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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Fish Out of Basin: Increased Stress Physiology and Reduced Performance of Salmon River Hatchery Chinook Salmon

Abstract Variation in rearing conditions across hatcheries and basins can affect the performance of hatchery salmonids in the wild. In 2008, the Shoshone-Bannock Tribes began planning an out-of-basin hatchery facility on the eastern Snake River Plain for rearing threatened Chinook Salmon Oncorhynchus tshawytscha for release in tributaries of the upper Salmon River, Idaho, USA. To help determine the viability of the planned out-of-basin hatchery, we reared 100,000 juvenile Chinook Salmon from the same genetic stock at one in-basin (Sawtooth Fish Hatchery on the Salmon River) and one out-of-basin (Springfield Fish Hatchery on the Snake River Plain) site in Idaho that are characterized by significant differences in water hardness and temperature regime. In October 2018 and April 2019, we tested whether fish condition, stress physiology, acute mortality, and downstream survival differed between the two groups at the parr and smolt life stages upon release in the Yankee Fork Salmon River, which is characterized by low water hardness. For both release groups, parr experienced low acute mortality during the 48 h after release; however, the out-of-basin group had a downstream survival rate through an unimpounded portion of the migration corridor that was an order of magnitude lower than that for the in-basin group. During the smolt release, the out-of-basin group showed signs of extreme physiological stress, acute mortality rates of 40–80%, and low survival in the unimpounded portion of the migratory corridor. The in-basin group recovered from the stress of transport and release, had no acute mortality, and survived through the unimpounded migratory corridor at a rate comparable to that of previous years’ releases. Based on the results of this comparative study, comanagers are evaluating alternatives to the proposed out-of-basin hatchery program. This case study highlights the effects of differences between rearing and release conditions on salmon physiology and survival as well as the value of conducting preliminary evaluations prior to implementing large-scale hatchery supplementation programs.

Ebel, Jonathan D.↗
DOE OSTI2023

Finding middle ground: Flow regimes designed for salmon and energy value

In regulated rivers, shaping seasonal flows to recover species at risk depends on understanding when to expect conflicts with competing water users and when their interests are aligned. Multi-objective optimization can be used to reveal such conflicts and commonalities. When species are involved, multi-objective optimization is challenged by the need to simulate complex species responses to flow regimes. Previously, we addressed that challenge by developing a simplified salmon model (Quantus) that defines cohorts of salmon by the river section and time in which they were spawned. Salmon in these space-time cohorts are tracked from the time redds (nests) are constructed until the cohort exits the tributary en route to the ocean. In this study, we modeled seasonal patterns in energy value and developed a Pareto-optimal frontier of seasonal flow patterns to maximize in-river salmon survival and hydropower value. Candidate flow regimes were characterized by two pulse flows varying in magnitude, timing, and duration and constrained by a total annual flow near the historical median. Our analysis revealed times when economic and salmon objectives were aligned and times when they differed. Pulse flows that favored higher energy value were timed to meet demand during extreme temperatures. Both salmon and hydropower objectives produced optimal flow regimes with pulse flows in early summer, but only solutions favoring hydropower value included high flows in mid-winter. Solutions favoring higher age-0 salmon survival provided an extended pulse flow in late winter/early spring, which suggests that access to productive floodplain habitat allowed faster growth and earlier out-migration and reduced the need for higher temperature-moderating flows later in spring. Minimum flows were also higher among solutions favoring salmon over energy. The tools used to produce these results can help to design simplified seasonal flow regimes by revealing compromise solutions that satisfy both fish and energy producers and highlighting when potential conflicts are likely.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Assessing the cumulative effects of nearshore habitat restoration actions for multiple populations of juvenile salmon in Whidbey Basin, Washington: foundation and approach for synthesis and evaluation

