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Results for “Annual Review of Earth and Planetary Sciences”

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1,694 records · Page 84Linked to original sources
USGS2025

Towards mobile wind measurements using joust configured ultrasonic anemometer for applications in gas flux quantification

Small uncrewed aerial systems (sUASs) can be used to quantify emissions of greenhouse and other gases, providing flexibility in quantifying these emissions from a multitude of sources, including oil and gas infrastructure, volcano plumes, wildfire emissions, and natural sources. However, sUAS-based emission estimates are sensitive to the accuracy of wind speed and direction measurements. In this study, we examined how filtering and correcting sUAS-based wind measurements affects data accuracy by comparing data from a miniature ultrasonic anemometer mounted on a sUAS in a joust configuration to highly accurate wind data taken from a nearby eddy covariance flux tower (aka the Tower). These corrections had a small effect on wind speed error, but reduced wind direction errors from 50° to >120° to 20–30°. A concurrent experiment examining the amount of error due to the sUAS and the Tower not being co-located showed that the impact of this separation was 0.16–0.21 ms − 1 "> ms − 1 , a small influence on wind speed errors. Lower wind speed errors were correlated with lower turbulence intensity and higher relative wind speeds. There were also some loose trends in diminished wind direction errors at higher relative wind speeds. Therefore, to improve the quality of sUAS-based wind measurements, our study suggested that flight planning consider optimizing conditions that can lower turbulence intensity and maximize relative wind speeds as well as include post-flight corrections.

Alaska↗
USGS2024

Imaging of seismic discontinuities using an adjoint method

For imaging of seismic discontinuities at depth, reverse time migration (RTM) is a powerful method to apply to recordings of seismic events. It is especially powerful when an extensive receiver array, numerous seismic sources, or both, permit adequate reconstruction of incident and scattered wavefields at depth. Reconstructing either the incident or scattered wavefield at depth becomes less accurate when relatively few recordings of seismic events are available. Here we explore an inverse scattering approach to imaging discontinuities based on an adjoint method, employing sensitivity kernels (Frechet derivatives) that represent jumps in material properties across seismic-discontinuity surfaces. When combined with ray-based requirements on scattering geometry, it constitutes a powerful approach to determining the locations and amplitudes of the discontinuities, recovering only those properties that can be resolved by a spatially limited source and/or receiver distribution. This is illustrated by synthetic examples with local sources followed by a field example in a subduction zone setting

Washington↗
USGS2026

Re-examining the growing degree day minimum for grass carp spawning initiation in Lake Erie: Have we missed the mark?

Understanding the timing of life history processes of invasive fish species, such as adult aggregations during spawning, allows natural resource managers to optimize targeted population control efforts. Temperature-based estimates of the timing of spawning initiation for grass carp ( Ctenopharyngodon idella ) exist from its native range, but have not previously been developed for grass carp reproduction in its invaded range in the Laurentian Great Lakes of North America. We accounted for differences among methods across studies and calculated cumulative growing degree days (GDD) for the dates of grass carp egg capture in Lake Erie tributaries (Sandusky, Maumee, and Huron rivers) during 2015–2024 and compared these values to the existing GDD base 15°C requirement estimate from the native range (633 GDD–15°C). The earliest egg detection in Lake Erie (Sandusky River) was 19 GDD–15°C or 361 GDD–5°C (latest egg detection was 2285 GDD–5°C from the Sandusky River), indicating that spawning was initiated up to 25 days earlier than would be predicted by the native range GDD. Moreover, spawning in Lake Erie tributaries occurred earlier than predicted for 58% of spawning events examined based on the native range GDD. The GDD values for spawning initiation in Lake Erie tributaries can be used to refine the timing of control efforts targeting pre-spawn and spawning adult fish, inform the timing of egg sampling, and provide linkages to existing early life stage models to infer the length of the growing season available for age-0 fish to reassess tributary suitability.

