kilometers. Eighty fish were collected at three sites (High Range [rkm 332.3], Dug Bar [rkm 315.4], and Three Creek [rkm 384.0]), which accounted for 23% of all collected fish in 2022. Most (333 fish) post-spawned salmon were collected from early to mid-November just after the peak of spawning. A summary of 2021 PBT results produced by the Idaho Power Company can be found in Appendix A.2. Beach seining and PIT tagging of subyearling fall Chinook salmon was conducted in Snake and Salmon rivers to obtain information on population metrics and growth as well as to provide data for ongoing life-cycle modeling. In the Snake River, we collected 7,496 subyearlings, tagged 4,139, and recaptured 502 (12.1%). Using 8-mm tags in 45–49-mm fish allowed us to represent an additional 25% of the juvenile population through PIT tagging beyond just using standard 9- and 12-mm tags. In the Salmon River, we captured 206 natural subyearlings with the majority (52%) of fish being captured at two sites: rkm 20 and 26. We tagged 145 subyearlings and recaptured 9 fish. Many of the subyearlings we tagged in the Snake River were detected passing Lower Granite Dam, but only 4 fish tagged in the Salmon River were detected. In total we detected 484 (11.3%) tagged fish at Lower Granite Dam, and detection rates varied by tag size and passage route. More subyearlings were detected passing via the removable spill weir (RSW) earlier in the season while more fish were detected passing through the juvenile fish bypass system (JBS) earlier in the season while more fish were detected passing via the removable spill weir (RSW) later in the season. In general, fish tagged with 12-mm PIT tags had higher detection rates than fish tagged with smaller tags. Survival to Lower Granite Dam was low and ranged from 0.22 to 0.36. Season-wide, growth of subyearlings was higher in the lower reach than in the upper reach of the Snake River.

Idaho, Oregon, Washington↗

Coproduction and modeling spatial contact networks prevent bias about infectious hematopoietic necrosis virus transmission for Snake River Basin salmonids

Much remains unknown about variation in pathogen transmission across the geographic range of a free-ranging fish or animal species and about the influence of movement (associated with husbandry practices or animal behavior) on pathogen transmission. Salmonid hatcheries are an ideal system in which to study these processes. Salmonid hatcheries are managed for endangered species recovery, supplementation of threatened or at-risk fish stocks, support of fisheries, and ecosystem stability. Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus of significant concern to salmon aquaculture. Landscape IHNV transmission dynamics previously had been estimated only for salmonid hatcheries in the Lower Columbia River Basin (LCRB). The objectives of this study were to estimate IHNV transmission dynamics in a unique geographic region, the Snake River Basin (SRB), and to quantitatively estimate the effect of model coproduction on inference because previous assessments of coproduction have been qualitative. In contrast to the LCRB, the SRB has hatchery complexes consisting of a main hatchery and ≥1 satellite facility. Knowledge about hatchery complexes was held by a subset of project researchers but would not have been available to project modelers without coproduction. Project modelers generated and tested multiple versions of Bayesian susceptible-exposedinfected models to realistically represent the SRB and estimate the effect of coproduction. Models estimated the frequency of transmission routes, route-specific infection probabilities, and infection probabilities for combinations of salmonid hosts and IHNV lineages. Model results indicated that in the SRB, avoiding exposure to IHNV-positive adult salmonids is the most important action to prevent juvenile infections. Migrating adult salmonids exposed juvenile cohort-sites most frequently, and the infection probability was greatest following exposure to migrating adults. Without coproduction, the frequency of exposure by migrating adults would have been overestimated by 70 cohort-sites, and the infection probability following exposure to migrating adults would have been underestimated by∼0.09. The coproduced model had less uncertainty in the infection probability if no transmission route could be identified (Bayesian credible interval (BCI) width = 0.12) compared to the model without coproduction (BCI width = 0.34). Evidence for virus lineage MD specialization on steelhead and rainbow trout (both Oncorhynchus mykiss) was apparent without model coproduction. In the SRB, we found a greater probability of virus lineage UC infection in Chinook salmon (Oncorhynchus tshawytscha) compared to in O. mykiss, whereas in the LCRB, UC more clearly exhibited a generalist approach. Coproduction influenced estimates that depended on transmission routes, which operated differently at main hatcheries and satellite sites within hatchery complexes. Hatchery complexes are found outside of the SRB and are not specific to salmonid hatcheries alone. There is great potential for coproduction and modeling spatial contact networks to advance understanding about infectious disease transmission in complex production systems and surrounding free-ranging animal populations.

