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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Performance of Subyearling Fall Chinook Salmon Tagged with 8-, 9-, and 12-mm Passive Integrated Transponder Tags in the Snake River

Abstract Inferences based on tagged individuals from a population are limited in part by the minimum size of fish that can be tagged. Smaller tags allow a greater proportion of a population to be represented by tagging and should reduce potential tag effects on fish performance. We evaluated different performance metrics of juvenile fall Chinook Salmon Oncorhynchus tshawytscha tagged with 8-, 9-, and 12-mm PIT tags in the Snake River. We did not find evidence that posttagging mortality of 45–49-mm-FL fish tagged with 8-mm tags was higher than the posttagging mortality of larger fish tagged with 9- and 12-mm tags. The incisions of fish tagged with 8-mm tags using 14-guage needles healed faster than those of fish tagged with larger tags using 12-guage needles. For individuals that received 8-mm tags, growth in length and mass was higher for 45–49-mm fish than for 50–59-mm fish and 60-mm and larger fish. Growth of the larger size-classes (50–59 and ≥60 mm) was also generally higher for those tagged with 8-mm tags compared to those tagged with 9- and 12-mm tags, respectively. There were no strong relationships between tag burden (i.e., tag weight expressed as a percentage of fish weight) at the time of tagging and growth metrics for any tag size or fish size-class. Releases made to compare the detection efficiency of the three tag types in the juvenile fish bypass at Lower Granite Dam, Washington, showed that 99–100% of all fish were detected. Survival of fish from rearing areas to Lower Granite Dam generally increased with fish size and varied by year, but there was no strong evidence of a tag size effect. The 8-mm PIT tag allowed us to represent a larger portion (i.e., 6.2–24.1%) of the subyearling fall Chinook Salmon population in the Snake River without compromising fish performance or detectability at the dam.

Tiffan, Kenneth F.↗
DOE OSTI2022

Improving Abundance Estimates of Spring–Summer Snake River Chinook Salmon for Fisheries Management

Abstract The Columbia River basin is home to a run of spring–summer Chinook Salmon Oncorhynchus tshawytscha that returns to the Snake River drainage of Idaho, Oregon, and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River basin. However, Snake River spring–summer Chinook Salmon have experienced declines in abundance due to overfishing, habitat degradation, and dams. Several stocks are listed as threatened under the U.S. Endangered Species Act and are supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan, and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, PIT-tagged as juveniles and detected at Lower Granite Dam, to generate adult abundance estimates. In season, these estimates inform state and tribal harvest shares and ensure that broodstock needs are met. Postseason, they provide smolt-to-adult survival and return rates. Since 2012, parentage-based tagging (PBT) has provided an alternative method to estimate stock- and age-specific returns at Lower Granite Dam, since returning hatchery adults sampled at Lower Granite Dam can be assigned to their parents. We compared stock-specific abundance estimates between PIT- and PBT-derived methodologies for return years 2016–2019. Across all years, PIT tag estimates accounted for 65% of the PBT-based estimates at Lower Granite Dam across all age-groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT-based estimates should aide in-season harvest management and postseason run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.

Coykendall, D. Katharine (ORCID:0000000211482397)↗
DOE OSTI2025

Emigration and Survival of Hatchery‐Reared Coho Salmon Released as Parr and Smolts in a Reintroduction Program

ABSTRACT Releasing fish at varied life stages is an underutilized hatchery‐rearing practice. Columbia River Treaty tribes have been working to reintroduce extirpated Coho Salmon to historical habitats in upper watersheds. This effort has included the release of hatchery‐origin fish at both the parr and smolt life stages in the Yakima River Basin (Washington State USA), a tributary to the Columbia River. We evaluated releases of parr and smolts tagged with passive integrated transponders over 11 brood years. We assessed emigration timing, fish survival, and age‐at‐return for the two release groups. Emigrating juveniles released as smolts had higher survival and arrived downstream earlier than fish released as parr. Survival from release locations to adult return did not significantly differ for the two release groups. However, we observed a difference in apparent marine survival as fish released as parr had mean juvenile‐to‐adult return rates greater than fish released as smolts. Parr releases also tended to return at older age than smolt releases. Our results indicate that implementing practices to reduce homogenization of hatchery releases may produce survival and diversity benefits as fish mature to later life stages. Given the rapid ecosystem changes Pacific Salmon are experiencing throughout their life cycles, practices such as this may have increasing utility and import.

