Geology topics

Shannon C. Waters-Dynes

Publications and source records attributed to Shannon C. Waters-Dynes.

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↗

USGS2025

Too hot for comfort: Elevated temperatures influence gene expression and exceed thermal tolerance of bigmouth shiners, Ericymba dorsalis

Environmental and associated ecosystem change may affect the persistence of fish species based on their ability to adapt to changing conditions, including decreasing flows and rising water temperatures. Exceeding the thermal tolerances of stream fish will likely result in a loss of ability to maintain metabolic processes. We evaluated the critical thermal maximum (CTmax) of bigmouth shiner ( Ericymba dorsalis ) and analysed the expression of heat shock protein 70 messenger RNA (mRNA) (HSP70) to quantify a thermal stress response over a gradient of temperatures (25°C–31°C). E. dorsalis HSP70 mRNA expression was upregulated in response to temperatures >25°C, indicating a stress response. This study supports the existence of a thermal stress threshold for E. dorsalis . The frequency at which this threshold is exceeded may increase under forecasted future climate scenarios for Nebraska.

Nebraska↗

USGS2025

Transcriptomics as an early warning of domoic acid exposure in Pacific razor clams (Siliqua patula)

As oceans warm, harmful algal blooms (HABs) are expected to increase, including blooms of Pseudo-nitzschia , a diatom that produces domoic acid (DA), which is a potent neurotoxin. Regulatory limits for human consumption (0.075–0.1 mg/kg/day; acute exposure) exist for the Pacific razor clam; however, fisheries currently do not have regulatory limits for chronic low-level exposure to DA even though razor clams can retain DA for over a year after an algal bloom. For bivalves, exposure to marine toxins may disrupt important cellular processes, leading to concerns about effects on their overall health and potential population- and ecosystem-level impacts. Transcriptomics was used to identify differentially expressed genes in razor clams (N = 30) from Long Beach, WA, collected prior to, during, and after a DA-producing bloom. Differentially expressed genes were identified that may indicate exposure of razor clams to DA, including clams with tissue DA concentrations that fall below regulatory limits for human consumption. Targeting these genes in real-time PCR assays may provide an early warning system for routine monitoring of DA in clams. Our results suggest DA exposure is associated with physiological responses ranging from decreased immune function to the potential disruption of cell communication, including retinoic acid catabolic processes, cell adhesion, collagen fibril organization, and immune effector processes. This work may also allow us to examine potential drivers of population-level change and whether chronic lower-level exposure to DA negatively impacts razor clam function, consequently affecting individual and population health.

Toxins↗

USGS2024

A comparison of eDNA sampling methods in an estuarine environment on presence of longfin smelt (Spirinchus thaleichthys) and fish community composition

The loss of tidal wetlands in the San Francisco Bay estuary have led to declines in native fish presence. Restoration of tidal wetlands in this area has intensified, with a primary goal of increasing the number of native fishes. We compared the presence of longfin smelt in naturally accreted and beneficial dredge reuse wetlands as a measure of successful restoration. We used environmental DNA (eDNA) analyses as our metric for fish presence and fish community composition, employing two different water sampling methods for comparison (standard and high-volume). Longfin smelt were present in multiple sites, but at numbers too low for accurate comparisons across sites. Community composition varied based on the water sampling method, but the presence/absence of longfin smelt was consistent across sampling methods. As this represents a pilot study, further refinement of methodology is necessary, but the use of high-volume water sampling methods is promising.

California↗

USGS2023

Differential heat shock protein responses in two species of Pacific salmon and their utility in identifying heat stress

Rapid and accelerating warming of salmon habitat has the potential to lower productivity of Pacific salmon ( Oncorhynchus species) populations. Heat stress biomarkers can indicate where warming is most likely affecting fish populations; however, we often lack clear classifications that separate individuals with and without heat stress needed to make these tools operational. We conducted a heat exposure experiment with trials lasting 12 or 36 h using juvenile Chinook salmon ( Oncorhynchus tshawytscha ) and coho salmon ( Oncorhynchus kisutch ) to validate heat stress biomarkers in white muscle. Following habituation to 13°C, individuals were exposed to water temperatures that increased to 15°C, 17°C, 19°C, 21°C or 23°C. Heat shock protein 70 abundance (HSP70 measured by ELISA) and transcription of 13 genes (mRNA measured by qPCR) including three heat shock protein genes ( hsp70, hsp90, hsp27 ) were measured. A distinct heat stress response was apparent by 21°C in juvenile Chinook salmon and 23°C in juvenile coho salmon using HSP70. A threshold for heat stress classification in Chinook salmon of > 2 ng HSP70 mg .1 total protein identified heat stress in 100% of 21 and 23°C treated individuals compared to 4% in cooler treatments. For coho salmon, > 3 ng HSP70 mg .1 total protein identified heat stress in 100% of 23°C treated individuals compared to 4% in cooler treatments. Transcription from a panel of genes separated individuals between cooler and stressful temperature experiences (≥21°C for Chinook salmon and ≥23°C for coho salmon) with ~ 85% correct classification. Our findings indicate that juvenile Chinook salmon were more temperature-sensitive than juvenile coho salmon and support the use of a HSP70 threshold sampled from muscle for assessing heat stress in individual wild Pacific salmon with an option for non-lethal biopsies for spawning adults.