Ecosystem restoration is a common tool for re-establishing ecosystem processes, structures, and functions to improve biodiversity and services in coastal and estuarine ecosystems. In the Salish Sea, salmon habitats have been fragmented, reduced in size, and diminished in quality, and the ecosystem processes that form and sustain these habitats have been degraded and disrupted as well. This loss is especially prevalent in estuaries, where up to 90% of former salmon habitat has been lost or compromised. Salmon species are integral to the identities and cultures of people in the Pacific Northwest, yet salmon abundances remain at historic lows, especially in urbanized areas. Recent investments in restoration are creating rearing habitat and repairing lost ecosystem function. However, restoration efforts in this region have largely proceeded at the site scale, with less attention to big-picture thinking regarding how restoration will effectively recover degraded or lost habitats for target species. As a result, no landscape-scale evaluation program exists, and the cumulative benefits of multiple interventions are unknown. We describe innovative methods for science synthesis related to the evaluation of cumulative effects of ecosystem restoration for Pacific salmon, using years of existing, but disparate data. Building from previous work on cumulative effects evaluation and incorporating a hierarchy of hypotheses approach, we propose using causal inference across numerous hypotheses in a framework to assess the cumulative benefits to Pacific salmon from multiple estuarine restoration projects. We present the framework as a method that can be used to address many complex questions and provide examples from the Salish Sea where the approach is being implemented. The framework draws on science synthesis from numerous fields and uses a hierarchy of hypotheses, causal analysis at multiple scales, and a new hierarchy of synthesis for assessing multiple lines of evidence documenting restoration effects on Pacific salmon. We propose causal inference to synthesize dissimilar data streams, in our case, to identify various manifestations of cumulative effects of restoration and benefits to salmon, and to further inform restoration and recovery planning. A unifying framework would allow for the detection of thresholds at which restoration provides measurable improvement and would greatly advance understanding of the effects of restoration on ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Stock-specific spatial overlap among seabird predators and Columbia River juvenile Chinook Salmon suggests a mechanism for predation during early marine residence

Abstract Objective Because predation is thought to be the primary source of natural mortality for juvenile salmon first entering the ocean, we sought to identify regions where, on average, stock-specific spatial overlap between the distribution of threatened and endangered juvenile Chinook Salmon Oncorhynchus tshawytscha and abundant fish-eating seabirds (common murres Uria aalge and sooty shearwaters Ardenna grisea) suggests the greatest potential for ocean predation risk to juvenile Chinook Salmon. Methods The relative abundance and spatial distribution of seabird predators and juvenile Chinook Salmon were quantified as part of long-term ecosystem surveys during May 2003–2012 and June 2003–2022. Genetic stock identification methods were used to assign individual fish to their respective stock groups. Stock-specific species distribution models then generated maps and indices of average annual spatial overlap between predators and prey within the survey area. Result There is unequivocal evidence for spatial overlap between common murres, sooty shearwaters, and five genetic groups of interior and lower Columbia River juvenile Chinook Salmon. We found strongly positive (≥0.70) spatial correlations between predator and prey densities in both May and June, although spatial overlap was, in general, greater during May. The region of highest spatial overlap occurred on the inner continental shelf between the Columbia River mouth (46.2°N) and Grays Harbor (47.0°N), a region at the beginning of the juvenile salmon migratory pathway that is strongly affected by freshwater outflow from the river. Conclusion Our findings support the idea that ocean avian predation during early marine residence has the potential to affect marine survival of juvenile Chinook Salmon and should be further investigated to better inform and implement ecological models and possible recovery actions for Chinook Salmon populations of the Columbia River basin.

Zamon, Jeannette E.↗
DOE OSTI2024

Implications of increased spatial and trophic overlap between juvenile Pacific salmon and Sablefish in the northern California Current

Abstract Objective The study was designed to assess long-term variability in the distribution of juvenile Pacific salmon Oncorhynchus spp. and Sablefish Anoplopoma fimbria. The study also evaluated whether Sablefish and Pacific salmon shared food resources and looked to characterize Sablefish during an understudied period of their life cycle. Methods To meet the objectives, the study used data from 26 years of surface trawls conducted in Oregon and Washington coastal waters (1998–2023). Spatial–temporal models were used to measure changes in abundance and distribution of Pacific salmon and Sablefish along with covariates of ocean temperature. The study evaluated trophic characteristics of Pacific salmon and Sablefish from 2020 for differences. The temporal variation in size and diets of Sablefish were also analyzed, along with energy density of fish caught in 2020. Result The spatial–temporal model demonstrated that there has been a nearshore expansion of juvenile Sablefish over the past 26 years that was correlated with increased ocean temperature. The nearshore expansion of Sablefish resulted in increased spatial and trophic overlap with juvenile Pacific salmon. While feeding in nearshore waters, juvenile Sablefish demonstrated competitive feeding advantages over juvenile Pacific salmon during a critical phase of salmonid early marine life history. Juvenile Sablefish exhibited significant ontogenetic diet and energetic shifts, and even the smallest (68–80 mm fork length) were piscivorous. Conclusions If juvenile Sablefish numbers continue to increase relative to Pacific salmon, they could exert more competitive pressure, especially if food resources become limited. Pacific salmon may experience adverse effects from competition, regardless of whether or not juvenile Sablefish, which have recently expanded into nearshore waters, successfully recruit to the adult population.