Idaho, Oregon, Washington↗

Tough places and safe spaces: Can refuges save salmon from a warming climate?

The importance of thermal refuges in a rapidly warming world is particularly evident for migratory species, where individuals encounter a wide range of conditions throughout their lives. In this study, we used a spatially explicit, individual-based simulation model to evaluate the buffering potential of cold-water thermal refuges for anadromous salmon and trout ( Oncorhynchus spp.) migrating upstream through a warm river corridor that can expose individuals to physiologically stressful temperatures. We considered upstream migration in relation to migratory phenotypes that were defined in terms of migration timing, spawn timing, swim speed, and use of cold-water thermal refuges. Individuals with different migratory phenotypes migrated upstream through riverine corridors with variable availability of cold-water thermal refuges and mainstem temperatures. Use of cold-water refuges (CWRs) decreased accumulated sublethal exposures to physiologically stressful temperatures when measured in degree-days above 20, 21, and 22°C. The availability of CWRs was an order of magnitude more effective in lowering accumulated sublethal exposures under current and future mainstem temperatures for summer steelhead than fall Chinook Salmon. We considered two emergent model outcomes, survival and percent of available energy used, in relation to thermal heterogeneity and migratory phenotype. Mean percent energy loss attributed to future warmer mainstem temperatures was at least two times larger than the difference in energy used in simulations without CWRs for steelhead and salmon. We also found that loss of CWRs reduced the diversity of energy-conserving migratory phenotypes when we examined the variability in entry timing and travel time outside of CWRs in relation to energy loss. Energy-conserving phenotypic space contracted by 7%–23% when CWRs were unavailable under the current thermal regime. Our simulations suggest that, while CWRs do not entirely mitigate for stressful thermal exposures in mainstem rivers, these features are important for maintaining a diversity of migration phenotypes. Our study suggests that the maintenance of diverse portfolios of migratory phenotypes and cool- and cold-water refuges might be added to the suite of policies and management actions presently being deployed to improve the likelihood of Pacific salmonid persistence into a future characterized by climate change.

