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Research about Yukon River

Source-linked reports with geographic coverage including Yukon River.

At least 19 recordsLinked to original sources
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↗
USGS2026

Biomarkers of mortality risks in Yukon Chinook salmon

Premature mortality of spawning adult Pacific salmon ( Oncorhynchus species) can strongly influence population dynamics and complicate escapement-based management. Heat stress and Ichthyophonus infections have been identified as probable drivers of premature mortality in Yukon River Chinook salmon ( Oncorhynchus tshawytscha ) and likely contributors to low spawning abundance. We leveraged a multiagency study focused on Ichthyophonus using lethally collected heart tissue as a rare opportunity to investigate these two stressors jointly in the same individuals to accomplish two tasks: (1) provide a more comprehensive premature mortality risk index that combines heat stress and Ichthyophonus detection and (2) investigate the feasibility of using skeletal muscle tissue gene transcription (mRNA of select genes) as a non-lethal biomarker of Ichthyophonus . Water temperatures ranged from ~12–22°C across four sites and two years. In both 2023 and 2024, effects were identified in ~30% of salmon at Pilot Station, Alaska, and ~70% of salmon by the time they reached mid river (Rapids, Fort Yukon). Mortality risk is presumably highest among fish with multiple stressors, which were detected in ~25% of Chinook salmon in the middle river sites in 2023 when it was warmer and 9—18% in 2024 when it was cooler. We explored Chinook salmon genes that respond to Ichthyophonus with a full transcriptome analysis that measured mRNA of 17,569 genes and identified 53 that were related to Ichthyophonus infection. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction– all processes known to be influenced by senescence during spawning migrations and imply accelerated senescence of infected fish. Primers were developed for 21 of the differentially expressed Chinook salmon genes for qPCR measurements of their mRNA that could be used in classification models. Attempts to statistically deduce Ichthyophonus infection from Chinook salmon gene transcription at the individual and group levels included some potential for separating fish where Ichthyophonus was not detected compared to those with high infection intensities (as judged by qPCR that directly detects Ichthyophonus DNA). Fish with relatively low infection intensities did not have a separate gene transcription signature and grouped with the undetected Ichthyophonus fish in two-thirds of the cases and high infection in onethird of cases. Among the genes with the most utility to predict Ichthyophonus infection were retinoic acid receptor beta (regulates cellular states) and lysozyme CII (immune system gene). Interannual variation in the gene transcription of fish with undetected Ichthyophonus was a complicating factor that demonstrated a need for additional refinement and testing. Overall, this study identified two broad findings: (1) The proportion of migrating fish with one or both of the assessed stressors ( Ichthyophonus infections and/or elevated levels of heat shock protein) can be very high (~70%) and (2) we recommend measuring interannual variation of gene transcription in any study that seeks to develop gene transcription as a biomarker.

Alaska↗
USGS2021

Comparison of historical water temperature measurements with landsat analysis ready data provisional surface temperature estimates for the Yukon River in Alaska

Water temperature is a key element of freshwater ecological systems and a critical element within natural resource monitoring programs. In the absence of in situ measurements, remote sensing platforms can indirectly measure water temperature over time and space. The Earth Resources Observation and Science (EROS) Center has processed archived Landsat imagery into analysis ready data (ARD), including Level-2 Provisional Surface Temperature (pST) estimates derived from the Landsat 4–5 Thematic Mapper (TM), Landsat 7 Enhanced Thematic Mapper Plus (ETM+), and Landsat 8 Thermal Infrared Sensor (TIRS). We compared in situ measurements of water temperature within the Yukon River in Alaska with 52 instances of pST estimates between June 2014 and September 2020. Agreement was good with an RMSE of 2.25 °C and only a slight negative bias in the estimated mean daily water temperature of −0.47 °C. For the 52 dates compared, the average daily water temperature measured by the USGS streamgage was 11.3 °C with a standard deviation of 5.7 °C. The average daily pST estimate was 10.8 °C with a standard deviation of 6.1 °C. At least in the case of large unstratified rivers in Alaska, ARD pST can be used to infer water temperature in the absence of or in tandem with ground-based water temperature monitoring campaigns.