Daly, Elizabeth A. (ORCID:0000000195334457)↗
DOE OSTI2024

Efficient species identification for Pacific salmon genetic monitoring programs

Abstract Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage‐based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species‐specific Genotyping‐in‐Thousands by sequencing (GT‐seq) panels. For laboratories involved in large‐scale genotyping efforts, diagnosing non‐target species and reassigning them to the appropriate monitoring program can be costly and time‐consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross‐species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species‐specific GT‐seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species‐informative amplicons (16) were newly identified from the four existing GT‐seq panels, thus demonstrating a low‐cost approach to species identification when using targeted sequencing methods. A species‐calling script was developed that is tailored for routine GT‐seq genotyping pipelines and automates the identification of non‐target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low‐frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost‐effective approach to species identification for genetic monitoring programs.

Robinson, Zachary L.↗
DOE OSTI2021

Characterizing juvenile salmon predation risk during early marine residence

Predation mortality can influence the distribution and abundance of fish populations. While predation is often assessed using direct observations of prey consumption, potential predation can be predicted from co-occurring predator and prey densities under varying environmental conditions. Juvenile Pacific salmon Oncorhynchus spp. (i.e., smolts) from the Columbia River Basin experience elevated mortality during the transition from estuarine to ocean habitat, but a thorough understanding of the role of predation remains incomplete. We used a Holling type II functional response to estimate smolt predation risk based on observations of piscivorous seabirds (sooty shearwater [ Ardenna griseus ] and common murre [ Uria aalge ]) and local densities of alternative prey fish including northern anchovy ( Engraulis mordax ) in Oregon and Washington coastal waters during May and June 2010–2012. We evaluated predation risk relative to the availability of alternative prey and physical factors including turbidity and Columbia River plume area, and compared risk to returns of adult salmon. Seabirds and smolts consistently co-occurred at sampling stations throughout most of the study area (mean = 0.79 ± 0.41, SD), indicating that juvenile salmon are regularly exposed to avian predators during early marine residence. Predation risk for juvenile coho ( Oncorhynchus kisutch ), yearling Chinook salmon ( O . tshawytscha ), and subyearling Chinook salmon was on average 70% lower when alternative prey were present. Predation risk was greater in turbid waters, and decreased as water clarity increased. Juvenile coho and yearling Chinook salmon predation risk was lower when river plume surface areas were greater than 15,000 km 2 , while the opposite was estimated for subyearling Chinook salmon. These results suggest that plume area, turbidity, and forage fish abundance near the mouth of the Columbia River, all of which are influenced by river discharge, are useful indicators of potential juvenile salmon mortality that could inform salmonid management.

Phillips, Elizabeth M. (ORCID:0000000327752563)↗
DOE OSTI2023

Export of macroinvertebrate prey from tidal freshwater wetlands provides a significant energy subsidy for outmigrating juvenile salmon

Tidal freshwater wetlands linking terrestrial, riverine, and saline habitats are critical areas for material processing and exchange. Once historically widespread, herbaceous marsh and forested tidal freshwater wetlands especially are now highly degraded worldwide. Additionally, quantitative assessments of hydrology and material exchange from these systems are lacking compared to lotic and estuarine (saltmarsh) habitats. Here we investigate macroinvertebrate and energy export from tidal marsh and forested wetlands and consider potential benefits from this ecological process to endangered Pacific salmon in a large tidal freshwater system, the Columbia River (USA). Macroinvertebrate (salmon prey) concentration, water velocity, and discharge were measured at several wetland habitat types (forested swamp, emergent marsh, and restored marsh). We used these data to compute prey flux and transport metrics. Then, applying literature values to calculate prey energy equivalents and juvenile salmon metabolic requirements, we estimated the potential energy subsidy available to juvenile salmon. Numerically, larval stages of aquatic insects were the predominant type of prey exported from the wetlands, with Diptera chironomid fly abundance exceeding other groups. Energetically, however, non-chironomid dipterans and hemipteran prey comprised most of energy transport due to their higher energetic content (energy density × mean weight). We determined the prey energy transported from the sampled tidal channels was sufficient to meet energetic needs of tens to thousands of juvenile salmon per day, depending on prey production and hydrography. The prey taxonomic composition differed among organisms exiting forested swamp, emergent marsh, and restored marsh habitats with corresponding differences in energy transport, but all habitat types supported similar numbers of juvenile salmon. We conclude that macroinvertebrate prey exported from varied tidal freshwater wetlands likely provide significant benefits to juvenile salmon over a larger ecological footprint than the wetland area would suggest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Population Dynamics and Temporal Trends of Bull Trout in the East Fork Salmon River, Idaho