Idaho, Oregon, Washington↗

Snake River fall Chinook salmon research and monitoring

In 2021, the U.S. Geological Survey (USGS) focused adult salmon survey efforts in the Snake River on deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses. We use used a boat-mounted underwater video camera to count 93 deepwater redds at 17 of the 28 sites surveyed. Redd depths averaged 3.9 m. In conjunction with the Idaho Power Company, we collected genetic samples from 346 live fall Chinook salmon ( Oncorhynchus tshawytscha ) and 15 carcasses at 48 unique geographic locations that spanned 90 river kilometers. Seventy-two fish were recovered at Eureka Bar (river kilometer [rkm] 307.1) and High Range (rkm 332.3), which accounted for 20% of all collected fish in 2021. Most (291 fish) post-spawned salmon were collected during the first two weeks of November around the peak of spawning. A summary of 2021 PBT results produced by the Idaho Power Company can be found in Appendix A.2. Beach seining and PIT tagging of subyearling fall Chinook salmon was conducted in Snake and Salmon rivers to obtain information on population metrics and growth as well as to provide data for ongoing life-cycle modeling. In the Snake River, we collected 13,710 subyearlings, tagged 6,299, and recaptured 981 (15.6%). Using 8-mm tags in 45–49-mm fish allowed us to represent an additional 40% of the juvenile population through PIT tagging beyond just using standard 9- and 12-mm tags. In the Salmon River, we captured 103 natural subyearlings with the majority (60%) of fish being captured at two sites: rkm 11 and 20. We tagged 27 subyearlings, and no fish were recaptured. In Lower Granite Reservoir, we captured 4,887 subyearlings, PIT tagged 2,585, and recaptured 312. Many of the subyearlings we tagged in the Snake River were detected passing Lower Granite Dam, but no fish tagged in the Salmon River were detected. In total we detected 673 (7.6%) tagged fish at Lower Granite Dam, and detection rates varied by tag size and passage route. More subyearlings were detected passing via the removable spill weir (RSW) earlier in the season while more fish were detected passing through the juvenile fish bypass system (JBS) later in the season. In general, fish tagged with 12-mm PIT tags had higher detection rates than fish tagged with smaller tags. Survival to Lower Granite Dam was low and ranged from 0.195 to 0.228. Growth of subyearlings was similar between riverine and reservoir reaches but was slightly lower in Lower Granite Reservoir. Only 19 subyearlings were recaptured at Lower Granite Dam in early autumn that predominantly originated from the Clearwater River (1 fish was from the Snake River). Mean standard deviation (SD) fork length and mass growth rates were 0.92±0.10 mm/d and 0.06±0.01 g/g/d, respectively.

Idaho, Oregon, Washington↗

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook salmon ESU

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2020 in response to U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on changes in population abundance and habitat use by natural- and hatchery-origin spawners. Typically, we also report on population attributes of natural-origin juveniles, but data on juveniles were not collected in 2020 due to Covid-19. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching the point that no more redds can be supported. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following changes: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr has declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate has increased. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir resulting from the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) programs. In 2020, the U.S. Geological Survey (USGS) focused survey efforts in the Snake River on deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses. We use a boat-mounted underwater video camera to count 170 deepwater redds at 19 of the 28 sites surveyed. Redd depths averaged 4.2 m. We collected genetic samples from 297 live fall Chinook salmon and 16 carcasses at 44 unique geographic locations that spanned 89 river kilometers. Seventy-two fish were recovered at Eureka Bar (rkm 307.1) and Corral Creek (rkm 349.7), which accounted for 23% of all collected fish in 2020. Most (238 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2020, we PIT tagged subyearling fall Chinook salmon in the Clearwater River to obtain population and growth data. In the Clearwater River, we tagged 2,192 subyearlings and recaptured 79 (3.6%) fish in the river and 187 fish (78 tagged by the U.S. Geological Survey, 109 tagged by the Nez Perce Tribe) at Lower Granite Dam during October which provided information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was generally lower in Lower Granite Reservoir than in riverine habitats. Information on prey resources and juvenile fall Chinook salmon prey consumption was collected to better understand the growth opportunity of late-migrating fish in Lower Granite Reservoir. Zooplankton and surface drifting prey were collected from three reservoir locations from July through October during 2019 and 2020. Fall Chinook salmon diet data were collected from angled fish using gastric lavage. Cladocera and Copepoda were the most abundant zooplankton taxa collected while Diptera was the most common invertebrate taxon collected in surface drift samples. Totals of 49 and 94 juvenile fall Chinook salmon were captured in 2019 and 2020, respectively, and most fish were caught in the lower reach of the reservoir in October of each year. Juvenile fall Chinook salmon consumed mainly dipterans in July and October 2019 and mainly Daphnia during August–October in 2020. Fish showed selection mainly for dipterans in 2019 but strong selection for Daphnia during October 2020. Stomach fullness values were relatively low (<1.1%) during both years. Results show that prey resources are adequate in Lower Granite Reservoir to support positive fish growth during late summer and early autumn.

