Adam Sepulveda

• United States Geological Survey

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 tr...

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 bene...

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...

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 precisel...

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 studi...

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...

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...

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...

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...

Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured deci...

Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and...

Invasive species are a major threat to global biodiversity, yet also represent large‐scale unplanned ecological and evolutionary experiments to address fundamental questions in nature. Here we analyzed both native and invasive populations of predatory northern pike (Esox lucius) to characterize landscape genetic variation, determine the most likely...

Invasion risk assessments of habitat suitability provide insight on early detection effort allocation; however, sufficient data are rarely available to inform assessments. We explored tradeoffs of leveraging big data from the National Water Quality Portal (WQP), a standardized water quality database in the United States, to inform calcium- and pH-b...

Knowledge of potential spread by introduced species is critical to effective management and conservation. The Smallmouth Bass Micropterus dolomieu is an example of a fish that has been introduced globally, often spreads after introduction, and has substantial predatory impacts on fish assemblages. Nonnative Smallmouth Bass in the free‐flowing Yello...

Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid dev...

Environmental (e)DNA methods have enabled rapid, sensitive, and specific inferences of taxa presence throughout diverse fields of ecological study. However, use of eDNA results for decision-making has been impeded by uncertainties associated with false positive tests putatively caused by sporadic or systemic contamination. Sporadic contamination is...

Invasive species surveillance programs can utilize environmental DNA sampling and analysis to provide information on the presence of invasive species. Wider utilization of eDNA techniques for invasive species surveillance may be warranted. This paper covers topics directed towards invasive species managers and eDNA practitioners working at the inte...

Environmental (e)DNA methods have enabled rapid, sensitive, and specific inferences of taxa presence throughout diverse fields of ecological study. However, use of eDNA results for decision-making has been impeded by uncertainties associated with false positive tests putatively caused by contamination. Sporadic contamination is a process that is in...

The relentless role of invasive species in the extinction of native biota requires predictions of ecosystem vulnerability to inform proactive management strategies. The worldwide invasion and range expansion of predatory northern pike (Esox lucius) has been linked to the decline of native fishes and tools are needed to predict the vulnerability of...

Misunderstandings regarding the term “false positive” present a significant hurdle to broad adoption of eDNA monitoring methods. Here, we identify three challenges to clear communication of false‐positive error between scientists, managers, and the public. The first arises from a failure to distinguish between false‐positive eDNA detection at the s...

Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory stu...

Proliferative kidney disease (PKD) is an emerging disease that recently resulted in a large mortality event of salmonids in the Yellowstone River (Montana, USA). Total PKD fish mortalities in the Yellowstone River were estimated in the tens of thousands, which resulted in a multi‐week river closure and an estimated economic loss of US$500,000. This...

Autonomous, robotic environmental (e)DNA samplers now make it possible for biological observations to match the scale and quality of abiotic measurements collected by automated sensor networks. Merging these automated data streams may allow for improved insight into biotic responses to environmental change and stressors. Here, we merged eDNA data c...

Invasive species surveillance programs can utilize environmental DNA sampling and analysis to provide information on the presence of invasive species. Wider utilization of eDNA techniques for invasive species surveillance may be warranted. This paper covers topics directed towards invasive species managers and eDNA practitioners working at the inte...

The rapid evolution of environmental (e)DNA methods has resulted in knowledge gaps in smaller, yet critical details like proper use of negative controls to detect contamination. Detecting contamination is vital for confident use of eDNA results in decision-making. We conducted two literature reviews to summarize (a) the types of quality assurance m...

The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dyna...

The American Bullfrog (Lithobates catesbeianus) is a non-native invader of aquatic habitats across the Northwestern United States. It recently invaded the Yellowstone River, Montana, and has spread to over 140 km of floodplain habitat. We analyzed seven microsatellites in 528 tadpoles sampled across nearly the entire Yellowstone River invasion (~14...

Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and across large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated wit...

Environmental DNA (eDNA) sampling is a promising tool for the detection of rare and cryptic taxa, such as aquatic pathogens, parasites and invasive species. Environmental DNA sampling workflows commonly rely on multi‐stage hierarchical sampling designs that induce complicated dependencies within the data. This complex dependence structure can be in...

Climate change may facilitate the expansion of non-native invasive species (NIS) in aquatic and terrestrial systems. However, empirical evidence remains scarce and poorly synthesized at scales necessary for effective management. We conducted a literature synthesis to assess the state of research on the observed and predicted effects of climate chan...

Multiple studies have demonstrated environmental (e)DNA detections of rare and invasive species. However, invasive species managers struggle with using eDNA results because detections might not indicate species presence. We evaluated whether eDNA methods have matured to a point where they can be widely applied to aquatic invasive species management...

Abstract Environmental DNA analysis has revolutionized the way we study rare, invasive, and endangered taxa. However, if eDNA testing is to become an increasingly reliable tool, high detection sensitivity is crucial. Current eDNA sampling methods, like filtration and precipitation, can only process small volumes of water per sample. If only a few s...