Abstract Because of their long-term listing under the Endangered Species Act, much interest has been placed on estimating population vital rates for Bull Trout Salvelinus confluentus, but the biotic and abiotic factors that influence the interannual variability in those vital rates have rarely been evaluated. We used mark–recapture data to estimate fish growth, survival, and trends in abundance for fluvial adult Bull Trout in the East Fork Salmon River, Idaho. Over an 8-year period, a total of 1,205 individual Bull Trout were collected at a weir on the East Fork Salmon River (29 km upstream of its confluence with the Salmon River) during June–September, of which 420 were recaptures from prior years. Bull Trout varied in length from 215 to 756 mm and achieved a slightly larger asymptotic length and a slightly lower rate of growth relative to other fluvial and adfluvial Bull Trout populations. Apparent survival averaged 0.42 across all years, which was similar to previous studies estimating apparent survival for Bull Trout. The number of emigrating anadromous salmonid smolts in the upper Salmon River basin positively influenced East Fork Salmon River Bull Trout growth and survival, and survival was higher in years with lower annual discharge. Assessment of population growth via linear regression analysis indicated that the Bull Trout population was increasing during the study period (λ = 1.08; 95% confidence interval = 1.03–1.14). Our findings highlight the ecological link between the abundance of wild and hatchery Chinook Salmon Oncorhynchus tshawytscha, Sockeye Salmon O. nerka, and steelhead O. mykiss smolts and growth and survival of adult Bull Trout in systems where these species occur in sympatry.

Roth, Curtis J.↗
DOE OSTI2023

Expansion of smallmouth bass distribution and habitat overlap with juvenile Chinook salmon in the Willamette River, Oregon

Abstract Smallmouth bass populations have expanded far beyond their native range and these predatory fish present a pervasive threat to native aquatic species throughout North America. In the western United States, smallmouth bass are now present in river and reservoir habitats where Pacific salmon are found and are considered a potential threat to salmon recovery in many locations. We conducted a study to determine if smallmouth bass are expanding their range in the mainstem Willamette River, Oregon, and developed a model to assess habitat overlap between smallmouth bass and juvenile Chinook salmon. Sampling during 2011–2022 revealed that the distribution of smallmouth bass had expanded throughout that timeframe to encompass the entire mainstem Willamette River, including important rearing habitats for juvenile Chinook salmon. The model predicted that smallmouth bass and juvenile Chinook salmon habitat overlap was substantial, highlighting the need for additional research to evaluate for potential negative impacts to salmon recovery in the basin. The model was also used to evaluate the efficacy of using flow management to reduce interactions between these two species, but the scenarios we examined suggested that this was not a viable option. These results highlight the need for continued research to assess interactions between smallmouth bass and juvenile salmon, and other native species of concern, in the Willamette River Basin. The development of the model is useful for resource managers to understand interactions between these species to prioritize locations for sampling in the future.