Bosch, William J. [Yakama Nation Fisheries Toppeni↗
DOE OSTI2023

Effects of volitional emigration timing and smolt size on survival and age-at-return in a Pacific salmon hatchery population

Abstract Many Pacific salmon populations are returning from sea at younger ages and smaller sizes. Hatchery culture, management practices, and environmental factors influence juvenile release size and emigration timing, which in turn affect important demographic characteristics in returning adults. We analyzed data from approximately 345,000 tagged spring Chinook Salmon juveniles exiting Cle Elum Supplementation and Research Facility (Yakima River, Washington, USA) acclimation sites over thirteen brood years (2002–2014), evaluating smolt size, emigration timing, river flow, juvenile survival, and age-at-return. We observed a relationship between size and volitional exit timing of smolts from acclimation sites, with larger fish tending to emigrate earlier than smaller fish. Early emigration was also coincident with lower river flows near acclimation sites. Later emigration timing was correlated with an increase in apparent survival of juveniles to Bonneville Dam (500–530 km downstream of acclimation sites), but also with a lower rate of survival to return from sea. In general, for juveniles successfully emigrating downstream of Bonneville Dam, age-at-return increased with decreasing juvenile fish size and later emigration timing. Our results support a growing body of evidence that hatchery practices may result in larger smolts that tend to return at younger ages. Given the biological and economic consequences of younger age-at-maturation, methods to reverse this trend should be further explored and implemented.

Bosch, William J. (ORCID:0000000300447390)↗
DOE OSTI2021

Evaluation of Juvenile Salmon Passage and Survival Through a Fish Weir and Other Routes at Foster Dam, Oregon, USA

Downstream passage for juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) through the fish weir at Foster Dam, Oregon, was evaluated to assess the weir’s efficacy as a long-term passage solution. Radio telemetry was used to estimate survival, passage, and effectiveness for the fish weir, spillway, and turbines. Survival of Chinook salmon through the fish weir varied by season and reservoir elevation (66–87%), passage proportions were low (8–20%), and fish weir effectiveness was low to moderate (0.5–2.0). Steelhead survival was lower (57–77%) but passed the fish weir in higher proportions (77%) and weir effectiveness was consistently high (3.0–5.5). Our results indicate the existing fish weir will not be a suitable long-term passage solution for all species. However, because of the high passage proportions and effectiveness observed for steelhead, further development of the surface flow concept appears to be promising for safely passing downstream-migrating fishes.

Hughes, James S.↗
DOE OSTI2023

Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Abstract The distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle. This study provides a high‐resolution portrait of genomic variation in Chinook salmon ( Oncorhynchus tshawytscha ) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered data set of ~13 million single nucleotide polymorphisms (SNPs) from low‐coverage whole genome resequencing of 53 populations (3566 barcoded individuals), we contrasted patterns of genomic structure within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Neutral variation provided support for fine‐scale structure of populations, while allele frequency variation in GREB1L/ROCK1 was highly correlated with mean return timing for early and late migrating populations within each of the lineages ( r 2 = .58–.95; p < .001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream‐type) compared to the other two major lineages, which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

Horn, Rebekah L.↗
DOE OSTI2021

Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon ( Oncorhynchus tshawytscha ) production in the Sacramento Valley

Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem health and valuation methods to predict ecosystem response to restoration actions. This process is particularly challenging for anadromous fish species such as California's Sacramento River winter-run Chinook salmon, due to their limited geographic range and diverse life history habitat requirements. Tools, such as life-cycle models, are needed to manage population dynamics and quantify the composite effects of processes across space and time. Nevertheless, complex institutions can hinder result interpretation and communication, and limit model use in decision-making. This paper focuses on the federally endangered and endemic Sacramento River winter-run Chinook (Oncorhynchus tshawytscha) by developing a Winter-Run Habitat-based Population Model (WRHAP). Additionally, WRHAP is a conceptual, freshwater rearing stage model that includes alternative rearing habitats reported in the literature (e.g., floodplains, off-channel and tributaries), defines rules of habitat use based on instream conditions, and incorporates a juvenile growth module that combines bioenergetics modeling with empirical growth rates. Model outputs reasonably follow observed out-migration patterns and provide a realistic smolt size distribution arriving at the San Francisco Bay. This effort demonstrates the importance of currently “non-critical” habitats (as defined by the Endangered Species Act) for juvenile development, with floodplain habitat contributing to a quarter of out-migrating biomass (despite < 18% availability and <10% of total rearing days), and off-channel growth being one of the most sensitive parameters (explaining ~13% of average juvenile weight variance). The model shows the utility of a simple population model to explore relationships between habitat quality/quantity and juvenile development, and to assist water/environmental management and decision-making processes focused on species recovery.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

How do Management Goals for Wild Chinook Salmon Align with Feasibility?

