Geology topics

Richard F. Lance

Publications and source records attributed to Richard F. Lance.

6 recordsLinked to original sources

USGS2023

The Government eDNA Working Group 6th Annual eDNA Technical Exchange Workshop

The 6th annual Environmental DNA (eDNA) Technical Exchange Workshop was a virtual workshop hosted and coordinated by the Government eDNA Working Group (GEDWG) on January 24–26, 2023. GEDWG is a no-cost consortium that focuses on bringing together stakeholders associated with federal, state, provincial, municipal, and other government and non-government agencies interested in eDNA and related fields, for the purposes of sharing technical expertise and experience during monthly discussion meetings and annual workshops. Over 400 participants registered for the virtual Workshop, which featured four keynote speakers, 23 platform talks, eight short-form poster presentations, and an extended discussion session. Workshop attendees represented a broad cross-section of disciplines and backgrounds, including research scientists, natural resource managers, and conservation policy experts, and many different government agencies, private environmental consulting firms, trade organizations, non-governmental organizations, and others in the environmental management sector. Key takeaways from the workshop included moving the application of eDNA into resource management and discovering ways to improve policy uptake in the development of nationwide biodiversity monitoring, some of which is happening in the development of eDNA networks and national strategies. Future research directions discussed include studies of fate and transport, autonomous sampling/sample processing, and reference library curation. Additionally, co-design of studies and improved engagement and communication among scientists and managers are needed to ensure clear expectations and outcomes.

Environmental DNA↗

USGS2023

Genetic analysis of North American Phragmites australis guides management approaches

Phragmites australis subsp. australis is an invasive and ecologically detrimental plant in multiple regions of North America. Its co-occurrence with the native subspecies, and multiple instances of hybridization, has created the need to differentiate Phragmites subspecies or haplotypes so that management can be appropriately targeted to the invader. We compiled a review of current genetic discrimination methods among the three Phragmites subspecies inhabiting the United States and Canada, and discussed how each method can contribute to control of the introduced subspecies while preserving the two endemic subspecies. We also discussed various control tools and the implications of Phragmites genetics for implementation. The Phragmites subspecies endemic to North America have environmental or infrastructure significance (e.g., habitat sustainability, biodiversity, storm surge and erosion protection). Thus, faster and more accurate differentiation among the endemic and introduced subspecies is needed. Additionally, more in-depth genetic information on Phragmites subspecies could support better management decisions, as well as the development of improved control treatments. This review highlights technologies and approaches currently available for genetic identification, recently collected genomic, transcriptomic and proteomic information, and implications for biological control and herbicide treatments.

Aquatic Botany↗

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

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↗

USGS2017

Experimental observations on the decay of environmental DNA from bighead and silver carps

Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore decay of eDNA associated with bighead carp ( Hypophthalmichthys nobilis ) biological waste collected from an aquaculture filtration system and with sperm collected from captive silver carp ( H. molitrix ), and how decay may be influenced by differing levels of water turbulence, temperature, microbial load, and pH. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in a decay half-life as much as 5.5× more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5×. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25×, despite relatively little apparent increase in the overall microbial load. This pattern indicated that species constituency of the microbial community, in addition to microbial load, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6× reduction in eDNA halflife. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay condition and a slow decay condition, and tracked eDNA decay over 91 days, we observed a 5.0× greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1× and 3.3×, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate and, thus, the interpretation of eDNA survey results.

Management of Biological Invasions↗

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↗