Geology topics

Adam Sepulveda

Publications and source records attributed to Adam Sepulveda.

At least 19 recordsLinked to original sources

USGS2026

Bright spot in eDNA monitoring: Early detection of invasive New Zealand mudsnails (Potamopyrgus antipodarum) prompted effective rapid response for fish hatchery

The New Zealand mudsnail (NZMS; Potamopyrgus antipodarum ) is a widespread aquatic invasive species that is parthenogenic, requiring only a single individual to initiate an infestation. Fish hatcheries–which are critical infrastructure that raise fish to support conservation, recreation, and subsistence fisheries–frequently use local water sources to provide cool water and are especially vulnerable to NZMS invasion from the contamination of water supplies. If an invasion proceeds undetected, hatcheries pose a risk for compounding the spread of NZMS because their operations transfer live organisms and associated water between hatchery facilities and, when stocking, to rivers and lakes. The U.S. Fish and Wildlife Service's Alchesay National Fish Hatchery, located on the Fort Apache Indian Reservation in Whiteriver, Arizona, produces trout to stock in Tribal reservoirs, lakes, and rivers across the southwestern U.S. New Zealand mudsnails were first documented in Arizona in 1995, are now widespread in this region, and occur at the confluence of the hatchery's outflow with the North Fork White River. Contamination of water supplies is the principal pathway for NZMS invasion into the hatchery. Here, we describe early detection environmental DNA (eDNA) surveillance efforts for NZMS at Alchesay National Fish Hatchery. Positive eDNA detections initiated a chain of events that ultimately led to four NZMS individuals being discovered and a rapid response eradication effort. Follow-up eDNA sampling and visual observation efforts after the eradication effort have yielded no detections of NZMS eDNA. We credit the success of this case with four key elements: rapid turnaround times, a robust quality assurance scheme, a proactive eDNA sampling design, and established partnerships. To our knowledge, this is the first published case of eDNA monitoring being used for early detection and successful rapid response for complete removal of an invasive species in a fish hatchery.

Arizona↗

USGS2026

Warming causes modest increase in the consumptive demands of invasive Northern Pike (Esox lucius) in Alaska freshwaters

Warming freshwaters can have profound effects on species composition and community structure and can increase the consumptive demand of predators. Here we explore synergistic impacts of warming and invasion within a freshwater community in Southcentral Alaska (USA). We quantified changes in population structure and predator diet composition using observed data for an introduced population of Northern Pike ( Esox lucius ) spanning a decade of warming temperatures and declining salmon returns. We used bioenergetics models to estimate past and contemporary predator consumptive demands and then estimated future consumption demands by applying forecasted future simulated temperatures under high emissions scenarios for the mid and late century compared to a baseline from the last twenty years. During the last decade, the population structure of Northern Pike shifted towards younger individuals with increased growth rates in young of year and Age-1 fish. The biomass of juvenile salmon in Northern Pike diets decreased 30–74% across all age classes of predators, corresponding to a 42% reduction of mean abundance of adult Chinook Salmon ( Oncorhynchus tshawytscha ) in the system from 2014–2018 to 2019–2023. Consumption of all fish species was highly variable and all increased, 5% to 63%, consistent with prey switching towards other fishes reflecting possible declines in availability of preferred salmon prey. Bioenergetic simulations revealed modest increases in total per-capita consumption of prey by Northern Pike across mid-century and late-century scenarios, with the largest increases in consumption predicted in individuals three years of age and greater. We also observed increased numbers of Coho Salmon ( Oncorhynchus kisutch ) in diets and smaller mean size suggesting a shift to young of year individuals as well as an absence of Sockeye Salmon ( Oncorhynchus nerka ) from diets, which differed from historical baseline data. These findings collectively suggest that changing thermal regimes may have modest but meaningful overall effects, disproportionately affecting the consumptive demands of larger Northern Pike, and may increase total consumption enough to appreciably increase mortality of salmon and other preferred prey.

