W. Lindsay Chadderton

Environmental Conditions Influence eDNA Persistence in Aquatic Systems

Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments.

In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.

Aquatic Invasive Species Transport via Trailered Boats: What is Being Moved, Who is Moving it, and What Can Be Done

Abstract Trailered boats have been implicated in the spread of aquatic invasive species. There has been, however, little empirical research on the type and quantity of aquatic invasive species being transported, nor on the efficacy of management interventions (e.g., inspection crews, boat washing). In a study of small-craft boats and trailers, we collected numerous aquatic and terrestrial organisms, including some species that are morphologically similar to known aquatic invasive species. Additionally, a mail survey of registered boaters (n = 944, 11% response rate) and an in-person survey of boaters in the field (n = 459, 90% response rate) both indicated that more than twothirds of boaters do not always take steps to clean their boats. Furthermore, we used a controlled experiment to learn that visual inspection and hand removal can reduce the amount of macrophytes on boats by 88% ± 5% (mean ± SE), with high-pressure washing equally as effective (83% ± 4%) and low-pressure washing less so (62% ± 3% remov...

Viability of Aquatic Plant Fragments following Desiccation

Abstract Desiccation following prolonged air exposure challenges survival of aquatic plants during droughts, water drawdowns, and overland dispersal. To improve predictions of plant response to air exposure, we observed the viability of vegetative fragments of 10 aquatic plant species (Cabomba caroliniana, Ceratophyllum demersum, Elodea canadensis, Egeria densa, Myriophyllum aquaticum, Myriophyllum heterophyllum, Myriophyllum spicatum, Potamogeton crispus, Potamogeton richardsonii, and Hydrilla verticillata) following desiccation. We recorded mass loss, desiccation rate, and plant fragment survival across a range of air exposures. Mass loss accurately predicted viability of aquatic plant fragments upon reintroduction to water. However, similar periods of air exposure differentially affected viability between species. Understanding viability following desiccation can contribute to predicting dispersal, improving eradication protocols, and disposing of aquatic plants following removal from invaded lakes or contaminated equipment. Nomenclature: Brazilian egeria, Egeria densa Planch., common elodea, Elodea canadensis Michx., coontail, Ceratophyllum demersum L., curlyleaf pondweed, Potamogeton crispus L., Eurasian watermilfoil, Myriophyllum spicatum L., fanwort, Cabomba caroliniana Gray, hydrilla, Hydrilla verticillata (L. f.) Royle, parrotfeather, Myriophyllum aquaticum (Vell.) Verdc., Richardsons pondweed, Potamogeton richardsonii (A. Bennett) Rydb., variable-leaf watermilfoil, Myriophyllum heterophyllum Michx Management Implications: A framework for assessing the vulnerability of ecosystems to invasion by aquatic weeds must consider many aspects of species invasions: which species will arrive, how will they get there, and will they establish and generate impacts following introduction. Knowledge about physiological responses to stressors provides critical input to such a framework. In our study, we compared the viability of vegetative fragments of 10 aquatic plant species following variable periods of desiccation. We found that while desiccation expectedly decreased plant viability, desiccation rates and tolerances differed significantly between plant species. The species-specific nature of desiccation warrants species-specific management actions. Our results suggest that boat launch inspection programs should be extra vigilant in their search for species that are relatively desiccation-resistant or –tolerant, such as emergent Myriophyllum aquaticum. On the other hand, our finding that some common invasive plants (Ceratophyllum demersum, Hydrilla verticillata) are comparatively intolerant to air exposure suggests that for these species, greater attention should be given to specific situations that promote insulation of vegetative material (e.g., entrainment in nets or anchor wells, burial in sediments), plant propagules that are more tolerant or resistant to desiccation (e.g., seeds or tubers), and alternative invasion pathways (e.g., water garden contaminants).

