Geology topics

Jayde A. Ferguson

Publications and source records attributed to Jayde A. Ferguson.

6 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

Disease-associated mortality drives reduction in Yukon River Chinook salmon escapement: A novel method for quantifying the negative impacts of ‘misfit’ parasites to improve fisheries management

Parasites can suppress host populations through parasite-induced mortality. However, the negative effects of parasites are difficult to measure in wild populations and we have few tools for quantifying the magnitude of parasite-induced mortality. This is especially true for many ‘misfit’ parasites that do not fit into standard classifications (e.g. fungal-like parasites and myxozoans). As such, we are limited in our ability to include the effects of parasites in fish and wildlife management strategies. Chinook salmon ( Oncorhynchus tshawytscha ) are a species of immense cultural and ecological significance but populations are declining across much of their range. In the Yukon River, Alaska, USA, episodic outbreaks of the ichthyosporean parasite Ichthyophonus have been linked to declines, but population-level effects of Ichthyophonus on Yukon Chinook salmon remain largely unknown. We developed a novel model that leverages changes in parasite intensity distributions to quantify the magnitude of disease-induced mortality occurring in host populations. We used it to address two questions to inform management of Yukon Chinook salmon: (i) Is parasite-induced mortality occurring in Chinook salmon and at what magnitude? (ii) What are the drivers of spatio-temporal variability in parasite-induced mortality? Using 3 years of surveys, we quantified the evidence for the presence, magnitude, and variability in Ichthyophonus -induced mortality in Chinook salmon. Our model predicted that Ichthyophonus was responsible for between 8% and 15% mortality of the migrating Chinook salmon population prior to reaching the Canadian border and could describe nearly 35% of unaccounted for mortality at the border. The model predicted that variability in mortality among years could largely be explained by differences in parasite acquisition in the marine environment rather than differences in infection dynamics in the river. Synthesis and applications . Alaska Department of Fish and Game is implementing an annual monitoring program at the mouth of the Yukon River where our model will estimate the proportion of fish at risk from parasite-induced mortality to inform annual management. Moreover, the model is broadly applicable to other fungal-like and myxozoan parasites of conservation concern, where improved estimates of parasite-induced mortality could be used to predict parasite suppression of wild and managed host populations.

Alaska↗

USGS2022

A phylogeny based on cytochrome-c oxidase gene sequences identifies sympatric Ichthyophonus genotypes in the NE Pacific Ocean

ABSTRACT: In recent decades, evidence has accumulated to suggest that the widespread and highly variable parasite Ichthyophonus hoferi is actually a species complex. Highly plastic morphology and a general lack of defining structures has contributed to the likely underestimate of biodiversity within this group. Molecular methods are a logical next step in the description of these parasites, but markers used to date have been too conserved to resolve species boundaries. Here we use mitochondrial encoded cytochrome-c oxidase (MTCO1) gene sequences and phylogenic analysis to compare Ichthyophonus spp. isolates from several marine and anadromous fish hosts. The resulting phylogeny displays lineage separation among isolates and possible host/niche segregation not previously described. The parasite type that infects Pacific herring Clupea pallasii , Atlantic herring C. harengus , Atlantic salmon Salmo salar , and Pacific staghorn sculpin Oligocottus maculosus (Clade A) is different from that which infects Chinook salmon Oncorhynchus tshawytscha, walleye pollock Gadus chalcogrammus , Greenland halibut Reinhardtius hippoglossoides , and Pacific halibut Hippoglossus stenolepsis (Clade B). MTCO1 sequences confirmed the presence of a more divergent Ichthyophonus sp. isolated from American shad Alosa sapidissima in rivers of eastern North America (Clade C), while American shad introduced to the Pacific Ocean are infected with the same parasite that infects Pacific herring (Clade A). Currently there are no consensus criteria for delimiting species within Ichthyophonidae , but MTCO1 sequences hold promise as a potential species identifying marker and useful epizootiological tool.