White, James S.↗
DOE OSTI2023

Spatial and temporal overlap between hatchery- and natural-origin steelhead and Chinook Salmon during spawning in the Klickitat River, Washington, USA

Abstract Objective A goal of many segregated salmonid hatchery programs is to minimize potential interbreeding between hatchery- and natural-origin fish. Our objective was to assess this on the Klickitat River, Washington, USA. Methods We used radiotelemetry to evaluate spatiotemporal spawning overlap between hatchery- and natural-origin steelhead Oncorhynchus mykiss and spring Chinook Salmon O. tshawytscha. We estimated percentages of tagged fish that spawned naturally in the Klickitat River subbasin, emigrated from the Klickitat River, or died before spawning. A kernel density analysis was used to estimate probability of spatiotemporal overlap between hatchery- and natural-origin spawners. Result For steelhead, 12% of hatchery-origin and 50% of natural-origin fish spawned naturally. For spring Chinook Salmon, 18% of hatchery-origin and 44% of natural-origin fish spawned naturally. Tag loss may result in underestimates in these percentages. Most hatchery-origin steelhead (90%) spawned downstream of river kilometer (rkm) 32, and 75% spawned from November to mid-March. The majority of natural-origin steelhead (64%) spawned upstream of rkm 32, and 75% spawned from mid-March to late May. Spawn timing of hatchery-origin Chinook Salmon (early August to mid-September) overlapped with that of natural-origin Chinook Salmon (late July to late September), and fish of both origins spawned in the same 30-km reach of the river. We estimated the percentage of hatchery-origin spawners (pHOS) on the natural spawning grounds to be 12% for steelhead and 40% for spring Chinook Salmon across all study years. For steelhead, we estimated the overlap probability to be 25% (95% CI = 22.5–28%). For spring Chinook Salmon, tight spatial clustering of hatchery-origin fish resulted in a lower overlap estimate of 21% (13–31%). Conclusion We suggest adjusting pHOS estimates using these overlap estimates or similar spatiotemporal data on actual spawner proximity and possible interactions, and that these types of analyses be used in conjunction with gene flow analysis to accurately evaluate effects of individual hatchery programs.

Zendt, Joseph S.↗
DOE OSTI2025

Genomic insights into local adaptation and migration success in reintroduced Coho Salmon of the Wenatchee River basin

ABSTRACT Objective Reintroduction of salmonids into regions where they have been extirpated is a common conservation strategy that is often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focused on the mid-Columbia River Coho Salmon reintroduction program managed by Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon into the Wenatchee and Methow River basins, Washington. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15-km, high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Methods Low-coverage whole-genome resequencing data were used to screen for genomic regions associated with the phenotypes of interest. Results A weak polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions occurring across eight chromosomes. Conclusions These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.

Horn, Rebekah L.↗
DOE OSTI2024

Restoring freshwater habitat mosaics to promote resilience of vulnerable salmon populations

Phenotypic diversity and abundance drive salmon resilience in the face of increasing environmental variability. But what happens when human activities fundamentally alter the habitat complexity that drives this diversity? And how can we restore habitats to recover both diversity and abundance to support salmon persistence in a warming climate? Here, we looked at the impact of a large watershed restoration effort on the abundance and climate resilience of the three remaining core natural spring-run Chinook Salmon populations in the California Central Valley (Butte, Mill, and Deer Creek). Butte Creek fish, which have floodplain access, had higher overall productivity and faster juvenile growth compared with Mill and Deer Creek populations, and the proportion of floodplain inundation was positively correlated with Butte Creek adult abundance two years later. While Butte Creek exhibited significant increases in abundance post-restoration (~2000%), it generally exhibited lower phenotypic diversity and only a marginal increase in population stability after restoration based on the coefficient of variation (CV). In particular, Butte Creek salmon tended to exhibit larger drops in escapement following dry years (e.g., return years 2010, 2017) compared with Mill and Deer Creek populations, presumably due to limited inundation of its downstream floodplain. The late-migrating juvenile strategy (i.e., yearling), which disproportionately supported Mill and Deer Creek populations during droughts, was uncommon among Butte Creek adults (averaging 60% of returns for Mill and Deer Creek vs. 0.3% for Butte Creek). Increased spring-run stock complex stability was found, post-restoration, when combining the three spring-run populations (i.e., lower aggregate CV). However, among-river pairwise correlations also suggested increased synchronization in population abundances post-restoration, potentially due to increasing frequency and severity of extreme climatic events (e.g., droughts and ocean warming). This study underscores the importance of restoring a connected mosaic of aquatic habitats across modified landscapes, such as cold water refugia and floodplains, to preserve multiple (across-population) life history pathways for increasing salmon stock complex stability and abundance. These landscape-scale process-based habitat restoration efforts are likely to be crucial for the successful long-term recovery of vulnerable species in a rapidly changing climate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Juvenile Salmon and Their Habitats in the Columbia River Estuary: A Review and Synthesis of Knowledge Development 2000–2025