Geographic selection bias of occurrence data influences transferability of invasive Hydrilla verticillata distribution models

Due to socioeconomic differences, the accuracy and extent of reporting on the occurrence of native species differs among countries, which can impact the performance of species distribution models. We assessed the importance of geographical biases in occurrence data on model performance using Hydrilla verticillata as a case study. We used Maxent to predict potential North American distribution of the aquatic invasive macrophyte based upon training data from its native range. We produced a model using all available native range occurrence data, then explored the change in model performance produced by omitting subsets of training data based on political boundaries. We also compared those results with models trained on data from which a random sample of occurrence data was omitted from across the native range. Although most models accurately predicted the occurrence of H. verticillata in North America (AUC > 0.7600), data omissions influenced model predictions. Omitting data based on political boundaries resulted in larger shifts in model accuracy than omitting randomly selected occurrence data. For well-documented species like H. verticillata, missing records from single countries or ecoregions may minimally influence model predictions, but for species with fewer documented occurrences or poorly understood ranges, geographic biases could misguide predictions. Regardless of focal species, we recommend that future species distribution modeling efforts begin with a reflection on potential spatial biases of available occurrence data. Improved biodiversity surveillance and reporting will provide benefit not only in invaded ranges but also within under-reported and unexplored native ranges.

A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America

Detection of invasive species before or soon after they establish in novel environments is critical to prevent widespread ecological and economic impacts. Environmental DNA (eDNA) surveillance and monitoring is an approach to improve early detection efforts. Here we describe a large-scale conservation application of a quantitative polymerase chain reaction assay with a case study for surveillance of a federally listed nuisance species (Ruffe, Gymnocephalus cernua) in the Laurentian Great Lakes. Using current Ruffe distribution data and predictions of future Ruffe spread derived from a recently developed model of ballast-mediated dispersal in US waters of the Great Lakes, we designed an eDNA surveillance study to target Ruffe at the putative leading edge of the invasion. We report a much more advanced invasion front for Ruffe than has been indicated by conventional surveillance methods and we quantify rates of false negative detections (i.e. failure to detect DNA when it is present in a sample). Our results highlight the important role of eDNA surveillance as a sensitive tool to improve early detection efforts for aquatic invasive species and draw attention to the need for an improved understanding of detection errors. Based on axes that reflect the weight of eDNA evidence of species presence and the likelihood of secondary spread, we suggest a two-dimensional conceptual model that management agencies might find useful in considering responses to eDNA detections.

A Spatial Modeling Approach to Predicting the Secondary Spread of Invasive Species Due to Ballast Water Discharge

Ballast water in ships is an important contributor to the secondary spread of invasive species in the Laurentian Great Lakes. Here, we use a model previously created to determine the role ballast water management has played in the secondary spread of viral hemorrhagic septicemia virus (VHSV) to identify the future spread of one current and two potential invasive species in the Great Lakes, the Eurasian Ruffe (Gymnocephalus cernuus), killer shrimp (Dikerogammarus villosus), and golden mussel (Limnoperna fortunei), respectively. Model predictions for Eurasian Ruffe have been used to direct surveillance efforts within the Great Lakes and DNA evidence of ruffe presence was recently reported from one of three high risk port localities identified by our model. Predictions made for killer shrimp and golden mussel suggest that these two species have the potential to become rapidly widespread if introduced to the Great Lakes, reinforcing the need for proactive ballast water management. The model used here is flexible enough to be applied to any species capable of being spread by ballast water in marine or freshwater ecosystems.

Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs

Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge - including limitations, research needs, and likely future developments - relevant to various aspects of planning and conducting comprehensive EDM. We begin with the scope of the effort, contrasting target-species with broad-spectrum monitoring, reviewing information to support prioritization based on species and locations, and exploring the challenge of moving beyond individual surveys towards a coordinated monitoring network. Next, we discuss survey design, including effort to expend and its allocation over space and time. A section on sample collection and analysis overviews the merits of collecting actual organisms versus shed DNA, reviews the capabilities and limitations of identification by morphology, DNA target markers, or DNA barcoding, and examines best practices for sample handling and data verification. We end with a section addressing the analysis of monitoring data, including methods to evaluate survey performance and characterize and communicate uncertainty. Although the body of science supporting EDM implementation is already substantial, research and information needs (many already actively being addressed) include: better data to support risk assessments that guide choice of taxa and locations to monitor; improved understanding of spatiotemporal scales for sample collection; further development of DNA target markers, reference barcodes, genomic workflows, and synergies between DNA-based and morphology-based taxonomy; and tools and information management systems for better evaluating and communicating survey outcomes and uncertainty.