Idaho, Oregon, Washington↗

Impact of smallmouth bass predation on subyearling fall Chinook salmon over a broad river continuum

Smallmouth bass ( Micropterus dolomieu ) predation on subyearling fall Chinook salmon ( Oncorhynchus tshawytscha ) was examined in the Snake River (USA) to identify seasonal and habitat-related changes in bass diets, and associated subyearling consumption and loss in various riverine and impounded reaches. Smallmouth bass diets reflected opportunistic foraging that at times showed predation on subyearlings is influenced by the consumption of other prey such as crayfish, sand roller ( Percopsis transmontana ), and smaller invertebrates. Estimated loss of subyearlings was influenced by bass abundance and consumption rates. The highest bass abundances (> 1,000 bass/river kilometer) were observed in the upper reach of Hells Canyon early in April and May, and in Lower Granite Reservoir. Peak consumption rates of subyearlings (≥ 0.12 subyearlings/bass/day) occurred in the upper reach of Hells Canyon during May and in most reservoir reaches in June. Predation losses accumulated evenly along the river continuum from riverine to reservoir habitats. We estimated that 869,371 subyearlings could be lost to smallmouth bass predation between riverine production areas and Lower Granite Dam in a given year. To provide a context for this estimated loss, we provide an illustration of its potential effect on the adult population. Assuming no juvenile mortality occurred downstream of the dam and depending on smolt-to-adult return rates, this represented up to 3.9–16.0% of the potential adult run that could have returned to Lower Granite Dam had no subyearling predation by smallmouth bass occurred upstream of the dam. Although this study was limited by a number of assumptions and constraints, it does provide an illustration of how predation affects juvenile and adult salmon loss over a broad, changing river landscape.

Idaho, Oregon, Washington↗

Groundwater quality in the Columbia Plateau basaltic-rock aquifers, northwestern United States

Groundwater provides nearly 50 percent of the Nation’s drinking water. To help protect this vital resource, the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Project assesses groundwater quality in aquifers that are important sources of drinking water. The Columbia Plateau basaltic-rock aquifers constitute one of the important resources being evaluated.

Idaho, Oregon, Washington↗

The Missoula and Bonneville floods—A review of ice-age megafloods in the Columbia River basin