Conservation Physiology↗

USGS2023

Gene expression and wildlife health: Varied interpretations based on perspective

We evaluated wildlife population health from the perspective of statistical means vs. variances. We outlined the choices necessary to provide the framework for our study. These consisted of spatial and temporal boundaries (e.g., choice of sentinel species, populations, time frame), measurement techniques (molecular to population level), and appropriate statistical analyses. We chose to assess the health of 19 sea otter populations, located in the north Pacific from the Aleutian Islands, AK, to Santa Barbara, CA, and varying in population growth rates and length of occupancy. Our focal metric was gene expression (i.e., mRNA transcripts) data that we had previously generated across sea otter populations as a measure of population health. We used statistical methods with different approaches (i.e., means vs. variances) and examined the subsequent interpretive outcomes and how these influence our assessment of “health.” Interpretations based on analyses using variances versus means overlapped to some degree. In general, sea otter populations with low variation in gene expression were limited by food resources and at or near carrying capacity. In populations where the variation in gene expression was moderate or high, four out of five populations were increasing in abundance, or had been recently increasing. Where we had additional information on sources of stressors at the level of the population, we were able to draw inferences from those stressors to specific gene expression results. For example, gene expression patterns of sea otters from Western Prince William Sound were consistent with long term exposure to petroleum hydrocarbons, whereas in Kachemak Bay, patterns were consistent with exposure to algal toxins. Ultimately, determination of population or ecosystem health will be most informative when multiple metrics are examined across disciplines in the context of specific scenarios and goals.

Alaska, British Columbia, California, Oregon, Wash↗

USGS2022

The mysterious case of the missing razor clams

Oceans are changing and these changes are affecting animals that live there. Animals respond differently to changes in water temperature, food availability, or contaminants. Those responses can be seen in their genes. Gene transcription is a tool that allows scientists to see the response of an animal’s genes to its environment. We used gene transcription to compare two populations of Pacific razor clams in Alaska: one that has lots of clams and one that used to have lots but doesn’t anymore. We were surprised when we didn't find any differences in their gene responses! So, we had to think about what else might be influencing the number of clams in these two populations. As we “dug” for answers, we found out that there are differences between the populations that don‘t influence their genes but may impact their numbers, such as predation.

Frontiers for Young Minds↗

USGS2022

Divergent gene expression profiles in Alaskan sea otters: An indicator of chronic domoic acid exposure?

An opportunistic investigation into ecosystem instability in Kachemak Bay (KBay), Alaska, has led us to investigate exposure to toxic algae in sea otters. We used gene expression to explore the physiological health of sea otters sampled in KBay in May 2019. We found altered levels of gene transcripts in comparison with reference sea otters from clinically normal, oil-exposed, and nutritionally challenged populations sampled over the past decade. KBay sea otters were markedly divergent from the other groups for five genes, which indicated the involvement of neurological, cardiac, immune, and detoxification systems. Further, analyses of urine and fecal samples detected domoic acid in the KBay sea otters. In combination, these results may point to chronic, low-level exposure to an algal toxin, such as domoic acid. With a warming climate, the frequency and severity of harmful algal blooms in marine environments is anticipated to increase, and novel molecular technologies to detect sublethal or chronic exposure to algal toxins will help provide an early warning of threats to the stability of populations and ecosystems.

