Geology topics

Caren S. Goldberg

Publications and source records attributed to Caren S. Goldberg.

At least 19 recordsLinked to original sources

USGS2024

Comparison of two methods to detect the northwestern pond turtle (Actinemys marmorata) and the invasive American bullfrog (Lithobates catesbeianus) in interior northern California

Knowledge about the distributions of species and the variables influencing their occurrence is important for their management and conservation, but factors affecting occurrence can vary across the range of a species. Northwestern pond turtles ( Actinemys marmorata ) are widespread generalist turtles, but are nonetheless of conservation concern throughout their range. To better understand the distribution of northwestern pond turtles and introduced American bullfrogs ( Lithobates catesbeianus ), we surveyed streams on private timberlands of the interior foothills of northern California using visual encounter surveys and collecting samples of environmental DNA. We found that northwestern pond turtle occurrence was negatively related to elevation in our sampling frame. Detection probabilities with environmental DNA were approximately twice those of visual encounter surveys, but both methods were effective for detecting turtles in streams. American bullfrogs were detected in a single sample at each of 2 sites (one by environmental DNA, one by visual encounter surveys). Management for northwestern pond turtles in forest streams within our sample area will likely have the largest effect at lower elevation sites where turtles are most likely to occur.

California↗

USGS2023

Successful eradication of invasive American bullfrogs leads to coextirpation of emerging pathogens

Interventions of the host–pathogen dynamics provide strong tests of relationships, yet they are still rarely applied across multiple populations. After American bullfrogs ( Rana catesbeiana ) invaded a wildlife refuge where federally threatened Chiricahua leopard frogs ( R. chiricahuensis ) were reintroduced 12 years prior, managers launched a landscape-scale eradication effort to help ensure continued recovery of the native species. We used a before-after-control-impact design and environmental DNA sampling of 19 eradication sites and 18 control sites between fall 2016 and winter 2020–2021 to measure community-level responses to bullfrog eradication, including for two pathogens. Dynamic occupancy models revealed successful eradication from 94% of treatment sites. Native amphibians did not respond to bullfrog eradication, but the pathogens amphibian chytrid fungus ( Batrachochytrium dendrobatidis ) and ranaviruses were coextirpated with bullfrogs. Our spatially replicated experimental approach provides strong evidence that management of invasive species can simultaneously reduce predation and disease risk for imperiled species.

Arizona↗

USGS2023

Empirical evidence for effects of invasive American Bullfrogs on occurrence of native amphibians and emerging pathogens

Invasive species and emerging infectious diseases are two of the greatest threats to biodiversity. American Bullfrogs ( Rana [ Lithobates ] catesbeiana ), which have been introduced to many parts of the world, are often linked with declines of native amphibians via predation and spreading emerging pathogens such as amphibian chytrid fungus ( Batrachochytrium dendrobatidis [Bd]) and ranaviruses. Although many studies have investigated the potential role of bullfrogs in declines of native amphibians, analyses that account for shared habitat affinities and imperfect detection have found limited support for clear effects. Similarly, the role of bullfrogs in shaping the patch-level distribution of pathogens is unclear. We used eDNA methods to sample 233 sites in the southwestern USA and Sonora, Mexico (2016–2018) to estimate how presence of bullfrogs affects occurrence of 4 native amphibians, Bd, and ranaviruses. Based on 2-species, dominant-subordinate occupancy models fitted in a Bayesian context, federally threatened Chiricahua Leopard Frogs ( R. chiricahuensis ) and Western Tiger Salamanders ( Ambystoma mavortium ) were 8 times (32% vs. 4%) and 2 times (36% vs. 18%), respectively, less likely to occur at sites where bullfrogs occurred. Evidence for negative effects of bullfrogs on Lowland Leopard Frogs ( R. yavapaiensis ) and Northern Leopard Frogs ( R. pipiens ) was less clear, possibly because of smaller numbers of sites where these native species still occur and because bullfrogs often occur at lower densities in streams, the primary habitat for Lowland Leopard Frogs. At the community level, Bd was most likely to occur where bullfrogs co-occurred with native amphibians, which could increase risk to native species. Ranaviruses were estimated to occur at 33% of bullfrog-only sites, 10% of sites where bullfrogs and native amphibians co-occurred, and only 3% of sites where only native amphibians occurred. Of the 85 sites where we did not detect any of the 5 target amphibian species, we also did not detect Bd or ranaviruses; this suggests other hosts do not drive the distribution of these pathogens in our study area. Our results provide landscape-scale evidence that bullfrogs reduce occurrence of native amphibians and increase occurrence of pathogens, information that can clarify risks and aid the prioritization of conservation actions.