Alaska↗
USGS2020

Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmon (Oncorhynchus tshawytscha)

Chinook salmon ( Oncorhynchus tshawytscha ) declines are widespread and may be attributed, at least in part, to warming river temperatures. Water temperatures in the Yukon River and tributaries often exceed 18°C, a threshold commonly associated with heat stress and elevated mortality in Pacific salmon. Untangling the complex web of direct and indirect physiological effects of heat stress on salmon is difficult in a natural setting with innumerable system challenges but is necessary to increase our understanding of both lethal and sublethal impacts of heat stress on populations. The goal of this study was to characterize the cellular stress response in multiple Chinook salmon tissues after acute elevated temperature challenges. We conducted a controlled 4-hour temperature exposure (control, 18°C and 21°C) experiment on the bank of the Yukon River followed by gene expression (GE) profiling using a 3′-Tag-RNA-Seq protocol. The full transcriptome was analysed for 22 Chinook salmon in muscle, gill and liver tissue. Both the 21°C and 18°C treatments induced greater activity in genes associated with protein folding (e.g. HSP70, HSP90 mRNA) processes in all tissues. Global GE patterns indicate that transcriptomic responses to heat stress were highly tissue-specific, underscoring the importance of analyzing multiple tissues for determination of physiological effect. Primary superclusters (i.e. groupings of loosely related terms) of altered biological processes were identified in each tissue type, including regulation of DNA damage response (gill), regulation by host of viral transcription (liver) and regulation of the force of heart contraction (muscle) in the 21°C treatment. This study provides insight into mechanisms potentially affecting adult Chinook salmon as they encounter warm water during their spawning migration in the Yukon River and suggests that both basic and more specialized cellular functions may be disrupted.

Alaska↗
USGS2020

Late Cenozoic climate change paces landscape adjustments to Yukon River capture

Late Cenozoic cooling and changes in glacial–interglacial cycle tempo are thought to increase global rates of erosion starting ~3 million years ago (Ma). Bedrock rivers set rates and patterns of erosion in most landscapes, but constraints on river response to late Cenozoic climate change remain elusive. Here, we determine cosmogenic isotope and luminescence ages of well-preserved bedrock terraces along the Fortymile River (Yukon River basin) to reconstruct an ~5 Myr history of fluvial adjustment to late Cenozoic climate and Yukon River headwater capture at 2.6 Ma. Post-capture Yukon River downcutting lowered the Fortymile River outlet, forcing subsequent bedrock incision throughout the Fortymile basin in two pulses, from 2.4 to 1.8 Ma and at ~1 Ma. These pulses of incision disrupted longer intervals of slow river channel sedimentation under near-consistent climate forcing from 4.8 to 2.4 Ma and from 1.8 to ~1 Ma. The Fortymile River delivers sediment to the Bering Sea, where provenance and accumulation rate changes since 4.3 Ma match observed variations in incision. Our results link alluviation and incision to late Cenozoic climate steadiness and change, respectively, and support the hypothesis that climate-forced changes in precipitation and runoff fundamentally control the pace of river incision and landscape erosion.

Alaska↗
USGS2020

Evidence of prevalent heat stress in Yukon River Chinook salmon

Migrating adult Pacific salmon ( Oncorhynchus spp.) are sensitive to warm water (>18 °C), with a range of consequences from decreased spawning success to early mortality. We examined the proportion of Yukon River Chinook salmon ( O. tshawytscha ) exhibiting evidence of heat stress to assess the potential that high temperatures contribute to freshwater adult mortality in a northern Pacific salmon population. Water temperatures greater than 18 °C have occurred almost annually in the Yukon River and correspond with low population abundance since the 1990s. Using gene transcription products and heat shock protein 70 biomarkers validated by field experiment, we identified heat stress in half of Chinook salmon examined (54%, n = 477) across three mainstem locations and three tributaries in 2016–2017. Biomarkers tracked wide variation in water temperature (14–23 °C) within a tributary. The proportion of salmon with heat stress differed between years at four of the six locations, with more prevalent heat stress in the warmer year. This work demonstrates that warming water temperatures are currently affecting northern populations of Pacific salmon.

