Geology topics

Adam J. Sepulveda

Publications and source records attributed to Adam J. Sepulveda.

At least 19 recordsLinked to original sources

USGS2022

Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database

To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for the verification of eDNA data by working closely with AIS eDNA community practitioners and natural resource managers across government, private and academic sectors. To better inform management decisions, verified AIS eDNA data will be displayed on a separate mapping layer alongside visual sighting data with the inclusion of additional information on the eDNA methods employed to collect and produce the data. To allow for eDNA data display, we produced consensus derived online documents including a submission application and data submission template and are developing a guidance document for detailing the eDNA data submission process. We also developed a communication plan including a mechanism for reporting detections to appropriate managers for consideration prior to display. The products of these efforts are an application and data submission process that will be used in the new environmental DNA data layer on the Nonindigenous Aquatic Species (NAS) database. Herein, we detail how we engaged the eDNA community for consensus of our standards, share lessons learned from the process, and describe the benefits of such an approach at instilling confidence among the research and decision-maker community.

Management of Biological Invasions↗

USGS2020

Robotic environmental DNA bio-surveillance of freshwater health

Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated with traditional sampling since it can automate water sample filtration and preservation of the captured material or homogenize it for immediate analyses in situ. The ESP was originally developed for marine environment applications. Here we evaluated whether the ESP can provide reliable, timely information on environmental (e)DNA detections of human and fish pathogens and introduced fishes at U.S. Geological Survey streamgage sites in freshwater rivers. We compared eDNA collected via ESP at high frequency (e.g., every 3 h) with manual eDNA collections collected at lower frequency (e.g., weekly). We found that water samples filtered and preserved by ESPs successfully detected the DNA of human pathogens, fish pathogens and introduced fishes. Both ESP and manually collected samples provided similar information about target DNA presence. We suggest that the greatest current benefit of the ESP is the cost savings of high frequency, bio-surveillance at remote or hard to access sites. The full potential of robotic technologies like the ESP will be realized when they can more easily execute in situ analyses of water samples and rapidly transmit results to decision-makers.

Idaho, Montana, Wyoming↗

USGS2020

msocc: Fit and analyse computationally efficient multi‐scale occupancy models in R

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 intuitively modelled with Bayesian multi‐scale occupancy models. However, current software for such models are computationally demanding, impeding their use. We present an r package, msocc , that implements a data augmentation strategy to fit fully Bayesian, computationally efficient multi‐scale occupancy models. The msocc package allows users to fit multi‐scale occupancy models, to estimate and visualize posterior summaries of site, sample and replicate‐level occupancy, and to compare different models using Bayesian information criterion. Additionally, we provide a supplemental web application that allows users to investigate study design for multi‐scale occupancy models and acts as a graphical user interface to the msocc package. The utility of the msocc package is illustrated on a published dataset and the functions in msocc are compared to the primary Bayesian toolkit for multi‐scale occupancy modelling, eDNAoccupancy , using various computational benchmarks. These benchmarks indicate that msocc is capable of fitting models 50 times faster than eDNAoccupancy . We hope that access to software that efficiently fits, analyses and conducts study design investigations for multi‐scale occupancy models facilitates their implementation by the research and wildlife management communities.

Methods in Ecology and Evolution↗

USGS2020

Climate-induced expansions of invasive species in the Pacific Northwest, North America: A synthesis of observations and projections

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 change on a suite of 398 aquatic and terrestrial NIS now present in or a major threat to aquatic and terrestrial ecosystems of the Pacific Northwest (PNW), USA and British Columbia. Surprisingly, very few studies (n = 15) have investigated the observed effects of climate change on the distribution, abundance, spread, or impact of the focal NIS, with only five studies focusing on terrestrial (n = 2) or aquatic (n = 3) species within the PNW. Only 93 studies predicted the future dynamics of the focal NIS somewhere in their non-native range using climate model projections, yielding 117 species-specific predictions. However, only 30 of those studies generated predictions that overlapped with the PNW, and only six focused specifically on the expansion or abundance of NIS (n = 11 species) entirely within the region. Although our understanding of how climate change may interact with biological invasions is notably lacking, some evidence suggests that climate-induced NIS expansions are already underway in the PNW, particularly in aquatic ecosystems, and will be exacerbated by future changes in temperature and precipitation regimes. Better information is urgently needed for managers to implement strategic prevention, early detection, and proactive actions that ameliorate ecologically and economically devastating impacts of NIS.