Ecological Applications↗

USGS2022

Scat as a source of DNA for population monitoring

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition, ecological impacts of removing scat, and zoonotic risks. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii , California, US, and Morafka's desert tortoise, G. morafkai , Arizona, US) and the common chuckwalla (Sauromalus atar ) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, varied between studies, with 15% for Agassiz's desert tortoise and 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study demonstrates that genotypes can successfully be obtained from swabs of herbivorous reptile scat collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for genetic identification of individuals from non-invasive samples.

Arizona, California↗

USGS2022

Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Estuaries and Coasts↗

USGS2022

Identifying factors linked with persistence of reintroduced populations: Lessons learned from 25 years of amphibian translocations

Conservation translocations are increasingly used to help recover imperiled species. However, success of establishing populations remains low, especially for amphibians. Identifying factors associated with translocation success can help increase efficiency and efficacy of recovery efforts. Since the 1990s, several captive and semi-captive facilities have produced Chiricahua Leopard Frogs ( Rana chiricahuensis ) to establish or augment wild populations in Arizona and New Mexico, USA. During this same time, personnel associated with several programs surveyed translocation and non-translocation sites for presence of amphibians. We used 25 years (1995–2019) of survey and translocation data for the federally threatened Chiricahua Leopard Frog to identify factors linked with population persistence. Our dataset included approximately 40,642 egg masses or animals translocated in 314 events to 115 distinct sites and > 5800 visual encounter surveys from 641 sites; 120 of these sites were also surveyed with environmental DNA methods in 2018. We used a hierarchical dynamic occupancy model that accounted for imperfect detection to identify patch- and landscape-level attributes associated with site occupancy, and then used predictions from that model to evaluate factors associated with population persistence at translocation sites. Across all sites, extinction probability for Chiricahua Leopard Frogs was higher in lotic (stream) than lentic (pond) habitats and when Western Tiger Salamanders ( Ambystoma mavortium ) were present. Restoration of sites specifically for frog conservation reduced extinction probability. Colonization of unoccupied sites increased moderately with increasing numbers of translocation sites within 2 km, indicating a benefit of translocation efforts beyond sites where frogs were stocked. At translocation sites, persistence was greater in lentic than lotic habitats and was negatively correlated with the proportion of years tiger salamanders were present. Increasing numbers of translocation events, especially of late-stage larvae, increased persistence. There was little difference in population persistence based on whether stock was from captive, semi-captive, or wild sources, but translocations during the dry season (January— July) succeeded more than those after the typical arrival of summer rains (August— December). Based on the number of years translocation sites were predicted to be occupied, 2 or more translocations produced, on average, a > 4-yr increase in predicted occupancy compared to sites without translocations. While translocations have increased the number of populations across the landscape, continued management of water availability and threats such as invasive predators and disease remain critical to recovery of the Chiricahua Leopard Frog.

Arizona, New Mexico↗

USGS2021

Distribution of tiger salamanders in northern Sonora, Mexico: Comparison of sampling methods and possible implications for an endangered subspecies

Many aquatic species in the arid USA-Mexico borderlands region are imperiled, but limited information on distributions and threats often hinders management. To provide information on the distribution of the Western Tiger Salamander ( Ambystoma mavortium ), including the USA-federally endangered Sonoran Tiger Salamander ( Ambystoma mavortium stebbinsi ), we used traditional (seines, dip-nets) and modern (environmental DNA [eDNA]) methods to sample 91 waterbodies in northern Sonora, Mexico, during 2015-2018. The endemic Sonoran Tiger Salamander is threatened by introgressive hybridization and potential replacement by another sub-species of the Western Tiger Salamander, the non-native Barred Tiger Salamander ( A. m. mavortium ). Based on occupancy models that accounted for imperfect detection, eDNA sampling provided a similar detection probability (0.82 [95% CI: 0.56-0.94]) as seining (0.83 [0.46-0.96]) and much higher detection than dip-netting (0.09 [0.02-0.23]). Volume of water filtered had little effect on detection, possibly because turbid sites had greater densities of salamanders. Salamanders were estimated to occur at 51 sites in 3 river drainages in Sonora. These results indicate tiger salamanders are much more widespread in northern Sonora than previously documented, perhaps aided by changes in land and water management practices. However, because the two subspecies of salamanders cannot be reliably distinguished based on morphology or eDNA methods that are based on mitochondrial DNA, we are uncertain if we detected only native genotypes or if we documented recent invasion of the area by the non-native sub-species. Thus, there is an urgent need for methods to reliably distinguish the subspecies so managers can identify appropriate interventions.