Alaska↗

USGS2026

Environmental DNA pilot monitoring program for invasive species and biodiversity assessments on Santa Cruz Island: Interim report, September 2025

The U.S. Geological Survey (USGS) and Southern California Coastal Water Research Project supported Channel Islands National Park, The Nature Conservancy’s (TNC) Santa Cruz Island Preserve, and University of California San Diego (UCSD) researchers in using environmental DNA sampling to monitor for invasive Argentine ant ( Linepithema humile ) and to describe spatial biodiversity patterns in a freshwater stream on Santa Cruz Island that is colloquially known as Cañada del Puerto Creek (hydrologic unit code 12 number 180600140201). An eDNA autosampler was deployed May 27–June 02, 2025, which filtered and preserved four 2-L water samples every 12 hours (n = 48 samples). These samples were extracted by USGS and shipped to UCSD for targeted eDNA analyses of Argentine ant. Environmental DNA sampling kits were used to filter and preserve water samples at four sites along the creek spanning ~ 5 km of stream distance. Six 1-L samples were collected at each site May 27–28 and samples were analyzed for eDNA metabarcoding using a comprehensive panel, which encompasses species across the tree of life. In these samples, eDNA from 2,134 unique taxa spanning 30 taxonomic groups (e.g., amoebas, insects, plants) were found. These sampling efforts demonstrated how eDNA autonomous and manual sampling approaches can be applied by National Park Service, TNC, and partners at scale to provide otherwise difficult and expensive to acquire information about biological threats and biodiversity.

California↗

USGS2026

Best practice guidelines for targeted environmental DNA-based proficiency testing in non-regulatory contexts

The effective use of environmental DNA (eDNA) tools is contingent on strict adherence to established and validated methods. Differences in eDNA methods and quality assurance protocols may contribute to variability in results. However, quality assurance measures such as proficiency testing can provide independent evaluation of laboratory performance against pre-established test criteria. With this commentary, we discuss how broad implementation of recurring proficiency testing in eDNA laboratories can build decision-maker confidence in eDNA results. It can also create a culture of continuous evaluation and improvement that minimizes error and meets performance requirements to inform the sustainable use or monitoring of natural resources. We provide an overview of proficiency testing across molecular disciplines, review the state of proficiency testing in eDNA applications, and draft a roadmap for the expanded application of proficiency testing informed by best practices for targeted eDNA detection. We suggest that best practice proficiency testing can be conducted by an independent, third-party sample provider. By demonstrating that laboratories are competent and capable of producing reliable results, implementation of proficiency testing best practices should foster confidence in eDNA measurements and its use in decision-making processes. Increased confidence in eDNA methods and a clear expectation of what is considered satisfactory performance are also likely to create more favorable conditions for investments in eDNA-based monitoring.

Environmental DNA↗

USGS2025

Turning trash into treasure: Leveraging discarded filters for national-scale aquatic eDNA biomonitoring

Monitoring biodiversity changes over large spatiotemporal scales is critical for effective ecosystem conservation and management. This study investigates the potential of environmental DNA (eDNA) metabarcoding to enhance national-scale biomonitoring of freshwater diversity by leveraging discarded filters associated with routine water quality sampling from the U.S. Geological Survey's (USGS) National Water Quality Network (NWQN). We tested 375 samples from 103 NWQN sites for eDNA of native and non-native fish and found that 52% of the filters yielded fish eDNA for a total of 70 fish species detections. Of the filters that had fish eDNA present, an average of 3.7 species were detected. Benchmarking these results to USGS's Aquatic Gap Analysis Project (AGAP)—which includes both field-verified observations along with predictive models derived from fish capture and landscape predictor datasets—we found that eDNA from these filters detected only a fraction of the observed and expected fish diversity for these sites. Our results indicate that these discarded filters may not be sufficient for eDNA sampling of fish communities and posit that alternative filter types more appropriate for eDNA sampling may yield more valuable biomonitoring data. Nevertheless, we tested the efficacy of two novel approaches to facilitate large-scale biomonitoring. Though these filters did not yield adequate fish eDNA, the AGAP database provides a useful method for ground truthing fish species presence. The potential of integrating eDNA sampling into existing monitoring frameworks, which, when paired with more optimal eDNA methods, could be a cost-effective strategy to enhance biodiversity monitoring at large scales.