Alaska↗

USGS2022

Using transcriptomics to predict and visualize disease status in bighorn sheep (Ovis canadensis)

Increasing risk of pathogen spillover coupled with overall declines in wildlife population abundance in the Anthropocene make infectious disease a relevant concern for species conservation worldwide. While emerging molecular tools could improve our diagnostic capabilities and give insight into mechanisms underlying wildlife disease risk, they have rarely been applied in practice. Here, employing a previously reported gene transcription panel of common immune markers to track physiological changes, we present a detailed analysis over the course of both acute and chronic infection in one wildlife species where disease plays a critical role in conservation, bighorn sheep ( Ovis canadensis ). Differential gene transcription patterns distinguished between infection statuses over the course of acute infection and differential correlation (DC) analyses identified clear changes in gene co-transcription patterns over the early stages of infection, with transcription of four genes—TGFb, AHR, IL1b and MX1—continuing to increase even as transcription of other immune-associated genes waned. In a separate analysis, we considered the capacity of the same gene transcription panel to aid in differentiating between chronically infected animals and animals in other disease states outside of acute disease events (an immediate priority for wildlife management in this system). We found that this transcription panel was capable of accurately identifying chronically infected animals in the test dataset, though additional data will be required to determine how far this ability extends. Taken together, our results showcase the successful proof of concept and breadth of potential utilities that gene transcription might provide to wildlife disease management, from direct insight into mechanisms associated with differential disease response to improved diagnostic capacity in the field.

Conservation Physiology↗

USGS2022

Baseline gene expression levels in Falkland-Malvinas Island penguins: Towards a new monitoring paradigm

Health diagnostics of wildlife have historically relied on the evaluation of select serum biomarkers and the identification of a contaminant or pathogen burden within specific tissues as an indicator of a level of insult. However, these approaches fail to measure the physiological reaction of the individual to stressors, thus limiting the scope of interpretation. Gene-based health diagnostics provide an opportunity for an alternate, whole-system, or holistic assessment of health, not only in individuals or populations but potentially in ecosystems. Seabirds are among the most threatened marine taxonomic groups in the world, with ~25% of this species currently listed as threatened or considered of special concern; among seabirds, the penguins (Family Spheniscidae) are the most threatened seabird Family. We used gene expression to develop baseline physiological indices for wild penguins in the Falkland-Malvinas Islands, and captive zoo penguins. We identified the almost complete statistical separation of penguin groups (gentoo Detroit Zoo, gentoo Falkland-Malvinas Islands, rockhopper Detroit Zoo, and rockhopper Falkland-Malvinas Islands) based on gene expression profiles. Implementation of long-term longitudinal studies would allow for the assessment of temporal increases or decreases of select transcripts and would facilitate interpretation of the drivers of change.

Life↗

USGS2021

Gene expression profiles in two razor clam populations: Discerning drivers of population status

With rapidly changing marine ecosystems, shifts in abundance and distribution are being documented for a variety of intertidal species. We examined two adjacent populations of Pacific razor clams ( Siliqua patula ) in lower Cook Inlet, Alaska. One population (east) supported a sport and personal use fishery, but this has been closed since 2015 due to declines in abundance, and the second population (west) continues to support commercial and sport fisheries. We used gene expression to investigate potential causes of the east side decline, comparing razor clam physiological responses between east and west Cook Inlet. The target gene profile used was developed for razor clam populations in Alaska based on physiological responses to environmental stressors. In this study, we identified no differences of gene expression between east and west populations, leading to two potential conclusions: (1) differences in factors capable of influencing physiology exist between the east and west and are sufficient to influence razor clam populations but are not detected by the genes in our panel, or (2) physiological processes do not account for the differences in abundance, and other factors such as predation or changes in habitat may be impacting the east Cook Inlet population.

Alaska↗

USGS2020

A manipulative thermal challenge protocol for adult salmonids in remote field settings

Manipulative experiments provide stronger evidence for identifying cause-and-effect relationships than correlative studies, but protocols for implementing temperature manipulations are lacking for large species in remote settings. We developed an experimental protocol for holding adult Chinook salmon ( Oncorhynchus tshawytscha ) and exposing them to elevated temperature treatments. The goal of the experimental protocol was to validate heat stress biomarkers by increasing river water temperature from ambient (~14°C) to a treatment temperature of 18°C or 21°C and then maintain the treatment temperature over 4 hours within a range of ±1.0°C. Our protocol resulted in a mean rate of temperature rise of 3.71°C h-1 (SD = 1.31) to treatment temperatures and mean holding temperatures of 18.0°C (SD = 0.2) and 21.0°C (SD = 0.2) in the low- and high-heat treatments, respectively. Our work demonstrated that manipulative experiments with large, mobile study species can be successfully developed in remote locations to examine thermal stress.