Sonora↗

USGS2021

Low occurrence of ranavirus in the Prairie Pothole Region of Montana and North Dakota (USA) contrasts with prior surveys

Ranaviruses are emerging pathogens that have caused mortality events in amphibians worldwide. Despite the negative effects of ranaviruses on amphibian populations, monitoring efforts are still lacking in many areas, including in the Prairie Pothole Region (PPR) of North America. Some PPR wetlands in Montana and North Dakota (USA) have been contaminated by energy-related saline wastewaters, and increased salinity has been linked to greater severity of ranavirus infections. In 2017, we tested tissues from larvae collected at 7 wetlands that ranged in salinity from 26 to 4103 mg Cl l -1 . In 2019, we used environmental DNA (eDNA) to test for ranaviruses in 30 wetlands that ranged in salinity from 26 to 11754 mg Cl l -1 . A previous study (2013-2014) found that ranavirus-infected amphibians were common across North Dakota, including in some wetlands near our study area. Overall, only 1 larva tested positive for ranavirus infection, and we did not detect ranavirus in any eDNA samples. There are several potential reasons why we found so little evidence of ranaviruses, including low larval sample sizes, mismatch between sampling and disease occurrence, larger pore size of our eDNA filters, temporal variation in outbreaks, low host abundance, or low occurrence or prevalence of ranaviruses in the wetlands we sampled. We suggest future monitoring efforts be conducted to better understand the occurrence and prevalence of ranaviruses within the PPR.

Montana, North Dakota↗

USGS2020

Occurrence of a suite of stream-obligate amphibians in timberlands of Mendocino County, California, examined using environmental DNA

Stream-obligate amphibians are important indicators of ecosystem health in the Pacific Northwest, but distributional information to improve forest management is lacking in many regions. We analyzed archived DNA extracted from water samples in 60 pools in streams on private timberlands in Mendocino County, California, for 3 California Species of Special Concern—Coastal Tailed Frogs ( Ascaphus truei ), Foothill Yellow-legged Frogs ( Rana boylii ), and Southern Torrent Salamanders ( Rhyacotriton variegatus )—to better understand their distributions in the region. Detection probabilities for eDNA of Foothill Yellow-legged Frogs and Coastal Tailed Frogs were positively influenced by water temperature. eDNA occurrence for both frogs was affected by whether silt or organic matter was a dominant substrate in the sampled pool, and Foothill Yellow-legged Frog eDNA occurrence was also affected by water temperature. Foothill Yellow-legged Frog eDNA occurrence had a strong, positive association with water temperature, with occurrence unlikely below 14°C and very likely above 16°C, and a positive association with silt or organic substrates in pools, which was likely an indicator of higher-order stream reaches. In contrast, Coastal Tailed Frogs had a negative association with silt or organic substrates. Historical visual detections were generally congruent with findings using eDNA, but differences highlight important areas for further study. We did not detect Southern Torrent Salamanders using eDNA at any sites. Our study reinforces that ecological relationships of these species are varied, and shows the importance of maintaining the integrity of streams with diverse characteristics for conserving stream amphibians.

California↗

USGS2019

Reporting the limits of detection and quantification for environmental DNA assays

Background Environmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully established, with one area being the calculation and interpretation of assay limit of detection (LOD) and limit of quantification (LOQ). Aims Here, we propose establishing consistent methods for determining and reporting of LOD and LOQ for single‐species quantitative PCR (qPCR) eDNA studies. Materials & Methods/ Results We utilize datasets from multiple cooperating laboratories to demonstrate both a discrete threshold approach and a curve‐fitting modeling approach for determining LODs and LOQs for eDNA qPCR assays. We also provide details of an R script developed and applied for the modeling method. Discussion/Conclusions Ultimately, standardization of how LOD and LOQ are determined, interpreted, and reported for eDNA assays will allow for more informed interpretation of assay results, more meaningful interlaboratory comparisons of experiments, and enhanced capacity for assessing the relative technical quality and performance of different eDNA qPCR assays.

