Geology topics

Erica L. Mize

Publications and source records attributed to Erica L. Mize.

3 recordsLinked to original sources

USGS2019

Environmental DNA assays for invasive populations of the Black Carp, Mylopharyngodon piceus, in North America

The Black Carp, Mylopharyngodon piceus, is an increasingly widespread invasive species in North America that threatens freshwater mussel populations. We developed four qPCR assays for detecting environmental DNA (eDNA) from these Black Carp populations. Assays were designed to target four mitochondrial DNA loci and were based on 34 complete mitochondrial genome sequences, including 29 generated in this study from samples obtained in three countries. Assays were validated for taxon specificity with in silico comparisons against archived DNA sequences and with in vitro tests of 41 DNA samples from Black Carp, as well as DNA samples from 30 non‐target fish species, all from the Mississippi River Basin. All four assays were able to detect the DNA of all Black Carp samples and did not exhibit any positive results with DNA from other tested species. Tests conducted in round‐robin fashion among three different laboratories found that all four assays were able to detect DNA at very low template concentrations (limits of detection = 3 copies/qPCR, limits of quantification = 16‐64 copies/qPCR) and, as part of in situ validation, were successful in detecting eDNA from Black Carp in aquaculture ponds. Despite some challenges with other attempts at in situ validation, the assays were also effective in detecting Black Carp eDNA in water samples from a drainage ditch in the upper reaches of the species’ range that was known to contain juvenile Black Carp, as well as in water samples from the Missisippi River and a connected oxbow lake in the lower reaches of the species range.

Transactions of the American Fisheries Society↗

USGS2019

Refinement of eDNA as an early monitoring tool at the landscape-level: Study design considerations

Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertainties created by imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR). Occurrence models can be used to address these challenges, thus we use an occurrence model to address two objectives: First, determine how many samples were required to detect species using eDNA; Second, examine when and where to take samples. We collected water samples from three different habitat types in the Upper Mississippi River when both Bighead Carp and Silver Carp were known to be present based on telemetry detections. Each habitat type (backwater, tributary, and impoundment) was sampled during April, May and November. Detections of eDNA for both species varied across sites and months, but were generally low, 0 - 19.3% of samples were positive for eDNA. Overall, we found that eDNA-based sampling holds promise to be a powerful monitoring tool for resource managers, however, limitations of eDNA-based sampling include different biological and ecological characteristics of target species such as seasonal habitat usage patterns as well as aspects of different physical environments that impact the implementation of these methods such as water temperature.

Ecological Applications↗

USGS2019

Sampling designs for landscape-level eDNA monitoring programs using three-level occurrence models

Resource managers conduct landscape-level monitoring using environmental DNA (eDNA). These managers must contend with imperfect detection in samples and sub-samples (i.e., molecular analyses). This imperfect detection impacts their ability to both detect species and estimate occurrence. Although occurrence (synonymously occupancy) models can estimate these probabilities, most models and guidance for their application do not consider three levels. We studied this with three aims. First, we examined the number of samples required to detect a species at a site given imperfect detection. Second, we examined the ability of a three-level occurrence model to recover parameter estimates. Third, we examined the number of samples required to reliably recover parameter estimates. We found detecting eDNA in 1 sample at a site required 12 samples under most condition, but detection eDNA in situations that might be expected when looking for species at very low abundance required >50 samples. We found our occupancy model generally recovered known parameters unless detection and sample occurrence probabilities were <0.3. In these situations, >50 samples per site and 8 molecular replicates were required. Conversely, estimating and comparing occurrence and detection probabilities for species with moderate to high abundance may require 4 molecular replicates and 20-30 samples per site. More broadly, our findings illustrate the importance of study design, sample sizes, and molecular replicates for eDNA-based research, monitoring, and management.

Integrated Environmental Assessment and Management↗