Conservation Physiology↗

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

Gene transcript profiling in desert bighorn sheep

Respiratory disease is a key factor affecting the conservation and recovery of bighorn sheep ( Ovis canadensis ) populations. Innovative, minimally invasive tools such as gene transcription–based diagnostics have the potential to improve our understanding of the broad range of factors that can affect the health of wild sheep. Evaluation of transcript levels for genes representative of multiple internal systems enables measurement of physiological responses of individuals as well as populations to environmental stressors such as pathogens, nutritional deficiency, or contaminants. We developed real‐time polymerase chain reaction assays for 14 genes of interest representing systems including inflammation, cell signaling, detoxification, antiviral, antibacterial, or general stress. Initial results from desert bighorn sheep ( O. c. nelsoni ) sampled from the River, Muddy, and Bare mountains as well as from the Pintwater Range, in southern Nevada, USA, indicated unique transcript profiles associated with each population. This initial study provides the framework from which controlled variable or longitudinal studies can be made, thus augmenting the potential to inform management actions in the future.

Nevada↗

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↗

USGS2019

Complex immune responses and molecular reactions to pathogens and disease in a desert reptile (Gopherus agassizii)

Immune function plays an important role in an animal's defense against infectious disease. In reptiles, immune responses may be complex and counterintuitive, and diagnostic tools used to identify infection, such as induced antibody responses are limited. Recent studies using gene transcription profiling in tortoises have proven useful in identifying immune responses to various intrinsic and extrinsic stressors. As part of a larger experiment with Mojave desert tortoises ( Gopherus agassizii ), we facilitated the transmission of the pathogenic bacteria, Mycoplasma agassizii (Myag), to naïve adults and measured innate and induced immune reactions over time. Specifically, we evaluated clinical condition, presence of Myag in the nasal/oral cavity, induced antibody responses specific to Myag, and measured molecular reactions (gene transcript profiles) in 15 captive tortoises classified as naïve, exposed, or infected and 14 wild tortoises for comparison. Myag was confirmed inside the nasal/oral cavity in exposed tortoises within 30–60 days of introduction to infected animals, yet we did not detect Myag specific induced antibody responses in these individuals until 420–595 days post exposure. Surprisingly, we found no overall differences in the gene transcript profiles between our experimental treatment groups throughout this study. This work highlights the complexities in assessing immune function and diagnosing pathogen related infections in tortoises and other reptiles.

Ecology and Evolution↗

USGS2018

Development and utility of a gene transcription panel for desert bighorn sheep (Ovis canadensis nelsoni)

Respiratory disease is a key factor impacting the success of the ongoing conservation and recovery of wild sheep populations (WAFWA 2017). Although the primary pathogens involved in the bighorn sheep pneumonia complex have been identified, the wide variability in herd response following infection is not well understood (Cassirer et al. 2018). The response of populations infected with Mycoplasma ovipneumoniae has been variable, from minimal to extensive herd mortality followed by years to decades of either poor lamb recruitment or little expression of disease and minimal impact on lamb survival (Coggins and Mathews 1992, Jorgenson et al. 1997, Cassirer et al. 2018). This variation is thought to be caused by differences in pathogen virulence, intrinsic or extrinsic factors that impact individual or herd immunity, including lungworm ( Protostrongylus spp.) or mite ( Psoroptes ovis ) infections, malnutrition, inbreeding, harsh weather conditions, or stress associated with overcrowding (Risenhoover et al. 1988, Bailey 1990, Jones and Worley 1994, Monello et al. 2001). Although substantial management strategies have been implemented, they have been ineffective in halting the spread of the epizootic (Cassirer et al. 2018).

Conference Paper↗

USGS2017

Using gene transcription to assess ecological and anthropological stressors in brown bears

Increasingly, population- and ecosystem-level health assessments are performed using sophisticated molecular tools. Advances in molecular technology enable the identification of synergistic effects of multiple stressors on the individual physiology of different species. Brown bears ( Ursus arctos ) are an apex predator; thus, they are ideal candidates for detecting potentially ecosystem-level systemic perturbations using molecular-based tools. We used gene transcription to analyze 130 brown bear samples from three National Parks and Preserves in Alaska. Although the populations we studied are apparently stable in abundance and exist within protected and intact environments, differences in transcript profiles were noted. The most prevalent differences were among locations. The transcript patterns among groups reflect the influence of environmental factors, such as nutritional status, disease, and xenobiotic exposure. However, these profiles also likely represent baselines for each unique environment by which future measures can be made to identify early indication of population-level changes due to, for example, increasing Arctic temperatures. Some of those environmental changes are predicted to be potentially positive for brown bears, but other effects such as the manifestation of disease or indirect effects of oceanic acidification may produce negative impacts.

Alaska↗