[This is a 90% discussion draft.] This is the third Synthesis Memorandum funded by the U.S. Army Corps of Engineers and developed for the Columbia Estuary Ecosystem Restoration Program (CEERP) on the topic of habitat restoration in the Columbia River Estuary (CRE) from Bonneville Dam to the river mouth. While the first two were developed by PNNL and NOAA without the benefit of stakeholder participation, for the current memo, two key activities were initiated: (1) review, by the Expert Regional Technical Group (ERTG), of status and trends monitoring and action effectiveness monitoring funded by CEERP, and (2) a workshop including representatives of the Bonneville Power Administration and the U.S. Army Corps of Engineers (the action agencies [AAs]), the National Oceanic and Atmospheric Administration (NOAA), major research agencies contributing to CEERP, and sponsors who implement CEERP restoration actions. A systematic literature review was conducted using ClarivateTM Web of ScienceTM database. The topics of interest for CRE relevant research included salmon ecology, physical processes, and wetland habitats, and therefore required the use of broad search terms. Our final search criteria included a combination of Boolean operators and an approach to combine different sets of search terms. The final search result yielded 669 records. The records were classified by groups and assigned to the relevant disciplinary expert for review. The review identified substantive advances in understanding the provision of salmon habitat functions through spatiotemporally dynamic physical and ecological processes, and the use of CRE habitats by numerous stocks of juvenile salmon. It also uncovered heretofore unincorporated historical documentation of riparian habitats across the CRE. The characterization of the structural components of floodplain habitat including plant associations and channel networks has advanced considerably, together with the understanding of seasonal changes and long-term trends. The relative influence of salmon-habitat location in the CRE as compared with temporal factors, mainly season, has been well described, which affects the prioritization of restoration. Stressors on the ecosystem and fish, and the drivers of these stressors, have been more carefully elucidated and predictive models are in various stages of development. The vision, aims, and design of restoration projects have advanced together with methods of data collection, analysis, and modeling that have seen substantial improvements. Experiments intended to inform the design of restoration projects are underway or have been completed. An important outstanding area of research that has lagged behind the advances in fundamental understanding of the ecosystem and salmon habitat functions remains the peer-reviewed documentation of the outcomes of restoration for both habitats and fish functions.

estuary↗
DOE OSTI2022

Riverscape heterogeneity in estimated Chinook Salmon emergence phenology and implications for size and growth

Abstract Many salmonid‐bearing rivers exhibit thermal and hydrologic heterogeneity at multiple spatial and temporal scales, but how this translates into spatiotemporal patterns of fry emergence is poorly understood. Understanding this variability is important because emergence timing determines the biophysical conditions fish first experience (e.g., temperature, flow, and food supply), thereby influencing growth opportunities and survival during this critical life stage. We predicted spring Chinook Salmon ( Oncorhynchus tshawytscha ) emergence phenology across four northeastern Oregon subbasins over 5–9 years using empirical spawning and temperature data. We then related interannual emergence timing estimates to juvenile salmon size and growth rates at consistent sampling locations. There were clear longitudinal patterns of predicted emergence timing in each subbasin: The shape of these patterns was consistent among years, but not among subbasins. In two subbasins, emergence occurred progressively later with distance upstream, whereas in the other two subbasins emergence was earliest at upstream sites. Within each year, median emergence dates among sites within each subbasin ranged between 44 and 58 days. This spatial variation was comparable to interannual variation, with median emergence dates for a given location in each subbasin ranging between 47 and 74 days among years. Contrary to our expectations, juvenile salmon were not larger in years with earlier emergence, owing to slower estimated spring and summer growth rates compared to years with later emergence. Despite large interannual variation in estimated emergence dates, these results suggest that other factors (e.g., stream flow, temperature, and density‐dependence) were more important than growth duration in determining juvenile salmon growth rates and size among years. We demonstrated considerable spatial and interannual variation in emergence phenology within these subbasins. Understanding how this variation translates to spatiotemporal patterns of juvenile salmon habitat use, growth, and survival has important implications for guiding restoration efforts and understanding how climate change may impact these populations.