Alaska↗
USGS2018

Satellite remote sensing estimation of river discharge: Application to the Yukon River Alaska

A methodology based on general hydraulic relations for rivers has been developed to estimate the discharge (flow rate) of rivers using satellite remote sensing observations. The estimates of discharge, flow depth, and flow velocity are derived from remotely observed water surface area, water surface slope, and water surface height, and demonstrated for two reaches of the Yukon River in Alaska, at Eagle (reach length 34.7 km) and near Stevens Village (reach length 38.3 km). The method is based on fundamental equations of hydraulic flow resistance in rivers, including the Manning equation and the Prandtl-von Karman universal velocity distribution equation. The method employs some new hydraulic relations to help define flow resistance and height of the zero flow boundary in the channel. Estimates are made both with and without calibration. The water surface area of the river reach is measured by using a provisional version of the U.S. Geological Survey (USGS) Landsat based product named Dynamic Surface Water Extent (DSWE). The water surface height and slope measurements require a self-consistent datum, and are derived from observations from the Jason-2 satellite altimeter mission. At both reach locations, the Jason-2 radar altimeter non-winter heights consistently tracked the stage recorded at USGS streamgages with a standard deviation of differences (error) during the non-winter periods of less than 7%. Part of the error may be due to differences in the gage and altimeter crossing locations with respect to the range of stage change and the response to changes in discharge at the upstream and downstream locations. For the non-winter periods, the radar derived slope estimates (mean = 0.0003) were constant over the mission lifetime, and in agreement with previously measured USGS water surface slopes and slopes determined from USGS topographic maps. The accuracy of the mean of the uncalibrated daily estimates of discharge varied between reaches, ranging from 13% near Stevens Village (N = 90) to −21% at Eagle (N = 246) based on the absolute error, and 5% to −6% based on the error of the log of the estimates. Calibrating to the mean of USGS daily discharge estimates from the streamflow rating for the same period of record at each streamgage resulted in mean absolute errors ranging from 1% to 2%, and log errors ranging from 1% or less. The error pattern of the estimates shows that without calibration, even though the mean is well simulated, the high and low end values over the range of estimates may have significant bias.

Alaska↗
USGS2015

Switching predominance of organic versus inorganic carbon exports from an intermediate-size subarctic watershed

Hydrologic exports of dissolved inorganic and organic carbon (DIC, DOC) reflect permafrost conditions in arctic and subarctic river basins. DIC yields in particular, increase with decreased permafrost extent. We investigated the influence of permafrost extent on DIC and DOC yield in a tributary of the Yukon River, where the upper watershed has continuous permafrost and the lower watershed has discontinuous permafrost. Our results indicate that DIC versus DOC predominance switches with interannual changes in water availability and flow routing in intermediate-size watersheds having mixed permafrost coverage. Large water yield and small concentrations from mountainous headwaters and small water yield and high concentrations from lowlands produced similar upstream and downstream carbon yields. However, DOC export exceeded DIC export during high-flow 2011 while DIC predominated during low-flow 2010. The majority of exported carbon derived from near-surface organic sources when landscapes were wet or frozen and from mineralized subsurface sources when infiltration increased.

Alaska↗
USGS2012

Synchronous cycling of Ichthyophoniasis with Chinook salmon density revealed during the annual Yukon River spawning migration

Populations of Chinook salmon Oncorhynchus tshawytscha in the Yukon River declined by more than 57% between 2003 and 2010, probably the result of a combination of anthropogenic and environmental factors. One possible contributor to this decline is Ichthyophonus , a mesomycetozoan parasite that has previously been implicated in significant losses of fish, including Chinook salmon. A multiyear epidemiological study of ichthyophoniasis in the Yukon River revealed that disease prevalence and Chinook salmon population abundance increased and decreased simultaneously (i.e., were concordant) from 1999 to 2010. The two values rose and fell synchronously 91% of the time for female Chinook salmon and 82% of the time for males; however, there was no significant correlation between Ichthyophonus prevalence and population abundance. This synchronicity might be explained by a single factor, such as a prey item that is critical to Chinook salmon survival as well as a source of Ichthyophonus infection. The host–parasite relationship between Ichthyophonus and migrating Chinook salmon from 2004 to 2010 was similar to that reported for the previous 5 years. During 2004–2010, overall disease prevalence was significantly higher among females (21%) than among males (8%), increased linearly with fish length for both males and females, and increased in both sexes as the fish progressed upriver. These regularly occurring features of host–parasite dynamics confirm a stable base of transmission for Ichthyophonus . However, from 2003 to 2010, disease prevalence decreased from 30% to just 8% in males and from 45% to 9% in females, paralleling a similar decline in Chinook salmon abundance during the same period. These findings may help clarify questions regarding the complex host–parasite dynamics that occur in marine species such as herrings Clupea spp., which have less well-defined population structures.