Abstract Resource managers may be hesitant to make decisions based on environmental (e)DNA results alone since eDNA is an indirect method of species detection. One way to reduce the uncertainty of eDNA is to identify laboratory‐based protocols that ensure repeatable and reproducible results. We conducted a double‐blind round‐robin analysis of probe...

Compensatory growth—when individuals in poor condition grow rapidly to catch up to conspecifics—may be a mechanism that allows individuals to tolerate stressful environmental conditions, both abiotic and biotic. This phenomenon has been documented fairly widely in laboratory and field experiments, but evidence for compensatory growth in the wild is...

The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year, so a critical tactic in minimizing the costs of invasive species is the development of effective, early‐detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS) s...

These are the Abstracts of the 2019 annual meeting of SNVB, WA TWS, and NW PARC. I have two abstracts in this compilation: Olson et al., Density Management and Riparian Buffer Study update, pp 154-155; Weil and Olson, NW PARC update, pp 162-163.

Environmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restrict the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may...

Climate change is increasing the severity and extent of extreme droughts events, posing a critical threat to freshwater ecosystems, particularly with increasing human demands for diminishing water supplies. Despite the importance of drought as a significant driver of ecological and evolutionary dynamics, current understanding of drought consequence...

The invasion of non-native fishes is a leading cause of extinction and imperilment of native freshwater fishes. Evidence suggests that introduced species with generalist diets have the potential for greatest impacts through competition and predation even though populations are often comprised of specialist individuals. The northern pike (Esox luciu...

In the original publication, the following disclaimer statement included in the first page should be ignored.

In Grand Teton and Yellowstone national parks wetlands offer critical habitat and play a key role in supporting biological diversity. The shallow depths and small size of many palustrine wetlands in these protected areas and elsewhere make them vulnerable to changes in climate compared with larger and deeper aquatic habitats. Here, we use a simple...

Nonnative trout are a considerable threat to native salmonids yet our understanding of the mechanisms behind interspecific interactions remains limited. We evaluated the impacts of nonnative Brown Trout Salmo salar on a population of Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri in Montana, USA. We contrasted diets, growth, and survival...

Environmental DNA (eDNA) has improved detection probabilities of aquatic invasive species but lab-based analytical platforms for eDNA analyses slow opportunities for rapid response. Effective approaches that address this analytical bottleneck and improve capacity for rapid response are urgently needed. We tested the sensitivity of a portable, field...

Conventional PCR is an established method to detect Tetracapsuloides bryosalmonae DNA in fish tissues and to confirm diagnosis of proliferative kidney disease (PKD) caused by T. bryosalmonae. However, the commonly used PKX5f‐6r primers were designed with the intention of obtaining sequence information and are suboptimal for determining parasite DNA...

Identification of suitable habitats, where invasive species can establish, is an important step towards controlling their spread. Accurate identification is difficult for new or slow invaders because unoccupied habitats may be suitable, given enough time for dispersal, while occupied habitats may prove to be unsuitable for establishment. To identif...

Introduced American Bullfrogs (Lithobates catesbeianus) have been present in Grand Teton National Park since approximately the 1950s, but little is known about their distribution and potential impacts. In this study, we surveyed the current bullfrog distribution and spatial overlap with sympatric native amphibians in the park, and characterized pos...

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably...

Despite the importance of hydrologic regimes to the phenology, demography, and abundance of fishes such as salmonids, there have been surprisingly few syntheses that holistically assess regional, species-specific trends in hydrologic regimes within a framework of climate change. Here, we consider hydrologic regimes within the Greater Yellowstone Ar...

[This corrects the article DOI: 10.1371/journal.pone.0162277.].

The importance of trophic linkages between aquatic and terrestrial ecosystems is predicted to vary as a function of subsidy quantity and quality relative to in situ resources. To test this prediction, I used multi-year diet data from Bonneville cutthroat trout Oncorhynchus clarki Utah in spring-fed and snowmelt-driven streams in the high desert of...

Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted tax...

Table A. Water quality data of lakes used in the caged and carcass experiments. Table B. eDNA detection and PCR results for the caged, carcass and rotenone experiments. Table C. Gillnetting data from the pre and post-rotenone treated lakes. (DOCX)

Freshwater wetlands are particularly vulnerable to climate change. Specifically, changes in temperature, precipitation, and evapotranspiration (i.e., climate drivers) are likely to alter flooding regimes of wetlands and affect the vital rates, abundance, and distributions of wetland-dependent species. Amphibians may be among the most climate-sensit...

Reconstructing historical colonization pathways of an invasive species is critical for uncovering factors that determine invasion success and for designing management strategies. The American bullfrog (Lithobates catesbeianus) is endemic to eastern North America, but now has a global distribution and is considered to be one of the worst invaders in...

Table S1. Lithobates spp. mitochondrial cytochrome b haplotypes used in this study. Table S2. Bullfrog haplotype composition by site along the Yellowstone River. Table S3. Summary of invasive Lithobates catesbeianus sampling and 923‐bp mitochondrial cytochrome b haplotypes by drainage. Figure S1. Lithobates catesbeianus native range sources of...

