Geology topics

Patrick Ross Hutchins

Publications and source records attributed to Patrick Ross Hutchins.

7 recordsLinked to original sources

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

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↗

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↗

USGS2021

Time to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies

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 a process that is inconsistent across samples and systemic contamination occurs consistently over a group of samples. Here, we used empirical data and laboratory experiments to (i) estimate the sporadic contamination rate for each stage of a common, targeted eDNA workflow employing best practice quality control measures under simulated conditions of rare and common target DNA presence, (ii) determine the rate at which negative controls (i.e., “blanks”) detect varying concentrations of systemic contamination, and (iii) estimate the effort that would be required to consistently detect sporadic and systemic contamination. Sporadic contamination rates were very low across all eDNA workflow steps, and, therefore, an intractably high number of negative controls (>100) would be required to determine occurrence of sporadic contamination with any certainty. Contrarily, detection of intentionally introduced systemic contamination was more consistent; therefore, very few negative controls (<5) would be needed to consistently alert to systemic contamination. These results have considerable implications to eDNA study design when resources for sample analyses are constrained.

Molecular Ecology Resources↗

USGS2021

Exploration of the 2016 Yellowstone River fish kill and proliferative kidney disease in wild fish populations

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 event shocked scientists, managers, and the public, as this was the first occurrence of the disease in the Yellowstone River, the only reported occurrence of the disease in Montana in the past 25 yr, and arguably the largest wild PKD fish kill in the world. To understand why the Yellowstone River fish kill occurred, we used molecular and historical data to evaluate evidence for several hypotheses: Was the causative parasite Tetracapsuloides bryosalmonae a novel invader, was the fish kill associated with a unique parasite strain, and/or was the outbreak caused by unprecedented environmental conditions? We found that T. bryosalmonae is widely distributed in Montana and have documented occurrence of this parasite in archived fish collected in the Yellowstone River prior to the fish kill. T. bryosalmonae had minimal phylogeographic population structure, as the DNA of parasites sampled from the Yellowstone River and distant water bodies were very similar. These results suggest that T. bryosalmonae could be endemic in Montana. Due to data limitations, we could not reject the hypothesis that the fish kill was caused by a novel and more virulent genetic strain of the parasite. Finally, we found that single‐year environmental conditions are insufficient to explain the cause of the 2016 Yellowstone River PKD outbreak. Other regional rivers where we documented T. bryosalmonae had similar or even more extreme conditions than the Yellowstone River and similar or more extreme conditions have occurred in the Yellowstone River in the recent past, yet mass PKD mortalities have not been documented in either instance. We conclude by placing these results and unresolved hypotheses into the broader context of international research on T. bryosalmonae and PKD, which strongly suggests that a better understanding of bryozoans, the primary host of T. bryosalmonae , is required for better ecosystem understanding.

Montana↗