The Channeled Scabland of eastern Washington State, USA, brought megafloods to the scientific forefront. A 30,000-km2 landscape of coulees and cataracts carved into the region’s loess-covered basalt attests to overwhelming volumes of energetic water. The scarred landscape, garnished by huge boulder bars and far-travelled ice-rafted erratics, spurred J Harlen Bretz’s vigorously disputed flood hypothesis in the 1920s. First known as the Spokane flood, it was rebranded the Missoula flood once understood that the water came from glacial Lake Missoula, formed when the Purcell Trench lobe of the last-glacial Cordilleran ice sheet dammed the Clark Fork valley in northwestern Idaho with ice a kilometer thick. Bretz’s flood evidence in the once-remote Channeled Scabland, widely seen and elaborated by the 1950s, eventually swayed consensus for cataclysmic flooding. Missoula flood questions then turned to some that continue today: how many? when? how big? what routes? what processes? The Missoula floods passed through eastern Washington by a multitude of valleys, coulees and scabland tracts, some contemporaneously, some sequentially. Which routings and their timing depended on the positions of various lobes of the multi-pronged Cordilleran ice sheet and the erosional development of the channels themselves. The first floods mostly followed the big bend of Columbia valley looping through north-central Washington. But the south-advancing Okanogan ice lobe soon blocked that path, forming long-lasting glacial Lake Columbia in the impounded Columbia valley. Missoula floods into this lake were diverted south out of the Columbia valley and into eastern Washington coulees and scabland tracts. At least four floods entered Moses Coulee, but then as the Okanogan lobe advanced over and blocked the head of that coulee, more eastern paths took the water, including Grand Coulee and the Telford-Crab-Creek and Cheney-Palouse scabland tracts. Flood routing also depended on the erosion of the coulees. At some point, headward erosion of upper Grand Coulee lowered the divide saddle between the west-running Columbia valley and the deep and wide Grand Coulee heading southwest. Still uncertain is when this happened and the consequences with respect to the stage and extent of glacial Lake Columbia and to flood access to the other, higher, flood routes. Downstream, all flood routes converged onto Pasco Basin, flowed through Wallula Gap and the Columbia River Gorge into the Pacific Ocean, following submarine canyons and depositing sediment layers on abyssal plains. Stratigraphic studies indicate dozens—likely more than a hundred—separate Missoula floods during the last glacial period. Over the length of the flood route, backwater areas and depositional basins preserve multiple flood beds, many of which are separated by signs of time, including volcanic ash layers and soil development in subaerial environments; and varve-like beds and pelagic mud layers in lacustrine and marine settings. Evidence also comes from the glacial Lake Missoula basin, where stratigraphy indicates dozens of filling and emptying cycles. Varve counts in conjunction of radiocarbon dating and paleomagnetic secular variation show the repeated filling-and-release cycles of glacial Lake Missoula had intervals possibly as long as 100 years early in the lake’s history but diminished to just one or two years for the last few floods. This behavior accords with jökulhlaup-style floods released by subglacial drainage from a self-dumping ice-dammed lake. But not yet clear is whether such a mechanism applies to all the floods or if some emptied more cataclysmically as hypothesized by some. Radiocarbon dating of sparse organic materials remains key to defining flood chronology but has been lately bolstered by analyses of terrestrial cosmogenic nuclides and optically stimulated luminescence. Varve counts and paleomagnetic secular variation studies help to define durations and intervals represented by sequences of flood beds. The ~16 ka Mount St. Helens Set S tephra is commonly interbedded within flood deposits, enabling correlation of deposits among sites. Tephra from the 13.7–13.4 ka eruption of Glacier Peak overlies all glacial Lake Missoula and Missoula flood deposits, defining an end time. Overall conclusions are that glacial Lake Missoula was extant and producing floods for at least 3–4 ky during 20–14 ka. At least ~75 floods preceded Mount St Helens Set S, followed by 30 or more after the tephra fall. Most floods entered glacial Lake Columbia, impounded by the Okanogan lobe, for 2–5 ky between about 18.5 and 15 ka. Glacial Lake Columbia outlived Lake Missoula by >200–400 yr but may have been born later since at least one flood came down the Columbia valley before the Okanogan ice lobe blocked the Columbia valley at 18.5–18 ka. The maximum extent of the Okanogan and Purcell Trench lobes, many Missoula floods, substantial erosion of upper Grand Coulee, and the widespread tephra falls from Mount St. Helens eruptions all happened about 17–15 ka. People, in the area since 16.6–15.3 ka, almost certainly witnessed the last of the Missoula floods and later large floods from other ice-dammed lakes in the Columbia River basin. Quantitative flow analyses give peak discharge estimates and support understanding of erosional and depositional processes. The first flow assessments were simple cross-section calculations but recent assessments employ two-dimensional hydrodynamic models. The general finding is that emplacement of the maximum stage evidence requires about 20 million m3/s near the Lake Missoula outlet and about 5–15 million m3/s through Wallula Gap and downstream in the Columbia River Gorge. These hydraulic analyses raise still-unresolved questions regarding canyon erosion and possible additional water sources. The large Pleistocene Bonneville flood entered the Columbia River system from the southeast from pluvial Lake Bonneville, the Pleistocene predecessor to Great Salt Lake in the eastern Great Basin. During the last glacial, the lake basin filled, covering >50,000 km2 with 10,400 km3 of water before reaching its maximum possible stage governed by Red Rock Pass, the lowest divide separating the basin from the Snake River basin to the north. The overtopping lake rapidly incised 108–125 m into the Red Rock Pass outlet, spilling half of its total lake volume. G.K. Gilbert described the essential sequence in the 1870s, but the flood was mostly forgotten until the late 1950s when Harold Malde linked the spectacular scabland topography and bouldery “melon gravel” on the Snake River Plain to the Lake Bonneville overflow. The Bonneville flood appears to have been a singular event at about 18 ka. No evidence of multiple or pre-last-glacial spillovers has yet been found. Its total volume was about twice that of a maximum Lake Missoula flood yet its peak discharge was ~1 million m3/s, less than a tenth of the largest Missoula floods. Its comparatively simple flow path and much steadier flow make the Bonneville flood ideal for new studies of erosional and depositional processes. At least two floods seem to have passed down the Columbia valley after the last of the Missoula floods, including a large flood about ~14 ka likely from cataclysmic demise of the thinning Okanogan ice lobe dam impounding glacial Lake Columbia. Floods from earlier glacial ages left scant yet clear evidence in the Channeled Scabland and Columbia valley. But their source, timing, and magnitudes are little understood. Some deposits are paleomagnetically reversed, thus older than ~800 ka. Last-glacial floods and perhaps older ones affected the Snake River Plain, some likely sourced in lakes dammed by alpine glaciers in central Idaho.