Idaho, Montana, Nevada, Oregon, Utah, Washington, ↗

USGS2020

A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels

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‐based assays for DNA of dreissenid ( Dreissena spp.) mussels, which are prolific aquatic invaders that can cause significant economic and ecological impacts. DNA extract from water samples spiked with known amounts of dreissenid DNA and from water samples collected from waters with and without dreissenids were analyzed by four independent research laboratories. We used results to calculate detection repeatability within laboratories and assays, detection reproducibility among laboratories and assays, and estimated dreissenid DNA copy number precision and accuracy. Laboratory and assay repeatability and reproducibility of detection results were high, 91% and 92%, respectively. The estimated copy numbers were neither precise nor accurate for samples spiked with <773 gene copies. These results suggest that eDNA surveillance of dreissenid mussels, using the protocols evaluated herein, can generate reliable detection data for decision‐making. However, managers should be cautious about using the quantitative information often associated with eDNA detections, especially when DNA is at lower abundance. Our results provide strong support that eDNA has the potential to provide repeatable and reproducible evidence under varying laboratory conditions and for different sample water chemistries. This is reassuring since the demand for eDNA surveillance is widespread and number of laboratories that process eDNA samples is growing steadily.

California, Montana, Nevada, New York, Oregon, Was↗

USGS2020

Are environmental DNA methods ready for aquatic invasive species management?

Multiple studies have demonstrated environmental (e)DNA detections of rare, invasive species. However, invasive species managers struggle with using eDNA results because detections might not indicate species presence. We evaluated if eDNA methods have matured to a point where they can be widely applied to aquatic invasive species management. We found that eDNA methods meet legal standards for being admissible as evidence in most courts, suggesting that eDNA method reliability is not the problem. Rather, we suggest that the interface between results and management needs attention since there are few tools for integrating uncertainty into decision-making. Solutions include decision support trees based on molecular best practices that integrate the temporal and spatial trends in eDNA positives relative to human risk tolerance.

Trends in Ecology and Evolution↗

USGS2019

Consistent compensatory growth offsets poor condition in trout populations

1. 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 scarce. 2. Cutthroat trout (Oncorhynchus clarkii subsp) are cold-water specialists that inhabit streams in montane ecosystems where seasonal conditions can be harsh and growth rates vary greatly among seasons. Understanding if individuals compensate for periods of reduced growth and body condition will improve understanding of the requirements of fish throughout their life-cycle and across freshwater habitats. 3. We quantified compensatory growth of juvenile cutthroat trout using extensive mark-recapture data from 11 stream populations (1,125 individuals) and two subspecies inhabiting a wide range of ecological settings in the northern Rocky Mountains, USA. Our objectives were to determine how growth was linked across seasons and determine if individuals behaviorally compensated for depressed body condition via emigration. 4. Fish in relatively poor condition consistently demonstrated compensatory growth in mass during subsequent seasons. In contrast, fish in relatively better condition responded with positive growth in length during the summer signaling these fish may be better suited to headwater environments; no compensatory growth in length was found during the winter. Furthermore, we found no evidence that individual condition mediated migration tendencies of fish to seek more favorable habitat. 5. Across a wide range of environmental conditions, we found consistent empirical support for compensatory growth in mass in the wild. A critical next step is to quantify how changing abiotic and biotic conditions influence the ability of stream fishes to compensate for locally or seasonally challenging conditions, thereby affecting long-term resiliency, viability, and adaptation in the face of changing environmental conditions.