Alaska↗
USGS2007

Water and sediment quality in the Yukon River and its tributaries between Atlin, British Columbia, Canada, and Eagle, Alaska, USA, 2004

The Yukon River basin is the fourth largest watershed in North America at 855,300 square kilometers (km 2 ). Approximately 126,000 people live within the basin and depend on the Yukon River and its tributaries for drinking water, commerce, subsistence and recreational fish and game resources. Climate warming in the Arctic and Sub arctic regions encompassing the Yukon basin has recently become a concern because of possible far-reaching effects on the ecosystem. Large amounts of carbon and nutrients are stored in permafrost and have potential for release in response to this warming. These changes in carbon and nutrient cycling may result in changes in stream chemistry and productivity, including salmon populations, and ultimately changes in the chemistry and productivity of the Bearing Sea. To address these concerns, the U.S. Geological Survey (USGS) conducted a 5-year comprehensive water-quality study of the Yukon River and its major tributaries starting in 2000. The study included frequent water-quality sampling at a fixed site network as well as intensive sampling along the Yukon River and its major tributaries. This report contains observations of water and sediment quantity and quality of the Yukon River and its tributaries in Canada during 2004. Chemical, biological, physical, and discharge data are presented for the reach of river between Atlin, British Columbia, Canada, and Eagle, Alaska, USA.

Alaska, British Columbia, Yukon↗
USGS2005

Non-lethal estimation of body composition of Yukon River salmon

Because of the importance of Chinook salmon to commercial and subsistence fisheries on the Yukon River, further study of the factors that may affect the success of this species and our ability to manage the fisheries is warranted. Critical to these studies is the determination of the amount of lipids (fat) stored and available to the fish as its primary energy source for migration and spawning. Recent developments of Bioelectrical Impedance Analysis (BIA) promise a simple, non-lethal means of estimating proximate composition (e.g. fat, protein, water content) for field applications with fish. The goal of the project was to develop BIA models for Chinook salmon from the Yukon River watershed that would permit the non-lethal estimation of body proximate composition for use in field studies. Our results clearly demonstrated that BIA can be used to estimate proximate composition and energy density of salmon. While some minor refinements were suggested, the methodology can be used in a wide variety of field applications. For instance, application of the BIA models to predict energy levels of fish during their migration will allow evaluation of management programs, while also yielding data that can be used to evaluate energy use along the migratory path. Correlations of energy level with ongoing tagging, radio-tracking, and genetic studies also have the potential to allow managers and scientists to understand the relationship between fat content and distance to spawning location. These models have the potential for application to this species in other river systems. They also provide tools for a variety of other scientific investigation such as: 1) differences in energy stores in spawning and recruitment success; 2) effects of global warming on migratory salmonid stocks; and 3) differences in annual flow and temperature regiments upon migratory energy costs and resulting recruitment success.

Alaska, Yukon↗
USGS2004

Ichthyophoniasis: An emerging disease of Chinook salmon in the Yukon River

Before 1985, Ichthyophonus was unreported among Pacific salmon Oncorhynchus spp. from the Yukon River; now it infects more than 40% of returning adult Chinook salmon O. tshawytscha . Overall infection prevalence reached about 45% in the Yukon River and about 30% in the Tanana River between 1999 and 2003. Mean infection prevalence was greater in females than males in the main-stem Yukon River during each of the 5 years of the study, but the infection prevalence in males increased each year until the difference was no longer significant. Clinical signs of ichthyophoniasis (presence of visible punctate white lesions in internal organs) were least at the mouth of the Yukon River (∼10%) but increased to 29% when fish reached the middle Yukon River and was 22% at the upper Tanana River. However, clinical signs increased each year from 7% in 1999 to 27% in 2003 at the mouth of the river. As fish approached the upper reaches of the Yukon River (Canada) and the spawning areas of the Chena and Salcha rivers (Alaska), infection prevalence dropped significantly to less than 15% in females on the Yukon River and less than 10% for both sexes in the Chena and Salcha rivers, presumably because of mortality among infected prespawn fish. Age was not a factor in infection prevalence, nor was the position of fish within the run. The source of infection was not determined, but Ichthyophonus was not found in 400 Pacific herring Clupea pallasi from the Bering Sea or in 120 outmigrating juvenile Chinook salmon from two drainages in Alaska and Canada. Freshwater burbot Lota lota from the middle Yukon River were subclinically infected with Ichthyophonus , but the origin and relationship of this agent to the Chinook salmon isolate is unknown.