Lake Erie, Maumee, River, Sandusky river↗
USGS2026

Deep groundwater total dissolved solids mapping in the Dakota Group, Williston Basin, USA

Growing concern about the quantity of available freshwater around the world has led to interest in surveying groundwater total dissolved solids (TDS) below water well depths. Deep TDS has not been systematically mapped, and there is much to learn about the distribution and controls on deeper groundwater. In sedimentary basins across the United States, groundwater resources often overlie hydrocarbon resources, providing an opportunity to use borehole geophysical data collected for hydrocarbons to characterize groundwater and pore space resources. This study adapts a recently developed subsurface geostatistical and geophysical modeling approach to continuously map groundwater TDS, porosity, and temperature in the Dakota Group of the Williston Basin—an undercharacterized regional aquifer system overlying deeper hydrocarbon reservoirs. Groundwater TDS in the Dakota Group ranges from approximately 4800 to 26,900 mg/L. TDS patterns are stratified with higher TDS in the lower and upper Dakota Group, and relatively lower TDS in the middle Dakota Group. The lower TDS in the middle zone may represent a preferential regional flow path for lower-TDS meteoric recharge from the west. The alternating pattern of TDS may also be evidence of higher-TDS inflows into the Dakota Group from underlying and potentially from overlying aquifers. Porosity is lower near the center of the Williston Basin and tends to be higher to the east, which may be related to grain size distributions. The new regional TDS and porosity modeling serves as a quantitative reference for water users and provides supporting evidence for hypotheses on Dakota Group recharge.

Montana, North Dakota, South Dakota↗
USGS2024

Twentieth century extreme precipitation detected in a high-resolution, coastal lake-sediment record from California

California faces increasing economic and societal risks from extreme precipitation and flooding associated with atmospheric rivers (ARs) under projected twenty-first century climate warming. Lake sediments can retain signals of past extreme precipitation events, allowing reconstructions beyond the period of instrumental records. Here, we calibrate AR-related extreme precipitation from the last century to proxy data from lake sediments collected in the latitudinal zone of the highest frequency landfall for modern ARs in California. Excursions in erosional proxy data (Ti/Al) are positively and significantly correlated (r median = 0.45, p median = 0.04) with modern records of integrated vapor transport (IVT, kg m −1 s −1 ), a key metric of AR intensity, using correlations that incorporate age-model uncertainty. Despite the land-use change near the study site, the data suggest intense and long-lasting AR storms are identifiable in this sedimentary record. These results allow conservative inferences concerning past extreme hydrology at this site.

California↗
USGS2024

Comparing subduction ground-motion models to observations for Cascadia

We evaluate Cascadia subduction ground-motion models (GMMs), considered for the 2023 US National Seismic Hazard Model (NSHM) update, by comparing observations to model predictions. The observations comprise regional recordings from intraslab earthquakes, including contributions from 2021 and 2022 events in southern Cascadia and global records from interface earthquakes. Since the 2018 NSHM update, new GMMs for Cascadia have been published by the Next Generation Attenuation (NGA)-Subduction Project that require independent evaluation. In the regional intraslab comparisons, we highlight a characteristic frequency dependence for Cascadia data, with short periods having lower ground motions and longer periods being comparable to other subduction zones. We evaluate differences in northern and southern Cascadia and find that the NGA-Subduction GMMs developed using southern Cascadia data perform better in this region than the model that did not consider these data. We compare ground-motion variability in Cascadia with the NGA-Subduction model predictions and find differences at short periods ( T = 0.1 s) due to the use of global versus regional data in the development of these models. Moreover, the within-event component of aleatory variability from the GMMs overpredicts the standard deviation of Cascadia recordings at very short periods ( T < 0.05 s). Using global interface earthquakes as a proxy to evaluate the Cascadia GMMs, we find long-period overprediction from a simulation-based GMM and some of the empirical GMMs. When comparing recent observations, we find a similar misfit to GMMs and the 2010 and 2022 Ferndale earthquakes. Finally, we observe different basin amplification factors arising in different subsets of the data, which indicate that differences in basin factors between empirical GMMs could arise from the data selection choices by the developers. As part of evaluating the regional basin terms, we apply basin amplification factors from the magnitude 9 Cascadia earthquake simulations to the empirical GMMs for interface earthquakes. The comparisons presented in this study indicate that the NGA-Subduction GMMs for Cascadia perform well relative to observations and older subduction GMMs.

British Columbia, California, Oregon, Washington↗
USGS2026

Subsurface vertical connectivity shapes solute transport to montane streams: Insights from watershed-scale geophysics-informed modeling

Headwater catchments provide essential water and nutrients to downstream ecosystems. The timing and evolution of their transport is shaped in part by the “invisible” subsurface structure but have been largely unexplored at the watershed scale. This raises a fundamental question: how and to what extent does subsurface structure influence streamflow and solute transport in montane watersheds? Here, we test controls of three-dimensionally resolved subsurface structure on solute transport, which reflects source waters and water residence time. We integrate the geophysically mapped architecture of Coal Creek, a headwater catchment in the Colorado River Basin, into numerical flow-transport models. Our results reveal greater vertical connectivity elongates flow paths and enhances deep groundwater contributions to streams, therefore substantially influencing the timing and magnitude of solute transport. In contrast, watershed-integrated outlet discharge can be predicted without high-resolution subsurface information. These findings demonstrate incorporating subsurface architecture is critical for predicting ecosystem health and contaminant transport.