Environmental DNA↗

USGS2018

An analytical framework for estimating aquatic species density from environmental DNA

Environmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. The modeling combines eDNA and animal count data from a subset of sites to estimate species density (and associated uncertainties) at other sites where only eDNA data are available. As a proof of concept, we first perform a cross-validation study using experimental data on carp in mesocosms. In these data, fish densities are known without error, which allows us to test the performance of the method with known data. We then evaluate the model using field data from a study on a stream salamander species to assess the potential of this method to work in natural settings, where density can never be known with absolute certainty. Two alternative distributions (Normal and Negative Binomial) to model variability in eDNA concentration data are assessed. Assessment based on the proof of concept data (carp) revealed that the Negative Binomial model provided much more accurate estimates than the model based on a Normal distribution, likely because eDNA data tend to be overdispersed. Greater imprecision was found when we applied the method to the field data, but the Negative Binomial model still provided useful density estimates. We call for further model development in this direction, as well as further research targeted at sampling design optimization. It will be important to assess these approaches on a broad range of study systems.

Ecology and Evolution↗

USGS2016

Critical considerations for the application of environmental DNA methods to detect aquatic species

Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

Methods in Ecology and Evolution↗

USGS2015

Environmental DNA sampling protocol - filtering water to capture DNA from aquatic organisms

Environmental DNA (eDNA) analysis is an effective method of determining the presence of aquatic organisms such as fish, amphibians, and other taxa. This publication is meant to guide researchers and managers in the collection, concentration, and preservation of eDNA samples from lentic and lotic systems. A sampling workflow diagram and three sampling protocols are included as well as a list of suggested supplies. Protocols include filter and pump assembly using: (1) a hand-driven vacuum pump, ideal for sample collection in remote sampling locations where no electricity is available and when equipment weight is a primary concern; (2) a peristaltic pump powered by a rechargeable battery-operated driver/drill, suitable for remote sampling locations when weight consideration is less of a concern; (3) a 120-volt alternating current (AC) powered peristaltic pump suitable for any location where 120-volt AC power is accessible, or for roadside sampling locations. Images and detailed descriptions are provided for each step in the sampling and preservation process.

Techniques and Methods↗

USGS2015

Assessment of environmental DNA for detecting presence of imperiled aquatic amphibian species in isolated wetlands

Environmental DNA (eDNA) is an emerging tool that allows low-impact sampling for aquatic species by isolating DNA from water samples and screening for DNA sequences specific to species of interest. However, researchers have not tested this method in naturally acidic wetlands that provide breeding habitat for a number of imperiled species, including the frosted salamander ( Ambystoma cingulatum ), reticulated flatwoods salamanders ( Ambystoma bishopi ), striped newt ( Notophthalmus perstriatus ), and gopher frog ( Lithobates capito ). Our objectives for this study were to develop and optimize eDNA survey protocols and assays to complement and enhance capture-based survey methods for these amphibian species. We collected three or more water samples, dipnetted or trapped larval and adult amphibians, and conducted visual encounter surveys for egg masses for target species at 40 sites on 12 different longleaf pine ( Pinus palustris ) tracts. We used quantitative PCRs to screen eDNA from each site for target species presence. We detected flatwoods salamanders at three sites with eDNA but did not detect them during physical surveys. Based on the sample location we assumed these eDNA detections to indicate the presence of frosted flatwoods salamanders. We did not detect reticulated flatwoods salamanders. We detected striped newts with physical and eDNA surveys at two wetlands. We detected gopher frogs at 12 sites total, three with eDNA alone, two with physical surveys alone, and seven with physical and eDNA surveys. We detected our target species with eDNA at 9 of 11 sites where they were present as indicated from traditional surveys and at six sites where they were not detected with traditional surveys. It was, however, critical to use at least three water samples per site for eDNA. Our results demonstrate eDNA surveys can be a useful complement to traditional survey methods for detecting imperiled pond-breeding amphibians. Environmental DNA may be particularly useful in situations where detection probability using traditional survey methods is low or access by trained personnel is limited.