Montana, Wyoming↗

USGS2019

Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network

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) streamgage network, which consists of > 8,200 streamgages nationwide systemically visited by USGS hydrologic technicians. Incorporating strategic eDNA sample collection during routine streamgage visits could provide early detection surveillance of aquatic invasive species with minimal additional cost. For this evaluation, USGS hydrologic technicians collected monthly eDNA water samples, May – September 2018, from streamgages downstream of reservoirs in the Columbia River Basin thought to be vulnerable to invasive dreissenid mussel ( Dreissenidae spp.) establishment. We tested water samples for dreissenid mussel DNA and also for kokanee ( Oncorhynchus nerka ) and yellow perch ( Perca flavescens ) DNA; the two fishes were used to assess if streamgages are adequately located to provide early-detection eDNA surveillance of taxa known to be present in upstream reservoirs. No Columbia River Basin streamgage samples met our criteria for being scored as positive for dreissenid DNA. We did detect kokanee and yellow perch DNA at all streamgages downstream of reservoirs where these species are known to occur. Field collection, laboratory analyses, and personnel time required for collection of four eDNA samples at a streamgage site cost US$500 -US$600 (net). Given these results, incorporating eDNA biosurveillance into routine streamgage visits might decrease costs associated with an invasion since early detection maximizes the potential for eradication, containment, and mitigation.

Ecosphere↗

USGS2019

Improved detection of rare, endangered and invasive trout using a new large-volume sampling method for eDNA capture

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 be to collect fewer, large volume water samples using coarse filters that do not clog as rapidly. We used mesocosm experiments and field evaluations to compare coarse filter‐large water volume samples (hereafter large volume filter samples) versus fine filter‐small water volume samples (hereafter small volume filter samples) for detection and quantification of rainbow trout ( Oncorhynchus mykiss ) and bull trout ( Salvelinus confluentus ) DNA. We found that large volume filter sampling can be an effective approach for detecting DNA of low‐density target taxa. In mesocosm experiments, large‐volume and small‐volume water samples detected similar quantities of rainbow trout DNA. In the field, large volume samples more frequently detected bull trout DNA, had higher bull trout DNA copy number, and higher total DNA concentrations than small volume samples. However, sampling higher water volumes increased the potential for PCR inhibition so the DNA workflow had to be altered for large volume samples. Combining larger water volume samples with other strategies, like increasing PCR sensitivity and the number of PCR replicates, will improve detection of rare species, which is crucial for advancing conservation and ecological understanding.

Montana↗

USGS2019

An integrated framework for ecological drought across riverscapes of North America

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 consequences for freshwater biodiversity is very limited. We describe key barriers that hinder integrative drought research and monitoring across riverscapes. The primary constraint limiting understanding of ecological drought is an existing monitoring framework focused on human water consumption and flood risk in mainstem rivers. This approach is misaligned with escalating needs for research and data collection that illuminate exposure, sensitivity, and adaptive capacity (i.e., vulnerability) of biota to drought across entire riverscapes. We present a hierarchical framework for integrated ecological drought monitoring and research that addresses drought vulnerability across riverscapes, and describe how this approach can directly inform natural-resource management.

BioScience↗

USGS2019

Trophic plasticity and the invasion of a renowned piscivore: A diet synthesis of northern pike (Esox lucius) from the native and introduced ranges in Alaska, U.S.A.

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 lucius), a predatory fish, has been widely introduced outside its native range for recreational fishing purposes, especially in western North America, and it has been implicated in declines and extirpations of native fishes. We synthesized over 2,900 individual northern pike diet records across 31 waterbodies from the native and introduced ranges in Alaska to quantify the extent of diet specialization and generalization relative to freshwater prey communities. To control for effects of ontogenetic diet shifts, we separately analyzed major size classes of northern pike and inferred and visualized trophic plasticity from Prey-Specific Abundance indices and ordination. Diet generalization was common in northern pike among waterbodies and usually consisted of individuals consuming macroinvertebrates. However, when available, individual northern pike diets showed specialization on fishes, amphibians, small mammals, and dragonflies. The reliance on macroinvertebrate prey by northern pike from small, isolated lakes in the native and invasive ranges suggests that dietary plasticity facilitates persistence of these predators in the absence of preferred fish prey. Broadly, this synthesis supports the hypothesis that trophic plasticity and diet generalization widely occur among invasive and native populations of northern pike which is likely to enhance the probability of introduction success, exacerbate their environmental impacts, and complicate management of this potentially invasive freshwater predator.