Colorado↗
USGS2025

Reservoir thermal energy storage pre-assessment for the United States

Storing thermal energy underground for later use in electricity production or direct-use heating/cooling is a promising, viable, and economical green energy option. Reservoir thermal energy storage (RTES) is one such option, which stores energy in underutilized permeable strata with low ambient groundwater flow rates and more geochemically evolved (e.g. brackish/saline) waters relative to overlying principal aquifer systems. The U.S. Geological Survey has begun assessing RTES potential nationally by focusing on five generalized geologic regions (Basin and Range, Coastal Plain, Illinois Basin, Michigan Basin, Pacific Northwest) across the United States. Hydrogeologic reservoir models are developed for the following eight metropolitan area cities within those regions to evaluate RTES performance across different climates and subsurface conditions: Albuquerque, New Mexico; Charleston, South Carolina; Chicago and Decatur, Illinois; Lansing, Michigan; Memphis, Tennessee; Phoenix, Arizona; and Portland, Oregon. Evaluated metrics include estimated required well spacing, thermal storage capacity, and thermal recovery efficiency through time. Also considered for each reservoir are potential complicating factors, including reservoir depth, thermally driven free convection, and groundwater salinity. This work focuses on direct-use cooling because the need for cooling modern office buildings greatly exceeds that for heating in most parts of the country (Falta and others, 2016); however, the evaluated metrics are also relevant to heating and electricity applications. Results indicate that favorable RTES conditions exist in each region, with the Coastal Plain and Basin and Range being especially favorable for thermal storage capacity, while the Pacific Northwest and Michigan Basin excel at energy recovery for the evaluated cooling application. The results underscore the utility of developing maps of thermal storage capacity, subsurface temperature models, and volumetric estimates of thermal storage capacity to serve as key RTES resource classification standards. Overall, this pre-assessment provides a basic understanding of RTES potential in several cities and geologic regions throughout the country and will aid ongoing thermal energy storage assessment efforts.

Arizona, Illinois, Michigan, New Mexico, Oregon, S↗
USGS2025

Megafaunal community structure on ferromanganese and phosphorite hardgrounds in the Southern California Borderland

The Southern California Borderland (SCB) is a topographically complex region on the active continental margin that hosts varied hardground habitats, including ferromanganese (FeMn) crusts and phosphorites, marine minerals being considered for resource extraction. The SCB is influenced by seasonal upwelling and terrestrial inputs, and has a well-defined oxygen-minimum zone (OMZ). We analyzed megafaunal community composition, density, and diversity across 41 ROV video transects at 10 SCB hard substrate sites spanning depth (378–2765 m), temperature (1.79–7.96 °C), and oxygen (3.91–105.67 μM) gradients, with varying rock types (FeMn crusts, phosphorites, other rocks). We counted 32,426 individuals representing 146 unique taxa over a total area of 21,935 m 2 . Echinodermata contributed 48 % of the total abundance; Cnidaria 24 %; Porifera 13 %; Annelida 6 %; Arthropoda 6 %; Chordata 2 %; Mollusca, Foraminifera, and Hemichordata <1 %. Megafauna communities showed clear heterogeneity, with density, diversity, and community composition varying among transects within sites and across sites. Rock type recorded no influence on megafaunal density, but habitats that included FeMn crusts had higher diversity and distinct taxonomic composition. Location, depth, and oxygen were the most important variables explaining variance among megafaunal communities, with distinct communities formed at deeper depths and within the OMZ. This study provides baseline information about the megafauna inhabiting SCB hardgrounds, particularly those associated with minerals considered for their resource potential. It extends existing documentation of such communities to greater depths, reveals increased representation of sponges and corals below 1000 m, and highlights the variability within and among deep-sea megafaunal communities, offering context for informed policy decisions.