Evaluation of goals is crucial for effective management to conserve viable and diverse fish populations and to support harvest. Management of wild Chinook Salmon Oncorhynchus tshawytscha in the Snake River basin exemplifies the struggle to meet fisheries goals. Considering contemporary production of juvenile emigrants, it is imperative to determine the survival from emigration to adult ( S e‐a ) required to meet abundance goals. Increased anthropogenic impact on spawning and rearing habitats leads to higher S e‐a required to attain goals. Wilderness populations exhibit viability and could sustain fisheries with S e‐a lower than required elsewhere. Conversely, populations targeted for habitat restoration demand higher S e‐a to fulfill goals, indicating a need to enhance egg‐to‐smolt survival. However, S e‐a has fallen below the threshold needed for replacement in all populations, even at current low abundances. Despite these challenges, most populations still possess the potential to achieve abundance goals, emphasizing the importance of strategic interventions to bolster their resilience.

Copeland, Timothy↗
DOE OSTI2022

Efficacy of a Short-Term Captive Broodstock Program Compared with Hatchery-Origin Spring Chinook Salmon Derived from the Same Population

Abstract We examined the efficacy of a one-generation (five brood years: 1997–2001) captive broodstock program for spring Chinook Salmon Oncorhynchus tshawytscha by comparing survival rates of captive broodstock progeny (CBP; F2) with that of hatchery-origin fish (HOR) from a conservation hatchery supplementation program in which both groups were derived from the Tucannon River (Washington State) population for the 2000–2006 brood years. Survival rates compared were egg to fry, fry to smolt, egg to smolt, total (ages 3–5) and adult (ages 4+) smolt-to-adult-return (SAR) survival, and total (ages 3–5) and adult (ages 4+) progeny-to-parent (P:P) ratio. Total escapement and adult P:P ratios were also examined to determine if observed demographic benefits to the population continued after the captive broodstock program ended. The CBP group had lower within-hatchery survival than the HOR group, with significant differences in survival at the egg-to-fry and egg-to-smolt stages due to poor egg viability. Mean untransformed total and adult SARs for the CBP were half those of the HOR group; however, SARs did not differ significantly. The CBP also had significantly lower total and adult P:P ratios than the HOR group and were below replacement for six of the seven brood years. While the captive broodstock provided additional fish for release that would not have been available otherwise, overall the CBP performed poorly and below expectations compared with the HOR group, both within the hatchery and after release. The captive broodstock program provided a short-term demographic boost, most notable in the 2008–2010 return years, but the benefit did not carry over after the program ended.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

State-Space Model to Estimate Salmon Escapement Using Multiple Data Sources

Abstract Accurate estimates of salmonids passing Lower Granite Dam on the Snake River, by species and origin, are a critical input to assessing the status and trends of various populations as well as successful management of fisheries in the Snake River basin. Here, we describe a state-space model that estimates such escapement past a dam by using window counts, PIT tag observations, and data from an adult fish trap, accounting for issues such as nighttime passage, fallback and reascension, potential observation error at the window, and uncertainty in the adult trap rate. We tested the approach using a simulation framework that mimicked several levels of observation error, differences between nighttime passage and reascension rates, and the possibility of the adult trap being closed for some period of time. Our results demonstrate that the model produced unbiased estimates across all tested scenarios. We also applied this model to empirical data from Lower Granite Dam to produce estimates of wild, clipped hatchery, and unclipped hatchery spring/summer-run Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss from spawn years 2010–2019.

See, Kevin E. (ORCID:0000000297626442)↗
DOE OSTI2022

Effects of Supplementation in Upper Yakima River Chinook Salmon

Abstract To promote recovery of natural salmonid populations, managers are utilizing hatchery supplementation programs to increase abundance of spawners on the spawning grounds. However, studies have provided evidence that captive breeding can result in domestication, demonstrated by lower fitness of hatchery‐origin compared with natural‐origin fish. Supplementation programs, therefore, typically use natural‐origin broodstock in an effort to minimize long‐term negative fitness impacts. Here we evaluated the upper Yakima River spring supplementation program for Chinook Salmon Oncorhynchus tshawytscha , which has broodstock comprised exclusively of unmarked fish presumed to be of natural‐origin. Using 5 years of spawner data, we tested for effects of hatchery breeding and rearing on total adult returns and their individual reproductive success when spawning naturally. Our study revealed that supplementation increased overall abundance of fish spawning naturally on the spawning grounds. However, on average, compared with natural‐origin spawners, hatchery‐origin fish had reduced reproductive success, which also translated to reduced reproductive success in three out of five return years for natural‐origin fish that spawned with hatchery‐origin fish. As expected, body length and return timing were also significant predictors of reproductive success. However, more generations of data are needed to establish the extent to which reduced reproductive success is passed on to naturally produced progeny.