Alaska↗

USGS2019

Wetland drying linked to variations in snowmelt runoff across Grand Teton and Yellowstone national parks

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 wetlands make them vulnerable to changes in climate compared with larger and deeper aquatic habitats. Here, we use a simple water balance model to generate estimates of biophysical drivers of wetland change. We then examine the relationship between wetland inundation status and four principal drivers (i.e., temperature, precipitation, evapotranspiration, and runoff) spanning varying meteorological conditions over an 8-year time series from Grand Teton and Yellowstone national parks. We found that a higher percentage of surveyed wetlands were dry in years characterized by lower snowmelt runoff. While runoff-based models were most supported, wetland drying was also related to variations in April to June precipitation and temperatures. Our work shows that wetland drying was widespread across both parks, but sub-regional variations were best described at the hydrologic subbasin-level. Documenting the varying responses of wetlands to meteorological drivers is a necessary first step to identifying which subbasins are most sensitive to recent change and contemplating how future change may alter the distribution of wetlands and their dependent taxa.

Idaho, Montana, Wyoming↗

USGS2019

Using environmental DNA to extend the window of early detection for dreissenid mussels

Tools that bolster early detection of invasive species are needed to prevent their spread. In this study, we assessed if environmental DNA (eDNA) can extend the seasonal window for dreissenid mussel early detection beyond that of plankton tows, which are limited to warmer seasons when mussel larvae are present. We focused eDNA sampling efforts at multiple sites in Tiber Reservoir (Montana) where dreissenid mussel abundance is hypothesized to be low. Samples were collected in June and October 2017, when water temperatures were cooler than thermal optima for dreissenid reproduction, and in July 2017 when water temperatures were warmer and conducive for reproduction. We detected dreissenid mussel DNA in June, July and October even though no dreissenid mussels were observed using non-molecular tools in 2017. A subset of positive and negative eDNA samples were analyzed by an independent lab and results were corroborated. We then estimated the effort needed for 95% probability detection of dreissenid DNA at each site within Tiber Reservoir and found that as many as 27, 14, and 34 samples needed to be collected in June, July and October, respectively. To further validate the utility of eDNA, we also present ancillary eDNA results from other waters in the Flathead Reservation (Montana) where dreissenid mussels have never been detected and from waters with established zebra mussel populations in the upper Mississippi River, which were sampled in the spring when water temperatures were cooler than thermal optima for dreissenid reproduction. All Flathead Reservation samples were negative for dreissenid mussel DNA, while all upper Mississippi River samples were positive. This study adds to a growing body of research that demonstrates eDNA is a highly sensitive tool for dreissenid mussel surveillance in newly invaded waters, including colder seasons when non-molecular tools are likely to be less effective or more challenging to employ.

Montana↗

USGS2019

The Yellowstone River fish-kill: Fish health informs and is informed by vital signs monitoring

Trout are socioeconomically and ecologically important in the Greater Yellowstone Area (GYA); yet these fish face numerous threats. Disease may begin to play a larger role in reducing fish populations, partly because many existing threats may interact to exacerbate the frequency, extent, and severity of fish diseases (Lafferty 2009). For example, habitat loss and low summer flows might interact to stress fish, making them more susceptible to disease while also increasing fish densities in microhabitats, thereby creating conditions where infectious diseases are more easily spread. Conservation and management efforts to mitigate these threats often involve reactionary measures to unforeseen events. Long-term monitoring of aquatic vital signs and fish health, however, may provide important insights for predicting the spread of fish diseases and the extent and severity of outbreaks.