Southern California borderland↗
USGS2025

Detecting hidden sedimentary geothermal systems in the Upper Colorado River Basin

Geothermal resources exist in sedimentary rock where circulation of water for efficient extraction or storage of heat is possible. Except in rare instances where hot water is expressed at the land surface, sedimentary geothermal resources are hidden, so the identification of these systems is optimally accomplished using predictive subsurface modeling. An integrated approach using detailed paleogeographic interpretations, subsurface geologic mapping, and numerical modeling has produced regional geologic and temperature models for the Upper Colorado River Basin, a large watershed in central North America that contains many sedimentary basins. These models identify areas of hidden sedimentary geothermal resource potential in low temperature (<90°C), moderate temperature (90–150°C), and high temperature (>150°C) fairways across the study area. These models incorporate maps of key horizons in outcrop and the subsurface to create a robust structural framework that can be used to target favorable geology for natural or engineered permeability. This framework is populated with lithologies derived from detailed palaeogeographical maps and over 40,000 bottom hole temperature (BHT) values were used to create a calibrated three-dimensional (3D) temperature model across the region. The resulting maps serve as a regional sedimentary geothermal play fairway screening tool for evaluating different grades of sedimentary geothermal resources and for identifying areas of interest where more detailed, prospect-scale studies can be undertaken.

Arizona, Colorado, New Mexico, Utah, Wyoming↗
USGS2026

Earthquake ground-motion model adjustments for the San Francisco Bay area

We develop adjustments to ergodic ground‐motion models (GMMs) to improve their performance in the San Francisco Bay Area (SFBA). GMMs are widely used in hazard assessments to estimate characteristics of ground shaking based on known properties of the source, path, and site. Such models are often developed using datasets containing records from various regions, resulting in models that represent median ground‐motion behavior, which may not adequately represent ground motions within subregions. This is true for the SFBA, where ground motions attenuate more rapidly with distance than in many other parts of California that dominate GMM databases. To support improved seismic hazard estimates in the SFBA, we calculate regional constants and anelastic attenuation coefficient adjustments relative to two commonly used ergodic GMMs: BSSA14 ( Boore et al. , 2014 ) and ASK14 ( Abrahamson et al. , 2014 ). These adjustments are obtained for a suite of ground‐motion intensity measures (peak ground acceleration, peak ground velocity, and 5%‐damped pseudospectral acceleration at oscillator periods ranging from 0.075 to 10 s) using mixed‐effects regression. Use of the regionally adjusted models reduces the overall bias by up to 0.5 natural log units for BSSA14 and up to 0.6 natural log units for ASK14. We demonstrate one application of our attenuation adjustments and their implications in an earthquake early warning case study of the 2014 M 6.0 South Napa earthquake. The predicted extent of shaking using the adjusted models better matches observed shaking at large source‐to‐site distances, especially for lower shaking intensities, thus potentially reducing overalerting. We encourage the use of our model adjustments when ergodic models are considered for seismic hazard studies in the SFBA.

California↗
USGS2024

Slip rate for the Rose Canyon fault through San Diego, California, based on analysis of GPS data: Evidence for a potential Rose Canyon–San Miguel-Vallecitos fault connection?

The Rose Canyon fault is the southern extension of the larger Newport–Inglewood–Rose Canyon fault system, which represents a major structural boundary in the Inner Continental Borderland (ICB) offshore of southern California. Ten to fifteen percent of total plate boundary motion in southern California is thought to be accommodated by the faults of the ICB, but the exact distribution of slip is uncertain. With an onshore segment, the Rose Canyon fault offers an opportunity to measure the slip rate using traditional geodetic methods. In this study, we use Global Positioning System (GPS) surface velocities from a combined campaign and continuous GPS network to constrain elastic models of the Rose Canyon fault. We then compare the observed surface velocities with proposed conceptual models of regional fault connections that facilitate the transfer of slip into the Rose Canyon fault to assess how well the observations are explained by the models. The results of elastic half‐space models suggest that the Rose Canyon fault may be slipping toward the higher end of geologic estimates, with the preferred model indicating a slip rate of 2.4 ± 0.5 mm/yr. Although limited in terms of near‐fault benchmarks, we find an improved model fit using an asymmetrical elastic half‐space model and a higher slip rate, suggesting a potential rheological contrast across the Rose Canyon fault, similar to observations from the northern Newport–Inglewood fault segments. Observed GPS surface velocities, background seismicity, and gravity anomalies south of San Diego Bay point toward a more easterly trace for the Rose Canyon fault, suggesting a possible connection with the San Miguel–Vallecitos fault system. Such a connection could increase the potential rupture lengths of future earthquakes and have important consequences for regional seismic hazards.