Diseases of Aquatic Organisms↗

USGS2017

A systematic surveillance programme for infectious salmon anaemia virus supports its absence in the Pacific Northwest of the United States

In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (BC), Canada, in 2011, U.S. national, state and tribal fisheries managers and fish health specialists developed and implemented a collaborative ISAV surveillance plan for the Pacific Northwest region of the United States. Accordingly, over a 3-1/2-year period, 4,962 salmonids were sampled and successfully tested by real-time reverse-transcription PCR. The sample set included multiple tissues from free-ranging Pacific salmonids from coastal regions of Alaska and Washington and farmed Atlantic salmon ( Salmo salar L.) from Washington, all representing fish exposed to marine environments. The survey design targeted physiologically compromised or moribund animals more vulnerable to infection as well as species considered susceptible to ISAV. Samples were handled with a documented chain of custody and testing protocols, and criteria for interpretation of test results were defined in advance. All 4,962 completed tests were negative for ISAV RNA. Results of this surveillance effort provide sound evidence to support the absence of ISAV in represented populations of free-ranging and marine-farmed salmonids on the northwest coast of the United States.

Pacific Northwest↗

USGS2017

Observations and first reports of saprolegniosis in Aanaakłiq, broad whitefish (Coregonus nasus), from the Colville River near Nuiqsut, Alaska

We report the first confirmed cases (2013–2016) of saprolegniosis caused by water mold from the genus Saprolegnia in Aanaakłiq, broad whitefish ( Coregonus nasus ), from the Colville River near Nuiqsut, Alaska. While this mold is known to be worldwide, these instances represent the first cases in Nuiqsut and only the second instance on a single fish on the North Slope, occurring in 1980. We describe the collaborative work on monitoring this emerging disease. Because fish constitute a critical component of the diet in Nuiqsut and fishing is an integral part of Inupiaq nutritional and cultural subsistence activities overall, individual subsistence fishers, local governmental entities, and Alaska Native organizations representing Nuiqsut requested an examination of affected fish and information on possible drivers of this emerging disease. The collaborative work described here ranges from recording fishermen observations, acquiring fish and mold specimens, histopathology, and molecular identification of the mold. This work, not currently grant-funded, begins with Native observation that incorporates western scientific methods and involves local, state, and federal departments as well as for-profit and non-profit organizations. Additionally, we report the more recent (2016) observation of this disease in a second species of whitefish, Pikuktuuq, humpback whitefish ( Coregonus pidschain ).

Alaska↗

USGS2011

Impacts of multispecies parasitism on juvenile coho salmon (Oncorhynchus kisutch) in Oregon

We are studying the impacts of parasites on threatened stocks of Oregon coastal coho salmon (Oncorhynchus kisutch). In our previous studies, we have found high infections of digeneans and myxozoans in coho salmon parr from the lower main stem of West Fork Smith River (WFSR), Oregon. In contrast parr from tributaries of this river, and outmigrating smolts, harbor considerably less parasites. Thus, we have hypothesized that heavy parasite burdens in parr from this river are associated with poor overwintering survival. The objective of the current study was to ascertain the possible effects these parasites have on smolt fitness. We captured parr from the lower main stem and tributaries of WFSR and held them in the laboratory to evaluate performance endpoints of smolts with varying degrees of infection by three digeneans (Nanophyetus salmincola, Apophallus sp., and neascus) and one myxozoan (Myxobolus insidiosus). The parameters we assessed were weight, fork length, growth, swimming stamina, and gill Na + ,K + -ATPase activity. We repeated our study on the subsequent year class and with hatchery reared coho salmon experimentally infected with N. salmincola. The most significant associations between parasites and these performance or fitness endpoints were observed in the heavily infected groups from both years. We found that all parasite species, except neascus, were negatively associated with fish fitness. This was corroborated for N. salmincola causing reduced growth with our experimental infection study. Parasites were most negatively associated with growth and size, and these parameters likely influenced the secondary findings with swimming stamina and ATPase activity levels.

Oregon↗