Koch, Ilana J.↗
DOE OSTI2024

Inferring precocial Chinook Salmon production through single‐parentage assignments

Abstract Objective Parentage analysis is a routine methodology in fisheries research, but study systems exist where it is impractical to sample both parents. The ability to reliably assign offspring to a single parent is beneficial in these situations. We applied single‐parentage assignments to a naturally spawning population of Chinook Salmon Oncorhynchus tshawytscha to quantify production of anadromous returns by unsampled precocial males. Methods We used an approach that focused on two important aspects of parentage analyses: (1) addressing the presence of family structure within the set of sampled parents and (2) controlling for false‐positive and false‐negative assignments. Result Results indicated that 30% of reproductively successful males were precocial males, which produced 20% of the returning anadromous offspring. Conclusion This study provides a framework for applying single‐parent assignments in a salmonid study system while explicitly addressing sources of assignment errors.

Steele, Craig A.↗
DOE OSTI2023

The Contribution of Subtropical Moisture Within an Atmospheric River on Moisture Flux, Cloud Structure, and Precipitation Over the Salmon River Mountains of Idaho Using Moisture Tracers

The impact of an atmospheric river (AR) on the flux of subtropical moisture across Idaho's Salmon River Mountains and precipitation over the mountains is evaluated using the Weather, Research, and Forecasting model with water vapor tracers (WRF-WVT). The AR impacted Idaho between 17 and 19 January 2017 during the Seeded and Natural Orographic Wintertime Clouds: The Idaho Experiment (SNOWIE) campaign. WRF-WVT is configured to isolate the subtropical moisture contribution to the AR, the moisture flux, and precipitation. Subtropical water vapor advected by the AR into Idaho is tagged and tracked in three-dimensional space throughout the run. This allows the contribution of the subtropical moisture to the vertical distribution of water vapor and the precipitation to be directly calculated. The simulated cloud structure is compared with airborne radar data collected during two SNOWIE intensive operation periods. This study found that more than 70% of the moisture flux and more than 80% of the precipitation across the Idaho Mountains during SNOWIE IOP 4 could be attributed to subtropical moisture within the AR. Nearly all of the moisture flux in the upper cloud and 50% of the moisture in the lower cloud was attributable to the subtropical moisture. The subtropical moisture contribution within the AR to precipitation ranged from 35% in northern Idaho to more than 90% in southern Idaho. Across the entire period of impact of the AR, more than 60% of precipitation in Idaho was attributable to the subtropical moisture within the AR, with this percentage increasing toward the south across the state.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Threatened salmon rely on a rare life history strategy in a warming landscape

We report that rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams. Despite the dominance of late migrants, other strategies played an important role in many years. Our results suggest that further loss of phenotypic diversity will have critical impacts on population persistence in a warming climate. Predicted thermally suitable river conditions for late migrants will shrink rapidly in the future and will be largely relegated above impassable dams. Reconnecting diverse habitat mosaics to support phenotypic diversity will be integral to the long-term persistence of this species.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A large dataset of detection and submeter-accurate 3-D trajectories of juvenile Chinook salmon

Abstract Acoustic telemetry has been used extensively to study the behavior of aquatic animals. The Juvenile Salmon Acoustic Telemetry System (JSATS) is one such system; it was developed for studying juvenile salmonids but has been used to study numerous species. A recent innovation of the JSATS system is an acoustic transmitter that is small enough to be implanted through injection or small incision that doesn’t require sutures. Use of the JSATS system involves deploying cabled acoustic receivers at hydroelectric dams, or other structures, and autonomous acoustic receivers in free-flowing sections of a river. The raw detections from acoustic-tagged fish are processed to remove potential false positives. The clean detections (5,147,996 total) are used to generate detection events and to compute 3-D trajectories (403,900 total), which are used to assign fish to a passage route through a dam. Controlled field testing involving a high-accuracy Global Positioning System receiver is done to validate the submeter accuracy of the trajectories. The JSATS dataset could be reused for expanding the understanding of near-dam fish behavior.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The incorporation of environmentally derived 87 Sr / 86 Sr and Sr/Ca in early otolith formation of Chinook salmon