Idaho, Montana, Wyoming↗

USGS2018

Impacts of nonnative Brown Trout on Yellowstone Cutthroat Trout in a tributary stream

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. We contrasted diets, growth, and survival of Yellowstone Cutthroat Trout occurring in allopatry (i.e., where no Brown Trout were present) with individuals sympatric (i.e., co‐occurring) with nonnative Brown Trout. We assessed summer and autumn diets using gastric lavage methods and survival and growth using mark–recapture analyses. Overlap in diets at sites where Yellowstone Cutthroat Trout were sympatric with Brown Trout was high during July (Horn's index: H = 0.94) and October ( H = 0.83). In the presence of Brown Trout, Yellowstone Cutthroat Trout growth rates were significantly lower for juvenile (<175 mm) length and adult (≥175 mm) length and mass than in allopatric sites. Allopatric Yellowstone Cutthroat Trout survival was greater across size‐classes; the most pronounced difference was in the age‐2 size‐class (125–175 mm). Together, these results in concert with observed changes in length‐frequency data, indicating a considerable lack of Yellowstone Cutthroat Trout recruitment where they are sympatric with Brown Trout, suggest the negative implications of Brown Trout are notable.

Montana↗

USGS2018

Improved conventional PCR assay for detecting Tetracapsuloides bryosalmonae DNA in fish tissues

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 presence. A new PCR assay to detect T. bryosalmonae 18s rDNA, PKX18s1266f‐1426r, is presented that demonstrates specificity, repeatability, and enhanced sensitivity over the PKX5f‐6r assay. The limit of detection of the PKX18s1266f‐1426r assay at 95% confidence was 100 template copies, and the new primers detected parasite DNA more consistently at template concentrations below 100 copies than did PKX5f‐6r. The PKX18s1266f‐1426r also achieved 100% detection at sample DNA concentrations one order of magnitude lower than PKX5f‐6r. Out of 127 salmonid fish with unknown T. bryosalmonae infection status, PKX5f‐6r detected 35 positive samples, while the new assay detected 43. The discrepancy in T. bryosalmonae detection between the two primer sets may be attributed to several differences between the assays, including oligonucleotide melting temperatures, the use of a touchdown PCR thermal cycle, and amplicon length.

Journal of Aquatic Animal Health↗

USGS2018

Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska

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-based eDNA platform relative to widely used lab-based eDNA approaches for detecting invasive northern pike (Esox lucius) in eight lakes on Alaska’s Kenai Peninsula. The portable, field-based platform takes ~ 1 hr from sample collection to final results and uses a field-based DNA extraction kit, a shelf-stable assay, and a portable real-time PCR thermocycler. Lab-based approaches take days to weeks to months for final results and use lab-based DNA extraction kits, lab-bound assays, and benchtop real-time thermocyclers. We found that the portable, field-based approach was less sensitive than lab-based approaches and was more prone to inhibition, thus increasing potential for false-negatives. Until sensitivity and inhibition issues can be resolved, this portable, field-based approach is best viewed as a complement to rather than a replacement of standard eDNA lab-based approaches.

Alaska↗

USGS2018

The northern pike, a prized native but disastrous invasive: Chapter 14

As the chapters in this book describe, the northern pike Esox lucius Linneaus, 1758 is a fascinating fish that plays an important ecological role in structuring aquatic communities (chapter 8), has the capacity to aid lake restoration efforts (chapter 11), and contributes substantially to local economies, both as a highlysought after sport fish (chapter 12) and as a commercial fishing resource (chapter 13). However, despite the magnificent attributes of this fish, there is another side to its story. Specifically, what happens when northern pike, a highly efficient predator, becomes established outside its natural range? To explore this question, this chapter will investigate observed consequences from many locations where northern pike (hereafter referred to as “pike”) have been introduced and discuss potential reasons why pike, under the right circumstances, can be considered an invasive species.

Book chapter↗