Idaho, Oregon, Washington↗

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook Salmon ESU: January 2019 - December 2019

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 19922019 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) progams. In 2019, the U.S. Geological Survey (USGS) shifted survey efforts in the Snake River toward deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses because all unmanned aerial system (UAS) activities were suspended by the Department of the Interior two weeks into the spawning season. We counted 81 deepwater redds at 17 of the 29 sites surveyed. Redd depths averaged 3.6 m. We collected a total of 123 live fall Chinook salmon from 16 unique geographic locations that spanned 55 river kilometers. Forty-six fish were recovered at Eureka Bar (rkm 307.1) and Kirby Creek (rkm 352.0), which accounted for 37% of all collected fish in 2019. Most (73 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2019, we PIT tagged subyearling fall Chinook salmon in both the Snake and Clearwater rivers. In the Snake River, we tagged 410 fish with 8-mm tags, 666 fish with 9-mm tags, and 1,082 fish 12-mm tags. During seining, our recapture rate of previously tagged fish was slightly higher in the lower reach at 11.4% than in the upper reach at 10.6%. In an effort to represent more of the population through tagging, we tagged fish as small as 45 mm with 8-mm tags at one site in the upper reach. This allowed us to increase the number of fish tagged in that reach by 17.7%. An additional 10.6% of collected fish could have been tagged in the lower reach had we used 8-mm tags in that reach. In the Clearwater River, we tagged 2,451 subyearlings and recaptured 260 (10.6%) fish in the river and 66 fish (48 tagged by USGS, 18 tagged by the Nez Perce Tribe) at Lower Granite Dam during October to provide information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was higher in Lower Granite Reservoir than in riverine habitats. We adapted existing statistical models used to estimate abundance of steelhead and spring/summer Chinook salmon for fall Chinook salmon passing Lower Granite Dam. Run reconstruction efforts to date at Lower Granite Dam for Snake River fall Chinook salmon have provided estimates of the number of returning adults but with no measure of uncertainty about the estimates. The objective of this study was to estimate the abundance, with uncertainty, of marked (coded-wire tagged CWT or adipose clipped) and unmarked fall Chinook salmon past Lower Granite Dam for return years 20032018. Estimating uncertainty is important for informing the state-space life cycle model (Chapter 5), which incorporates both observation and process uncertainty into parameter estimates. The coefficient of variation (CV) for log- abundance was 1.0% or less in all years, whereas the CV for abundance averaged 4.2% and ranged from 1.4% to 10.4% among years. Over the past five years, we have been developing a two-stage state-space life-cycle model for naturally produced fall Chinook salmon in the Snake River basin. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model. In this report we 1) describe the statistical life-cycle model and improvements made since our last report to the Independent Scientific Advisory Board (ISAB), 2) estimate the effects of covariates on key demographic parameters, and 3) use the fitted life- cycle model to simulate population trajectories under hydrosystem actions proposed for the NOAA 2020 Biological Opinion (hereafter, the Proposed Action). Major recent advancements to the model include revised juvenile abundance estimates, the ability to estimate smolt-to-adult return rates (SAR) separately for subyearling and yearling juvenile fall Chinook salmon, and improvements in the observation model for estimating age, sex, and outmigration structure in adult returns. We examined the effect of numerous environmental, hydrosystem, and ocean covariates on key demographic parameters but only a few covariates were significant. For the adult-to-juvenile transition, we found the maximum weekly river flows during the winter egg- incubation period had a significant negative effect on the juvenile outmigrant abundance from that brood year. For subyearling outmigrants, percent spill during the summer had a significant positive effect on SAR and the mean winter PDO (Pacific Decadal Oscillation) had a significant negative effect on SAR. For yearling outmigrants, NPGO (North Pacific Gyre Oscillation) had a significant positive effect on SAR. We used the fitted model to simulate population trajectories under the Proposed Action, and the median 10-year geometric mean abundance was 8,222 female spawners (interquartile range: 2,592 26,714). Overall, the probability of quasi- extinction (probability of falling below 50 female spawners for 4 consecutive years) was low, with only 1.6% of all simulations having a quasi-extinction probability >0.95. Although quasi-extinction probability was low, we did not assess the additional effect of climate change, which would be expected to increase quasi-extinction probability.