Yukon River↗
USGS2003

A 2,000-mile partnership with the USGS, Kayaks down the Yukon

Early in 2001, Bill Barber and Jay Klinck, avid kayakers and scientists, began planning a northern expedition that would take them across more than 2,000 miles of mostly untamed wilderness along the Yukon River. At the same time, USGS scientists were making plans to study the last, unregulated great river in North America, spanning one of the largest and most diverse ecosystems in the world. Soon, the paths of kayakers and scientists would cross.

Alaska↗
USGS1998

DNA and allozyme markers provide concordant estimates of population differentiation: Analyses of U.S. and Canadian populations of Yukon River fall-run chum salmon ( Oncorhynchus keta )

Although the number of genetic markers available for fisheries research has steadily increased in recent years, there is limited information on their relative utility. In this study, we compared the performance of different "classes" of genetic markers (mitochondrial DNA (mtDNA), nuclear DNA (nDNA), and allozymes) in terms of estimating levels and partitioning of genetic variation and of the relative accuracy and precision in estimating population allocations to mixed-stock fisheries. Individuals from eight populations of fall-run chum salmon ( Oncorhynchus keta ) from the Yukon River in Alaska and Canada were assayed at 25 loci. Significant differences in mitochondrial haplotype and nuclear allele frequencies were observed among five drainages. Populations from the U.S.-Canada border region were not clearly distinguishable based on multilocus allele frequencies. Although estimates of total genetic diversities were higher for the DNA loci ( H t = 0.592 and h = 0.647 for nDNA and mtDNA, respectively) compared with protein allozymes ( H t = 0.250), estimates of the extent of population differentiation were highly concordant across marker classes (mean theta = 0.010, 0.011, and 0.016 for allozymes, nDNA, and mtDNA, respectively). Simulations of mixed-stock fisheries composed of varying contributions of U.S. and Canadian populations revealed a consistent bias for overallocation of Canadian stocks when expected Canadian contributions varied from 0 to 40%, due primarily to misallocations among genetically similar border populations. No single marker class is superior for differentiating populations of this species at the spatial scale examined.

Yukon River↗
USGS1972

The hydraulic geometry of some Alaskan streams south of the Yukon River

Channel geometry surveys were conducted to determine bankfull stage, discharge, and other hydraulic parameters at 22 locations along the proposed route of the trans-Alaska pipeline corridor south of the Yukon River. Combined with the records from gaging stations located at some of the sites, the data are sufficient to describe some of the channel and flow characteristics typical of each of two major hydrologic areas, the Yukon River Region and the South-Central Region. Although each region follows general hydrologic trends, least squares relations indicate each exhibits its own particular deviations. Average values of the hydraulic and geometric properties of rivers were used to illustrate their application to practical engineering problems, namely the computation of depth of channel scour and of bedload discharge. For design purposes, caution is recommended when making computations based on average values. In the absence of other data, however, the average data become useful predictive tools.

Alaska↗
USGS1964

Magnitude and frequency of floods in Alaska south of the Yukon River

This report presents a method for evaluating the magnitude and frequency of floods on the basis of the analysis of flood records. One composite frequency curve is applied to the entire study region. This curve relates floods of various magnitudes at any site within the region to probable recurrence intervals (from 1.1 to 50 years) for those floods. Flood magnitudes are reduced to dimensionless form by expressing them as a ratio to mean annual flood. Magnitudes of mean annual floods vary with the flood-producing characteristics of stream basins. On the basis of the limited data available, drainage-area size is found to be the only significant factor affecting the magnitude of the mean annual flood. Trial and error groupings of gaging-station records show that the region can be split into three hydrologic areas: one curve defines the relation within each area between mean annual flood and drainage area. These three curves in combination with the composite flood-frequency curve permit, for natural-flow conditions at any site, the determination of flood magnitude for a given recurrence interval, or the determination of recurrence interval for a flood of known magnitude.

Alaska↗
USGS1956

Radiometric traverse along the Yukon River from Fort Yukon to Ruby, Alaska, 1949

In 1949, a radiometric traverse was made of rocks exposed along the banks of and near the Yukon River about Fort Yukon to Ruby, Alaska. Granitic rocks of Tertiary age and of Devonian or Carboniferous age and sandstone beds of Cretaceous age gave the highest readings obtained in the field. Other rock types examined were greenstone of Devonian or Carboniferous age and metamorphic rocks of Devonian and pre-Devonian age, sedimentary rocks, and liginite of Tertiary age, and alluvial deposits of Quaternary age. The most radioactive sample, from Melozitna River canyon, contained only 0.017 percent equivalent uranium.

Alaska↗