Abstract Effective species management often requires understanding patterns of movement and habitat use. A common approach in identifying where individuals reside relies upon chemical tracers from the environment that are incorporated into an individual's tissues. For fish, isotopes in their otoliths, specifically the portion of their otolith formed during their larval stage, have been used to identify the natal origin. Complicating this work, however, is the fact that during this life stage, there is a shift in the source of isotopes deposited onto the growing otolith from maternally to environmentally derived. The objective of this study was to identify the portion of the otolith representing this transition to environmentally derived isotopes so as to accurately investigate questions of natal origin for a threatened population of fall Chinook salmon ( Oncorhynchus tshawytscha ). We exposed developing larvae to four treatments that differed in terms of their water strontium isotope ratio ( 87 Sr/ 86 Sr) and used change‐point analysis of otolith 87 Sr/ 86 Sr and strontium to calcium ratio (Sr/Ca) to identify the otolith radius corresponding to the transition to environmentally derived isotopes. Our results indicated this transition occurred, on average, at 132 μm ( 87 Sr/ 86 Sr; ±50 μm standard deviation) and 127 μm (Sr/Ca; ±29 μm) from the otolith core, which corresponded to the developmental time between hatching and exogenous feeding. A substantial proportion of our otoliths (i.e., 61%) did not show convergence between otolith and water 87 Sr/ 86 Sr by the end of the 113‐day experiment, which was likely due to the dietary contribution of marine‐based feed. Therefore, we were unable to recommend an otolith radius to target for the purposes of reconstructing natal origin apart from being beyond approximately 130 μm.

Chittaro, Paul↗
DOE OSTI2023

A correlation between seasonally changing photoperiod, whole body lipid, and condition factor in juvenile spring Chinook salmon (Oncorhynchus tshawytscha)

The regulation of lipid stores is a central process for the physiology and ecology of fishes. Seasonal variation in lipid stores has been directly linked to survival of fishes across periods of food deprivation. We assessed whether a seasonally changing photoperiod was correlated to seasonal changes in energetic status to help better understand these important processes. Groups of first feeding Chinook salmon fry were introduced to a seasonal photoperiod cycle, but the point of entrance into the seasonal cycle varied from near the winter solstice (December), to either side of the spring equinox (February & May). Temperature and feeding rate were similar for all treatments. Subsequently, condition factor and whole body lipid content were assessed through a seasonal progression. Throughout most of the experiment, length and weight did not differ between the different photoperiod treatments, however whole body lipid and Fulton’s condition factor did. Furthermore, changes in both whole body lipid and Fulton’s condition factor in all treatment groups followed a similar seasonal pattern that was inversely related to day length (highest K and lipid levels found during days with the least light). These results suggest that regardless of age or size, there is a correlation between seasonal changes in photoperiod and changes in body composition in juvenile Chinook salmonids.

Spangenberg, Dina K. (ORCID:000000018861395X)↗
DOE OSTI2022

Hanford Reach Fall Chinook Salmon Productivity Analysis, Brood Years 1975–2016

Updating the Hanford Reach fall Chinook salmon productivity analysis to include seven additional years of data (BY 2010–2016), including three years of record escapements (>150,000 adults), reaffirmed the highly productive nature of this population and the positive effect of flow fluctuation constraints as implemented at Priest Rapids Dam by the VBSA and HRFCPP. The addition of several years of high escapements also revealed that competition among juveniles (and not spawning habitat limitations) is likely the mechanism driving density dependence in the Hanford Reach. The addition of the high escapement brood years also provided evidence for the high recruitment capacity of the population. As such, the WDFW may consider increasing the maximum escapement goal from 42,000 adults to 49,000 adults, which would be more in-line with SMSY as estimated from this update. Given the in-river protections that are in place as part of the HRFCPP, ocean conditions appear to be the primary factor controlling adult production. Therefore, the success of any additional management actions taken in freshwater are likely to be dependent on survival in the ocean. As such, the most effective management actions may be those that limit juvenile competition and density dependent growth effects in the Hanford Reach. Limiting competition would be expected to increase growth, resulting in larger smolts that would be less likely to suffer size-dependent mortality in the marine environment, even during years of poor ocean conditions. Increasing terminal harvest rates when high escapements are anticipated (from downstream dam counts) is one management option that could help to curtail juvenile competition.

Harnish, Ryan A.↗