Idaho, Oregon, Washington↗

Pacific Northwest Aquatic Monitoring Partnership 2018 Annual Report

The Pacific Northwest Aquatic Monitoring Partnership (PNAMP) continued to promote the integration of monitoring resources and development of tools to support monitoring in 2018. Improved coordination and integration of goals, objectives, and activities among Pacific Northwest monitoring programs is essential to improving the quality and consistency of monitoring in the region.

Idaho, Oregon, Washington↗

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook Salmon ESU

The portion of the Snake River fall Chinook Salmon Oncorhynchus tshawytscha ESU that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2018 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence has been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E). In 2018, the U.S. Geological Survey (USGS) searched 10 shallow-water spawning sites and 25 deepwater spawning sites in conjunction with the Idaho Power Company (IPC). A total of 103 redds were counted at shallow-water sites and 61 redds were counted at deepwater sites. We recovered 17 carcasses and 13 live fish, which were spawned out, and collected biological information and tissue samples that are currently being analyzed for parentage to determine the percentage of hatchery-origin spawners on the spawning grounds.

Idaho, Oregon, Washington↗

Transmission routes maintaining a viral pathogen of steelhead trout within a complex multi-host assemblage

This is the first comprehensive region wide, spatially explicit epidemiologic analysis of surveillance data of the aquatic viral pathogen infectious hematopoietic necrosis virus (IHNV) infecting native salmonid fish. The pathogen has been documented in the freshwater ecosystem of the Pacific Northwest of North America since the 1950s, and the current report describes the disease ecology of IHNV during 2000–2012. Prevalence of IHNV infection in monitored salmonid host cohorts ranged from 8% to 30%, with the highest levels observed in juvenile steelhead trout. The spatial distribution of all IHNV-infected cohorts was concentrated in two sub-regions of the study area, where historic burden of the viral disease has been high. During the study period, prevalence levels fluctuated with a temporal peak in 2002. Virologic and genetic surveillance data were analyzed for evidence of three separate but not mutually exclusive transmission routes hypothesized to be maintaining IHNV in the freshwater ecosystem. Transmission between year classes of juvenile fish at individual sites (route 1) was supported at varying levels of certainty in 10%–55% of candidate cases, transmission between neighboring juvenile cohorts (route 2) was supported in 31%–78% of candidate cases, and transmission from adult fish returning to the same site as an infected juvenile cohort was supported in 26%–74% of candidate cases. The results of this study indicate that multiple specific transmission routes are acting to maintain IHNV in juvenile fish, providing concrete evidence that can be used to improve resource management. Furthermore, these results demonstrate that more sophisticated analysis of available spatio-temporal and genetic data is likely to yield greater insight in future studies.

Idaho, Oregon, Washington↗