California↗
USGS2025

Fossil diatoms in Arctic marine surface sediments

Diatoms are one of the main constituents of marine phytoplankton in the Arctic, and thanks to their siliceous skeletons, diatom fossils are relatively well preserved in sediments. Due to their species-specific sensitivity to different ocean conditions, their abundance and assemblages in sediments are routinely used by paleoceanographers to reconstruct the state of the surface ocean in the past (Koç 2007). By using statistical methods, we can obtain valuable knowledge about their ecological preferences (Oksman et al. 2019) and generate quantitative reconstructions of various parameters, such as sea-surface temperature and sea-ice concentration through time (Krawczyk et al. 2021; Sha et al. 2014). The Marine Arctic Diatoms (MARDI) working group (WG) ( pastglobalchanges.org/mardi ) aims to advance knowledge on marine-diatom ecology and diatom-based reconstructions by compiling and harmonizing data from surface-sediment samples across the Arctic.

Pages Magazine↗
USGS2024

Parsimonious high-resolution landslide susceptibility modeling at continental scales

Landslide susceptibility maps are fundamental tools for risk reduction, but the coarse resolution of current continental-scale models is insufficient for local application. Complex relations between topographic and environmental attributes characterizing landslide susceptibility at local scales are not transferrable across areas without landslide data. Existing maps with multiple susceptibility classifications under-represent landslide potential in moderate and gently sloping terrain. We leverage an extensive landslide database ( N = 613,724), a high-resolution digital elevation model (10-m), and high-performance computing resources, to develop a new nationwide susceptibility map for the contiguous United States, Hawaii, Alaska, and Puerto Rico. We calculate four alternative linear and nonlinear thresholds of topographic slope and relief using an objective split-sample calibration. We down-sample our results to a 90-m grid to account for uncertainty in the digital elevation model and landslide position, and evaluate these thresholds' ability to differentiate areas of greater susceptibility. The less conservative nonlinear model optimally balances our priorities of capturing observed landslides (99%) while minimizing area covered by susceptible terrain (43%). Independent evaluation with four statewide landslide inventories ( N = 172,367) reinforces our model selection but highlights spatially variable performance. Therefore, we propose a novel approach to susceptibility classification using the concentration of landslide-prone terrain within each down-sampled grid. While landslides are possible within any cells containing susceptible terrain, those with the highest concentration capture the majority of observed landslides. Our new map characterizes landside susceptibility more consistently than prior models; our transparent classification approach also provides flexibility for accommodating different tolerances in risk reduction measures.

AGU Advances↗
USGS2026

Riverscape heterogeneity shapes population diversity for a migratory fish

Habitat patch dynamics can scale up to influence population demography and diversity with implications for resilience to environmental stochasticity. But how the spatial arrangement and size of habitat patches interact with other components of habitat heterogeneity to shape population diversity at larger spatial scales is not well understood. For riverine fishes, there is increasing evidence that tributary streams provide critical demographic support to main stem rivers. However, the extent to which main stem rivers rely on demographic contributions from tributaries, and the factors underlying this dependence, have not been assessed. Here, we used genetic stock identification to evaluate the effect of tributaries on population diversity of Yellowstone cutthroat trout ( Oncorhynchus virginalis bouvieri ) occupying the main stem Snake River, Wyoming, USA. We found that the main stem relied almost entirely on tributaries for demographic support, but main stem composition varied spatially among river sections. Distance between habitat patches, catchment area, and groundwater availability acted in concert to determine the contribution of specific tributaries to the main stem, but contributions were ultimately modulated by habitat connectivity. We also found evidence for multi-scale spatial structure in tributary contributions, providing insight into untested drivers of main stem river population diversity. Our results demonstrate how spatially discrete and distributed riverscape attributes influence population diversity at broader spatial scales, illustrating how ecosystem resilience emerges from the dynamic, two-way exchange of individuals and energy across habitat networks. Management plans for large rivers that address the ecological contributions of tributaries may be needed to achieve optimal outcomes. Similarly, conservation strategies that exclusively focus on headwater streams may fail to capture the broader habitat requirements necessary to maintain robust cold-water fish populations and associated recreational fisheries, particularly under global environmental change.

