Geology topics

John A. Darling

Publications and source records attributed to John A. Darling.

7 recordsLinked to original sources

USGS2025

What is eDNA method standardization and why do we need it?

The rapid advancement of environmental DNA ( eDNA ) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.

Metabarcoding and Metagenomics↗

USGS2024

National Aquatic Environmental DNA Strategy

Aquatic life is the engine of ecosystems and economies. In environments ranging from freshwater through marine, this biodiversity underpins the health, culture, opportunities, and economic wellbeing of the Nation -- from local communities to the entire country. The ability to evaluate the status, trends, and future projections of nature is key to maintaining national prosperity, and this requires timely and trusted information about the condition of aquatic biodiversity on a vast scale. With one of the largest Exclusive Economic Zones in the world and extensive estuaries, lakes, rivers and streams, it is a grand challenge for the United States to explore, monitor, and understand aquatic life.

Report↗

USGS2021

What do you mean by false positive?

Misunderstandings regarding the term “false positive” present a significant hurdle to broad adoption of eDNA monitoring methods. Here, we identify three challenges to clear communication of false-positive error between scientists, managers, and the public. The first arises from a failure to distinguish between false-positive eDNA detection at the sample level and false-positive inference of taxa presence at the site level. The second is based on the large proportion of false positives that may occur when true-positive detections are likely to be rare, even when rates of contamination or other error are low. And the third misunderstanding occurs when conventional species detection approaches, often based on direct capture, are used to confirm eDNA approaches without acknowledging or quantifying the conventional approach's detection probability. The solutions to these issues include careful and consistent communication of error definitions, managing expectations of error rates, and providing a balanced discussion not only of alternative sources of species DNA, but also of the detection limitations of conventional methods. We argue that the benefit of addressing these misunderstandings will be increased confidence in the utility of eDNA methods and, ultimately, improved resource management using eDNA approaches.

Environmental DNA↗

USGS2021

Satellite remote sensing to assess cyanobacterial bloom frequency across the United States at multiple spatial scales

Cyanobacterial blooms can have negative effects on human health and local ecosystems. Field monitoring of cyanobacterial blooms can be costly, but satellite remote sensing has shown utility for more efficient spatial and temporal monitoring across the United States. Here, satellite imagery was used to assess the annual frequency of surface cyanobacterial blooms, defined for each satellite pixel as the percentage of images for that pixel throughout the year exhibiting detectable cyanobacteria . Cyanobacterial frequency was assessed across 2,196 large lakes in 46 states across the continental United States (CONUS) using imagery from the European Space Agency’s Ocean and Land Colour Instrument for the years 2017 through 2019. In 2019, across all satellite pixels considered, annual bloom frequency had a median value of 4% and a maximum value of 100%, the latter indicating that for those satellite pixels, a cyanobacterial bloom was detected by the satellite sensor for every satellite image considered. In addition to annual pixel-scale cyanobacterial frequency, results were summarized at the lake- and state-scales by averaging annual pixel-scale results across each lake and state. For 2019, average annual lake-scale frequencies also had a maximum value of 100%, and Oregon and Ohio had the highest average annual state-scale frequencies at 65% and 52%. Pixel-scale frequency results can assist in identifying portions of a lake that are more prone to cyanobacterial blooms, while lake- and state-scale frequency results can assist in the prioritization of sampling resources and mitigation efforts. Satellite imagery is limited by the presence of snow and ice, as imagery collected in these conditions are quality flagged and discarded. Thus, annual bloom frequencies within nine climate regions were investigated to determine whether missing data biased results in climate regions more prone to snow and ice, given that their annual summaries would be weighted toward the summer months when cyanobacterial blooms tend to occur. Results were unbiased by the time period selected in most climate regions, but a large bias was observed for the Northwest Rockies and Plains climate region. Moderate biases were observed for the Ohio Valley and the Southeast climate regions. Finally, a clustering analysis was used to identify areas of high and low cyanobacterial frequency across CONUS based on average annual lake-scale cyanobacterial frequencies for 2019. Several clusters were identified that transcended state, watershed, and eco-regional boundaries. Combined with additional data, results from the clustering analysis may offer insight regarding large-scale drivers of cyanobacterial blooms.

