Geology topics

Jacob R. Williams

Publications and source records attributed to Jacob R. Williams.

5 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

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↗

USGS2021

Quantifying the spatial structure of invasive lake trout in Yellowstone Lake to improve suppression efficacy

Invasive Lake Trout Salvelinus namaycush have altered the once-pristine Yellowstone Lake ecosystem through top-down effects by consuming Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri . To conserve Yellowstone Cutthroat Trout and restore the ecosystem, a Lake Trout gillnetting program was implemented to suppress the invasive population. We evaluated the spatial structure of Lake Trout in Yellowstone Lake with the intent of increasing suppression efficiency. Specifically, we addressed questions related to adult Lake Trout aggregation and movement during summer and autumn (spawning) periods and how Lake Trout used locations in the context of suppression efforts. We tracked 373 Lake Trout (>500 mm TL) during the summer and autumn of 2016 and 2017. Based on kernel density estimates, Lake Trout were highly aggregated at 9 locations during summer and 22 locations during the spawning period. Using a novel metric, individual days (product of mean individuals per survey and mean length of stay), five summer locations and five spawning locations had at least 30 individual days. These locations are suggested as priority areas for targeting Lake Trout suppression. Lake Trout were less aggregated and moved less during the summer, making them less vulnerable to a passive gear in the summer than during the autumn spawning period. Lake Trout exhibited low spawning site fidelity compared to populations elsewhere, possibly due to decades of intensive gill netting at spawning locations. Given the aggregation and movement patterns observed in Yellowstone Lake, continuing to target adult Lake Trout during the spawning period is the most cost-effective approach to Lake Trout suppression.

Wyoming↗

USGS2020

Targeting aggregations of telemetered Lake Trout to increase gillnetting suppression efficacy

Conserving Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri by suppressing invasive Lake Trout Salvelinus namaycush in Yellowstone Lake is a high priority for Yellowstone National Park resource managers. Here, we tested whether targeting telemetered Lake Trout could increase the efficacy of Lake Trout suppression by gill netting. Mobile acoustic tracking surveys were performed to identify aggregations of tagged Lake Trout in summer (June–August) 2017. Lake Trout aggregations were relayed daily to suppression crews by phone, radio, or text and a printed map. Suppression crews set 30 large-mesh gill nets targeting telemetered Lake Trout aggregations (target treatment) and 124 large-mesh gill nets not targeting telemetered aggregations (nontarget treatment). Mean log e (CPUE) was higher for the target treatment (0.37; 95% credible interval [CRI] = 0.08–0.65) than for the nontarget treatment (−0.37; 95% CRI = −0.51 to −0.21). Mean of the target treatment was higher than the mean of the nontarget treatment for over 99% of the 1,000 draws from the joint posterior distribution. Because of telemetry costs, mean CPUE per US$10,000 spent was similar between the target treatment (0.20; 95% CRI = 0.15–0.26) and the nontarget treatment (0.15; 95% CRI = 0.13–0.17). Telemetry is an effective strategy for improving Lake Trout CPUE, which corresponds to an increased efficiency in the Lake Trout suppression program.

Wyoming↗