Wyoming↗
USGS2024

Predicting hydrothermal reservoir depth from chemical geothermometers using a three-dimensional temperature model in the Great Basin, USA

Recent work in the Great Basin region of the western United States has made it possible to predict the depth of hydrothermal reservoirs (i.e., the depth at which heat is accumulated prior to ascent via hydrothermal upflow) identified through geochemistry and to contextualize the spatial patterns of these reservoir depths. Chemical geothermometers use the chemical and mineral constituents of hydrothermal fluids to predict the temperature at which fluids equilibrated with the host rocks at depth. Assuming that most of the Great Basin is dominated by conductive conditions until a vertically connected hydrothermal flow path is created (e.g., by faulting), geothermometers reflect the chemical and thermal conditions at the depth interval that the fluid has conductively equilibrated over a long period before a vertical conduit allows convective upflow. By pairing geothermometer temperature estimates with our recent three-dimensional temperature model of conductive heat flow in the Great Basin, we estimate the corresponding reservoir depths and construct a map of circulation depths. The predicted depths from geothermometers have spatial patterns across the Great Basin that relate to patterns seen in other geologic and geophysical data. Deeper springs generally occur disproportionately in areas with higher strain rates and in basins. We posit that current elevated strain rates reflect patterns of historic deformation where ongoing tectonic activity maintains permeable pathways to deeper reservoirs, some of which are estimated to exceed 6 km depth. Basins, as expected, contain a disproportionate number of these deep systems, because the underlying aquifers are closer to the surface in basins, thus requiring less water pressure to reach the surface than in mountain ranges. Most springs estimated to have their source in a deep reservoir occur at places known to host a hydrothermal system; these refined depth estimates of the source reservoir can help to better constrain the source depth for many known hydrothermal systems across the Great Basin.

Arizona, California, Idaho, Nevada, Oregon, Utah↗
USGS2026

Microtextural characteristics of adularia in banded quartz veins from the Midas low-sulfidation epithermal deposit, Nevada

High-grade ores at the Miocene Midas low-sulfidation epithermal deposit in northern Nevada are confined to crustiform quartz veins containing abundant adularia. Micro-X-ray fluorescence elemental mapping reveals that adularia is a common gangue mineral occurring in colloform bands, bands showing bladed textures, and bands with dendritic terminations. The adularia aggregates have delicate shapes and are comprised of stacked, submillimeter crystals hosted by fine-grained quartz. The textural evidence suggests that the adularia aggregates originally formed within a gel-like, noncrystalline silica matrix, which subsequently transformed into quartz. This indicates that the adularia did not precipitate in open space along the vein walls. Correlative microscopy, involving scanning electron microscopy-based automated mineralogy and optical petrography, demonstrates that bands containing abundant adularia are not the primary host to ore minerals. The ore minerals occur in different bands within the crustiform veins, implying that adularia and ore mineral precipitation did not always occur simultaneously. It is hypothesized here that fluid flow at Midas involved intermittent short-lived events of fluid flashing, causing rapid solute supersaturation in the liquid. During each flashing event, different amounts of vapor were produced along a given vein. Compositional differences between adjacent bands in the crustiform quartz veins may, therefore, be linked to variations in the amount of vapor formed during each flash event.

Nevada↗
USGS2026

Transcriptional changes in wild Yukon River Chinook Salmon associated with Ichthyophonus infections

Objective We compared differentially expressed genes in Chinook Salmon Oncorhynchus tshawytscha with three divergent Ichthyophonus statuses (undetected, subclinical infections, or clinical disease; n = 100) to investigate associated transcriptomic responses. Disease associated with the fish parasite Ichthyophonus sp. was first diagnosed in adult Chinook Salmon from the Yukon River in the late 1980s and has subsequently been implicated in premature host mortality. Methods Chinook Salmon tissue sample collections and Ichthyophonus infection data were leveraged from a multi-agency collaboration during summer 2022 at three locations along the main-stem Yukon River that spanned nearly 2,000 km of freshwater migration (lower, middle, and upper river). We sequenced the transcriptome and compared this to infection status based on routine diagnostic procedures. Results Among the 17,569 genes for which messenger RNA was detected, we identified a transcription signature in the skeletal muscle that was associated with Ichthyophonus infections and included 53 differentially expressed genes. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction—all processes that are known to be influenced by senescence during spawning migrations. Conclusions Results demonstrate a clear transcriptional difference between diseased fish (clinical disease group) and those in which Ichthyophonus was undetected, including identifying candidate markers for infection in this population. These results provide a foundation for development of nonlethal biomarkers to evaluate potential Ichthyophonus infections in Chinook Salmon based on gene transcription, protein products, or gene variants (e.g., polymorphisms).

Journal of Aquatic Animal Health↗