Aquaculture, Fish and Fisheries↗

USGS2025

Native Yellowstone cutthroat trout Oncorhynchus virginalis bouvieri growth and survival in a headwater stream primarily driven by warming stream temperatures, with non-native brown trout Salmo trutta posing an additional threat to survival

Warming rivers and interactions with non-native species impact salmonid species globally. Understanding how hydroclimatic conditions synergistically and independently interact with non-native species is critical for effectively managing salmonids into the future. We used a 10-year mark–recapture dataset to assess how native Yellowstone cutthroat trout (YCT) Oncorhynchus virginalis bouvieri and non-native brown trout Salmo trutta growth rates and apparent survival were affected by hydroclimatic conditions and (for YCT) the presence of brown trout in a tributary. Growth (YCT) and survival (both species across size classes) were negatively related to warming stream temperatures. Brown trout growth was positively related to increasing daily streamflow variability (a proxy for streamflow), but this variable was not included in the top YCT growth model. Density-dependent effects appeared to be non-existent (growth) or weakly positive (survival). When sympatric with brown trout, YCT displayed worse survival than allopatric YCT across environmental conditions. Broadly, we found native and non-native trout respond to different hydroclimatic conditions that shift with changing climatic conditions, and brown trout represent an additional threat to YCT survival.

Montana↗

USGS2025

What is eDNA method standardization and why do we need it?

The rapid advancement of environmental DNA ( eDNA ) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.

Metabarcoding and Metagenomics↗

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2024

A hierarchical model for eDNA fate and transport dynamics accommodating low concentration samples

Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of ecological inference from eDNA sampling. Two particular challenges are (1) determining species source location(s) and (2) accurately and precisely measuring low concentration eDNA samples in the presence of multiple sources of ecological and measurement variability. The recently introduced eDNA Integrating Transport and Hydrology (eDITH) model provides a framework for relating eDNA measurements to source locations in riverine networks, but little empirical work has been done to test and refine model assumptions or accommodate low concentration samples, that can be systematically undermeasured. To better understand eDNA fate and transport dynamics and our ability to reliably quantify low concentration samples, we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as a latent variable with a count distribution and conditioning detection and quantification on replicate copy number. We provide evidence that the eDNA removal rate declined through time, estimating that over 80% of eDNA was removed over the first 10 m, traversed in 41 s. After this initial period of rapid decay, eDNA decayed slowly with consistent detection through our farthest site 1 km from the release location, traversed in 67.8 min. Our model further allowed us to detect extra-Poisson variation in the allocation of copies to replicates. We extended our hierarchical model to accommodate a continuous effect of inhibitors and used our model to provide evidence for the inhibitor hypothesis and explore the potential implications. While our model is not a panacea for all challenges faced when quantifying low-concentration eDNA samples, it provides a framework for a more complete accounting of uncertainty.

Environmental and Ecological Statistics↗

USGS2024

Field trials of an autonomous eDNA sampler in lotic waters

Environmental DNA (eDNA) analysis has become a transformative technology, but sample collection methods lack standardization and sampling at effective frequencies requires considerable field effort. Autonomous eDNA samplers that can sample water at high frequencies offer potential solutions to these problems. We present results from four case studies using a prototype autonomous eDNA sampler as part of the U.S. Geological Survey’s Rapid Environmental eDNA Assessment and Deployment Initiative & Network (READI-Net) project. These case studies involved short-term deployments of an eDNA autosampler (Smith-Root) across a range of riverine habitats with the objectives of (a) identifying what insights could be gained from high-frequency autosampling and (b) benchmarking these autosamples against manually collected samples. The high frequency autosampling revealed high temporal variability of eDNA concentrations and provided valuable insights about eDNA associations with environmental covariates, such as discharge and turbidity. Benchmarking assessments indicated autosamples had similar detection rates to manual samples and obtained similar or greater eDNA quantities. We did find minimal carryover contamination in autosampler field controls. We conclude that eDNA autosamplers have potential to improve freshwater biosurveillance by reducing logistical sampling barriers, standardizing collection methods, and clarifying the influence of environmental covariates on eDNA results.