Alabama, Florida, Georgia, South Carolina↗

USGS2015

Characterizing the distribution of an endangered salmonid using environmental DNA analysis

Determining species distributions accurately is crucial to developing conservation and management strategies for imperiled species, but a challenging task for small populations. We evaluated the efficacy of environmental DNA (eDNA) analysis for improving detection and thus potentially refining the known distribution of Chinook salmon ( Oncorhynchus tshawytscha ) in the Methow and Okanogan Subbasins of the Upper Columbia River, which span the border between Washington, USA and British Columbia, Canada. We developed an assay to target a 90 base pair sequence of Chinook DNA and used quantitative polymerase chain reaction (qPCR) to quantify the amount of Chinook eDNA in triplicate 1-L water samples collected at 48 stream locations in June and again in August 2012. The overall probability of detecting Chinook with our eDNA method in areas within the known distribution was 0.77 (±0.05 SE). Detection probability was lower in June (0.62, ±0.08 SE) during high flows and at the beginning of spring Chinook migration than during base flows in August (0.93, ±0.04 SE). In the Methow subbasin, mean eDNA concentration was higher in August compared to June, especially in smaller tributaries, probably resulting from the arrival of spring Chinook adults, reduced discharge, or both. Chinook eDNA concentrations did not appear to change in the Okanogan subbasin from June to August. Contrary to our expectations about downstream eDNA accumulation, Chinook eDNA did not decrease in concentration in upstream reaches (0–120 km). Further examination of factors influencing spatial distribution of eDNA in lotic systems may allow for greater inference of local population densities along stream networks or watersheds. These results demonstrate the potential effectiveness of eDNA detection methods for determining landscape-level distribution of anadromous salmonids in large river systems.

British Columbia, Washington↗

USGS2015

Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms

The discovery that macroorganisms can be detected from their environmental DNA (eDNA) in aquatic systems has immense potential for the conservation of biological diversity. This special issue contains 11 papers that review and advance the field of eDNA detection of vertebrates and other macroorganisms, including studies of eDNA production, transport, and degradation; sample collection and processing to maximize detection rates; and applications of eDNA for conservation using citizen scientists. This body of work is an important contribution to the ongoing efforts to take eDNA detection of macroorganisms from technical breakthrough to established, reliable method that can be used in survey, monitoring, and research applications worldwide. While the rapid advances in this field are remarkable, important challenges remain, including consensus on best practices for collection and analysis, understanding of eDNA diffusion and transport, and avoidance of inhibition in sample collection and processing. Nonetheless, as demonstrated in this special issue, eDNA techniques for research and monitoring are beginning to realize their potential for contributing to the conservation of biodiversity globally.

Biological Conservation↗

USGS2013

Factors influencing detection of eDNA from a stream-dwelling amphibian

Environmental DNA (eDNA) methods for detecting and estimating abundance of aquatic species are emerging rapidly, but little is known about how processes such as secretion rate, environmental degradation, and time since colonization or extirpation from a given site affect eDNA measurements. Using stream-dwelling salamanders and quantitative PCR (qPCR) analysis, we conducted three experiments to assess eDNA: (i) production rate; (ii) persistence time under different temperature and light conditions; and (iii) detectability and concentration through time following experimental introduction and removal of salamanders into previously unoccupied streams. We found that 44–50 g individuals held in aquaria produced 77 ng eDNA/h for 2 h, after which production either slowed considerably or began to equilibrate with degradation. eDNA in both full-sun and shaded treatments degraded exponentially to <1% of the original concentration after 3 days. eDNA was no longer detectable in full-sun samples after 8 days, whereas eDNA was detected in 20% of shaded samples after 11 days and 100% of refrigerated control samples after 18 days. When translocated into unoccupied streams, salamanders were detectable after 6 h, but only when densities were relatively high (0.2481 individuals/m 2 ) and when samples were collected within 5 m of the animals. Concentrations of eDNA detected were very low and increased steadily from 6–24 h after introduction, reaching 0.0022 ng/L. Within 1 h of removing salamanders from the stream, eDNA was no longer detectable. These results suggest that eDNA detectability and concentration depend on production rates of individuals, environmental conditions, density of animals, and their residence time.

Molecular Ecology Resources↗

USGS2013

Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.

Canadian Journal of Fisheries and Aquatic Sciences↗