Kaylor, Matthew J.↗
DOE OSTI2022

Density Dependence in Three Snake River Sockeye Salmon Nursery Lakes in Central Idaho

Abstract Snake River Sockeye Salmon Oncorhynchus nerka, listed as an endangered species in 1991, currently inhabit three nursery lakes (Redfish, Pettit, and Alturas lakes) in the Sawtooth Valley, Idaho. Conspecific kokanee (lacustrine Sockeye Salmon) are also present in the lakes. Snake River Sockeye Salmon recovery efforts, initially focused on genetic conservation, are now attempting to rebuild naturally spawning populations using hatchery supplementation. However, in Sockeye Salmon nursery lakes, density dependence is frequently observed when elevated O. nerka abundance leads to declines in zooplankton biomass, body size, and shifts in community composition. In turn, these changes lead to reductions in juvenile O. nerka growth rates, survival, and adult returns. We examined a long-term data set of O. nerka population metrics and associated zooplankton community metrics. We found evidence of density dependence within and among nursery lakes. We detected differences in zooplankton biomass, lengths of preferred zooplankton prey (Daphnia spp. and cyclopoid copepods), parr growth rates, and age-1 smolt size among the three lakes. We found negative relationships between O. nerka density and zooplankton biomass and size. We identified positive relationships between zooplankton biomass and two response variables: smolt size at migration and growth rates of hatchery parr. The relationships were generally similar among lakes. Variable outcomes were a result of differences in O. nerka density (or zooplankton biomass), controlled primarily by the relative proportion of spawning and rearing habitat in each lake. Understanding unique lake habitats, ecological interactions, and the role of density dependence is germane to management of Snake River Sockeye Salmon populations.

Griswold, Robert G.↗
DOE OSTI2021

Genomic region associated with run timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Abstract Conserving life‐history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early‐ and late‐migrating forms of Chinook salmon ( Oncorhynchus tshawytscha ) face unequal pressure from natural and anthropogenic forces that may alter the impacts of genetic variation underlying heritable migration timing. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among diverse lineages and populations in large basins such as the Columbia River. With high‐throughput genotyping (GT‐seq) and phenotyping methods, we examined the association of genetic variation in 28 markers (spanning GREB1L to ROCK1 of chromosome 28) with individual adult migration timing characteristics gleaned from passive integrated transponder recordings of over 5000 Chinook salmon from the three major phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them in putatively neutral genomic regions, each of the three lineages exhibited very similar genetic variants in the chromosome 28 region that were significantly associated with adult migration timing phenotypes. This is particularly notable for the interior stream‐type lineage, which exhibits an earlier and more constrained freshwater entry than the other lineages. In both interior stream‐type and interior ocean‐type lineages of Chinook salmon, heterozygotes of the most strongly associated linkage groups had largely intermediate migration timing relative to homozygotes, and results indicate codominance or possibly marginal partial dominance of the allele associated with early migration. Our results lend support to utilization of chromosome 28 variation in tracking and predicting run timing in these lineages of Chinook salmon in the Columbia River.

Willis, Stuart C.↗
DOE OSTI2023

Utility of parentage‐based tagging for monitoring Coho salmon ( Oncorhynchus kisutch ) in the interior Columbia River basin

Abstract By the 1980s, after decades of declining numbers in the mid‐1900s, Coho salmon ( Oncorhynchus kisutch ) were considered extirpated from the interior Columbia River. In the mid‐1990s, the Confederated Tribes of the Umatilla Indian Reservation, the Confederated Tribes and Bands of the Yakama Nation, and the Nez Perce Tribe began successful reintroduction programs of Coho salmon upstream of Bonneville Dam, but which were initially sourced from lower Columbia River hatcheries. Here we present the first Coho salmon parentage‐based tagging (PBT) baseline from seven hatchery programs located in the interior Columbia River basin, and two sites at or downstream of Bonneville Dam, composed of over 32,000 broodstock samples. Analyses of baseline collections revealed that genetic structure followed a temporal pattern based on 3‐year broodlines rather than geographic location or stocking history. Across hatchery programs, similar levels of genetic diversity was present. The PBT baseline provided multiple direct applications such as identification of origin for Coho salmon collected in a mixed stock at Priest Rapids Dam and the detection of the proportion and distribution of hatchery‐origin fish on the spawning grounds in the Methow River basin. The PBT baseline for Coho salmon is freely available for use and can be downloaded from FishGen.net .

Horn, Rebekah L.↗