Idaho, Missouri, Montana, New York↗

USGS2024

Autonomous samplers and environmental DNA metabarcoding: Sampling day and primer choice have greatest impact on fish detection probabilities

Unprecedented rates of biodiversity loss and ecosystem function necessitate the use of rapid, efficacious, and cost-effective biomonitoring tools. The combination of autonomous samplers and high throughput sequencing (i.e., “metabarcoding”) of environmental DNA ( eDNA ) samples enables characterization of entire communities at high frequency and can be an important tool for conservation and management, allowing researchers to track fluctuations in biodiversity. We deployed two autonomous samplers at two U.S. Geological Survey streamgage sites in the upper Snake River (Wyoming and Idaho, USA) to collect eDNA samples from July-September 2021 and 2022 to characterize fish diversity. We used a probabilistic approach to evaluate the effects of water temperature, water discharge, filter pore size, water volume filtered, number of samples collected, timing, and primers on the probability of detecting eDNA from fish species known to be present. We detected eDNA from 13/15 species present in these areas of the Snake River. Overall, we did not find evidence that filter pore size, water volume filtered, water discharge, and water temperature affected the probability of detecting fish species’ eDNA . By contrast, primers and sampling day affected fish detection probabilities, indicating that primer choice and sampling day can either over- or under- estimate species diversity. These results indicate that users would ideally consider sampling on non-consecutive days and which primer set will maximize species detections.

Metabarcoding & Metagenomics↗

USGS2024

Realizing the potential of eDNA biodiversity monitoring tools in the marine environment with application to offshore renewable energy

The U.S. Geological Survey (USGS) researches the biological diversity and distribution of species to support management, conservation, and resource use decisions. USGS scientists advance detection and monitoring technologies to assess changes in fish and wildlife populations, biodiversity, and the health of ecosystems. The United States is planning to install 30 gigawatts of offshore marine and wind energy by 2030. However, the effects on fish and wildlife and their habitats are not well understood. The USGS is a leader in the field of eDNA technologies and has helped advance robotic eDNA samplers, has extensive experience working in the offshore environment, and has developed novel and actionable statistical methods and standards for eDNA monitoring applications. This fact sheet presents key eDNA research and development advances needed for realizing the potential of eDNA biodiversity monitoring tools in the marine environment and applying eDNA monitoring to offshore renewable energy development. New and cost-effective tools for measuring changes in biodiversity in response to offshore renewable energy development can help to inform natural resource management and project planning and permitting decisions.

Fact Sheet↗

USGS2024

Zebra and Quagga mussels in the United States—Dreissenid mussel research by the U.S. Geological Survey

The U.S. Geological Survey (USGS) delivers high-quality data, technologies, and decision-support tools to help managers both reduce existing populations and control the spread of dreissenid mussels. The USGS researches ecology, biology, risk assessment, and early detection and rapid response methods; provides decision support; and develops and tests control measures.

conterminous United States↗

USGS2024

Critical considerations for communicating environmental DNA science

The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess and monitor aquatic environments. However, instances of inadequate communication from the scientific community about confidence levels, knowledge gaps, reliability, and appropriate parameters of eDNA-based methods have hindered their uptake in environmental monitoring programs and, in some cases, has created misperceptions or doubts in the management community. To help remedy this situation, scientists convened a session at the Second National Marine eDNA Workshop to discuss strategies for improving communications with managers. These include articulating the readiness of different eDNA applications, highlighting the strengths and limitations of eDNA tools for various applications or use cases, communicating uncertainties associated with specified uses transparently, and avoiding the exaggeration of exploratory and preliminary findings. Several key messages regarding implementation, limitations, and relationship to existing methods were prioritized. To be inclusive of the diverse managers, practitioners, and researchers, we and the other workshop participants propose the development of communication workflow plans, using RACI (Responsible, Accountable, Consulted, Informed) charts to clarify the roles of all pertinent individuals and parties and to minimize the chance for miscommunications. We also propose developing decision support tools such as Structured Decision-Making (SDM) to help balance the benefits of eDNA sampling with the inherent uncertainty, and developing an eDNA readiness scale to articulate the technological readiness of eDNA approaches for specific applications. These strategies will increase clarity and consistency regarding our understanding of the utility of eDNA-based methods, improve transparency, foster a common vision for confidently applying eDNA approaches, and enhance their benefit to the monitoring and assessment community.