New Zealand mud snails (NZMS) are exotic mollusks present in many waterways of the western United States. In 2009, NZMS were detected in Redwood Creek in Redwood National Park, CA. Although NZMS are noted for their ability to rapidly increase in abundance and colonize new areas, after more than 5 years in Redwood Creek, their distribution remains l...

Electric barriers can inhibit passage and injure fish. Few data exist on electric barrier parameters that minimize these impacts and on how body size affects susceptibility, especially to nontarget fish species. The goal of this study was to determine electric barrier voltage and pulse-width settings that inhibit passage of larger bodied rainbow tr...

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to d...

Knowledge of climatic variability at small spatial extents (< 50 km) is needed to assess vulnerabilities of biological reserves to climate change. We used empirical and modeled weather station data to test if climate change has increased the synchrony of surface air temperatures among 50 sites within the Greater Yellowstone Area (GYA) of the interi...

Results and discussion for data sets 2–5. (PDF)

The proportion of sites in each season with significant trends for each descriptive statistic for minimum and maximum temperature distributions using the modeled SNOTEL + COOP data, 1948–2012. (PDF)

Description of snowpack telemetry (SNOTEL) and Cooperative Observer Network (COOP) weather stations used in this study. (PDF)

Slopes and intercepts for seasonal Tmin and Tmax distribution metrics using the modeled SNOTEL + COOP data, 1948–2012. (PDF)

Slopes and intercepts for monthly Tmin and Tmax distribution metrics using the modeled SNOTEL + COOP data, 1948–2012. (PDF)

Management prioritization of species relative to their climate change sensitivity. (PDF)

American Bullfrogs (Lithobates catesbeianus) have been introduced across the globe, including in many northern latitude habitats where wetlands are ice-covered for part of the year. Because bullfrogs are less mobile at low temperatures, greater knowledge about their overwintering habitat may provide additional opportunities for control. Here, we de...

The accumulation of fine-grained sediments impairs the structure and function of streams, so removing fine sediments may be required to achieve restoration objectives. There has been little work on methods of removing excess sediment or on the efficacy of the methods. We used a 4-year before-after-control-impact design in southeastern Idaho streams...

Introduced American Bullfrogs (Lithobates catesbeianus) have been present in Grand Teton National Park since approximately the 1950s, but little is known about their distribution and potential impacts. In this study, we surveyed the current bullfrog distribution and spatial overlap with sympatric native amphibians in the park, and characterized pos...

The impacts of introduced northern pike (Esox lucius) on salmonid populations have attracted much attention because salmonids are popular subsistence, sport and commercial fish. Concern over the predatory effects of introduced pike on salmonids is especially high in Southcentral Alaska, where pike were illegally introduced to the Susitna River basi...

Excessive fine sediment is a focus of stream restoration work because it can impair the structure and function of streams, but few methods exist for removing sediment in spring-fed streams. We tested a novel method of sediment removal with the potential to have minimal adverse effects on the biological community during the restoration process. The...

Aquaculture and hatchery industries are in need of effective control methods to reduce the risk of spreading aquatic invasive species, such as the Asian clam Corbicula fluminea, through aquaculture and hatchery activities. The planktonic nature of Asian clam veligers enables this life stage to enter water-based infrastructure undetected, including...

Northern pike (Esox lucius) are opportunistic predators that can switch to alternative prey species after preferred prey have declined. This trophic adaptability allows invasive pike to have negative effects on aquatic food webs. In Southcentral Alaska, invasive pike are a substantial concern because they have spread to important spawning and reari...

1. Stream salamanders and fish often co-occur even though fish prey on and outcompete salamanders. However, the mechanisms that allow palatable salamanders to coexist with fish are unknown. 2. We tested mechanisms in the field that promote coexistence between Idaho giant salamanders (Dicamptodon aterrimus) and stream salmonid fishes in headwater st...

New Zealand mudsnails (NZMS) have spread rapidly across the globe, but little is known about mechanisms that drive their secondary spread within invaded streams. We used a field experiment to test if upstream movement is a potential mechanism of spread and how this movement is modified by flow velocity and resource availability. We found that movem...

Theory suggests that source-sink dynamics can allow coexistence of intraguild predators and prey, but empirical evidence for this coexistence mechanism is limited. We used capture-mark-recapture, genetic methods, and stable isotopes to test whether source-sink dynamics promote coexistence between stream fishes, the intraguild predator, and stream s...

New Zealand mudsnails (NZMS) have spread rapidly across the western United States, but little is known about mechanisms that drive their spread within invaded streams. We used a field experiment to test if upstream movement is a potential vector of NZMS spread and how this movement is modified by flow velocity and resource availability. We found mo...

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively...

Interior cutthroat trout occupy small fractions of their historic ranges and existing populations often are relegated to headwater habitats. Conservation requires balancing protection for isolated genetically pure populations with restoration of migratory life histories by reconnecting corridors between headwater and mainstem habitats. Identificati...

Significant reductions in juvenile stream salmonid growth have been observed in association with low summer flow, but underlying mechanisms are poorly understood and predictive power is limited. We conducted a stage-specific analysis of the relationship between summer flow and the growth of age-0 Atlantic salmon Salmo salar in two rearing sites in...