Ecological Indicators↗

USGS2018

Trends in nonindigenous aquatic species richness in the United States reveal shifting spatial and temporal patterns of species introductions

Understanding the spatial and temporal dynamics underlying the introduction and spread of nonindigenous aquatic species (NAS) can provide important insights into the historical drivers of biological invasions and aid in forecasting future patterns of nonindigenous species arrival and spread. Increasingly, public databases of species observation records are being used to quantify changes in NAS distributions across space and time, and are becoming an important resource for researchers, managers, and policy-makers. Here we use publicly available data to describe trends in NAS introduction and spread across the conterminous United States over more than two centuries of observation records. Available data on first records of NAS reveal significant shifts in dominance of particular introduction patterns over time, both in terms of recipient regions and likely sources. These spatiotemporal trends at the continental scale may be subject to biases associated with regional variation in sampling effort, reporting, and data curation. We therefore also examined two additional metrics, the number of individual records and the spatial coverage of those records, which are likely to be more closely associated with sampling effort. Our results suggest that broad-scale patterns may mask considerable variation across regions, time periods, and even entities contributing to NAS sampling. In some cases, observed temporal shifts in species discovery may be influenced by dramatic fluctuations in the number and spatial extent of individual observations, reflecting the possibility that shifts in sampling effort may obscure underlying rates of NAS introduction.

Aquatic Invasions↗

USGS2017

Satellite monitoring of cyanobacterial harmful algal bloom frequency in recreational waters and drinking water sources

Cyanobacterial harmful algal blooms (cyanoHAB) cause extensive problems in lakes worldwide, including human and ecological health risks, anoxia and fish kills, and taste and odor problems. CyanoHABs are a particular concern in both recreational waters and drinking water sources because of their dense biomass and the risk of exposure to toxins. Successful cyanoHAB assessment using satellites may provide an indicator for human and ecological health protection. In this study, methods were developed to assess the utility of satellite technology for detecting cyanoHAB frequency of occurrence at locations of potential management interest. The European Space Agency's MEdium Resolution Imaging Spectrometer (MERIS) was evaluated to prepare for the equivalent series of Sentinel-3 Ocean and Land Colour Imagers (OLCI) launched in 2016 as part of the Copernicus program. Based on the 2012 National Lakes Assessment site evaluation guidelines and National Hydrography Dataset, the continental United States contains 275,897 lakes and reservoirs >1 ha in area. Results from this study show that 5.6% of waterbodies were resolvable by satellites with 300 m single-pixel resolution and 0.7% of waterbodies were resolvable when a three by three pixel (3 × 3-pixel) array was applied based on minimum Euclidian distance from shore. Satellite data were spatially joined to U.S. public water surface intake (PWSI) locations, where single-pixel resolution resolved 57% of the PWSI locations and a 3 × 3-pixel array resolved 33% of the PWSI locations. Recreational and drinking water sources in Florida and Ohio were ranked from 2008 through 2011 by cyanoHAB frequency above the World Health Organization’s (WHO) high threshold for risk of 100,000 cells mL −1 . The ranking identified waterbodies with values above the WHO high threshold, where Lake Apopka, FL (99.1%) and Grand Lake St. Marys, OH (83%) had the highest observed bloom frequencies per region. The method presented here may indicate locations with high exposure to cyanoHABs and therefore can be used to assist in prioritizing management resources and actions for recreational and drinking water sources.

Florida, Ohio↗

USGS2013

Geographic range and structure of cryptic genetic diversity among Pacific North American populations of the non-native amphipod Grandidierella japonica

Reconstructing the invasion history of aquatic invasive species can enhance understanding of invasion risks by recognizing areas most susceptible to invasion and forecasting future spread based on past patterns of population expansion. Here we reconstruct the invasion history of the Japanese amphipod Grandidierella japonica Stephensen 1938 combining information from historical collection data with molecular genetic data to better understand post-invasion range expansion and anthropogenic connectivity across the Pacific coast of North America. Compilation of collection data from bays and estuaries of the Pacific North American coast show many new localities have been colonized in the last two decades, moving outward from harbors and bays with high commercial traffic into smaller coastal locations dominated by local recreational traffic. DNA barcode sequence data for G. japonica reveals two distinct clades: one found in San Francisco Bay and sites to the north, and one also found in San Francisco Bay and sites to the south. The two clades differ by an average 7.28 % genetic distance, large enough to consider these invasive amphipods two separate species. Both northern and southern clades exhibit low levels of genetic diversity, suggesting a single introduction event for each. The presence of cryptic diversity within this invasive amphipod highlights the need for more extensive study of the invasive and native populations of aquatic invasive invertebrates to address questions of taxonomy, diversity, and invasion history.

California, Oregon, Washington↗