Environmental DNA↗

USGS2024

A hierarchical model for eDNA fate and transport dynamics accommodating low concentration samples

Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of ecological inference from eDNA sampling. Two particular challenges are 1) determining species source location(s) and 2) accurately and precisely measuring low concentration eDNA samples in the presence of multiple sources of ecological and measurement variability. The recently introduced eDNA Integrating Transport and Hydrology (eDITH) model provides a framework for relating eDNA measurements to source locations in riverine networks, but little empirical work has been done to test and refine model assumptions or accommodate low concentration samples, that can be systematically undermeasured. To better understand eDNA fate and transport dynamics and our ability to reliably quantify low concentration samples, we developed a hierarchical model and used it to evaluate a fate and transport experiment. Our model addresses several low concentration challenges by modeling the number of copies in each PCR replicate as a latent variable with a count distribution and conditioning detection and quantification on replicate copy number. We provide evidence that the eDNA removal rate declined through time, estimating that over 80% of eDNA was removed over the first 10 meters, traversed in 41 seconds. After this initial period of rapid decay, eDNA decayed slowly with consistent detection through our farthest site 1km from the release location, traversed in 250 seconds. Our model further allowed us to detect extra-Poisson variation in the allocation of copies to replicates. We extended our hierarchical model to accommodate a continuous effect of inhibitors and used our model to provide evidence for the inhibitor hypothesis and explore the potential implications. While our model is not a panacea for all challenges faced when quantifying low-concentration eDNA samples, it provides a framework for a more complete accounting of uncertainty.

BioRxiv↗

USGS2024

A workshop to advance invasive species early detection capacity of The Rapid Environmental DNA Assessment and Deployment Initiative & Network (READI-Net)

Early detection and rapid response (EDRR) can minimize the impacts of invasive species, which cost billions of dollars globally. To bolster EDRR across the United States, the U.S. Department of the Interior is working with the U.S. Geological Survey and other partners to advance a National EDRR Framework that strengthens tools, actions, and processes to find and eradicate invasive species before they establish and cause negative impacts. An important component of this framework is to strengthen molecular tools for detecting new invasions. The Rapid Environmental (e)DNA Assessment and Deployment Initiative & Network (READI-Net) project is developing automating eDNA sampling tools, processes to ensure that eDNA results are reliable for management decision-making, and information structures to deliver eDNA results to end-users. To improve the potential uptake of this molecular EDRR toolbox, READI-Net investigators met with a group of end-users, partners, developers and subject-matter experts from federal agencies, tribes, universities, and an NGO representing state agencies from February 28 to March 1, 2023, in Moss Landing, CA. Here, we summarize the READI-Net project and the corresponding participant feedback.

Management of Biological Invasions↗

USGS2024

National Aquatic Environmental DNA Strategy

Aquatic life is the engine of ecosystems and economies. In environments ranging from freshwater through marine, this biodiversity underpins the health, culture, opportunities, and economic wellbeing of the Nation -- from local communities to the entire country. The ability to evaluate the status, trends, and future projections of nature is key to maintaining national prosperity, and this requires timely and trusted information about the condition of aquatic biodiversity on a vast scale. With one of the largest Exclusive Economic Zones in the world and extensive estuaries, lakes, rivers and streams, it is a grand challenge for the United States to explore, monitor, and understand aquatic life.

Report↗

USGS2023

Validation of a species-specific probe-based qPCR assay for the threatened meltwater stonefly, Lednia tumana, in environmental samples

A probe-based quantitative real-time PCR assay was developed to detect meltwater stonefly ( Lednia tumana ) environmental (e)DNA in water samples. The limits of detection and quantification, respectively, were 12.1 and 58.4 gene copies for calibration standards and these values were similarly low in a relevant environmental sample matrix (8.6 and 174.2, respectively). The assay’s utility was demonstrated in situ on water samples with concomitant manual invertebrate surveys from a wide range of alpine streams across L. tumana ’s native range.

Conservation Genetics Resources↗