Weed Risk Assessment for Aquatic Plants: Modification of a New Zealand System for the United States

We tested the accuracy of an invasive aquatic plant risk assessment system in the United States that we modified from a system originally developed by New Zealand’s Biosecurity Program. The US system is comprised of 38 questions that address biological, historical, and environmental tolerance traits. Values associated with each response are summed to produce a total score for each species that indicates its risk of invasion. To calibrate and test this risk assessment, we identified 39 aquatic plant species that are major invaders in the continental US, 31 species that have naturalized but have no documented impacts (minor invaders), and 60 that have been introduced but have not established. These species represent 55 families and span all aquatic plant growth forms. We found sufficient information to assess all but three of these species. When the results are compared to the known invasiveness of the species, major invaders are distinguished from minor and non-invaders with 91% accuracy. Using this approach, the US aquatic weed risk assessment correctly identifies major invaders 85%, and non-invaders 98%, of the time. Model validation using an additional 10 non-invaders and 10 invaders resulted in 100% accuracy for the former, and 80% accuracy for the latter group. Accuracy was further improved to an average of 91% for all groups when the 17% of species with scores of 31–39 required further evaluation prior to risk classification. The high accuracy with which we can distinguish non-invaders from harmful invaders suggests that this tool provides a feasible, pro-active system for pre-import screening of aquatic plants in the US, and may have additional utility for prioritizing management efforts of established species

Development and Field Validation of an Environmental DNA (eDNA) Assay for Invasive Clams of the Genus Corbicula

Early detection is imperative for successful control or eradication of invasive species, but many organisms are difficult to detect at the low abundances characteristic of recently introduced populations. Environmental DNA (eDNA) has emerged as a promising invasive species surveillance tool for freshwaters, owing to its high sensitivity to detect aquatic species even when scarce. We report here a new eDNA assay for the globally invasive Asian clam Corbicula fluminea (Müller, 1774), with field validation in large lakes of western North America. We identified a candidate primer pair for the Cytochrome c oxidase subunit 1 (COI) gene for C. fluminea. We tested it for specificity via qPCR assay against genomic DNA of the target species C. fluminea, and synthetic DNA gBlocks for other non-target species within and outside of the genus Corbicula. Our best identified primer amplifies a 208-bp fragment for C. fluminea and several closely related species within the genus, but was specific for these non-native Asian clams relative to native mollusks of western North America. We further evaluated this assay in application to eDNA water samples for the detection of C. fluminea from four lakes in California and Nevada, United States, where the species is known to occur (including Lake Tahoe) relative to seven lakes where it has never been observed. Our assay successfully detected C. fluminea in all four lakes with historic records for this species, and did not detect C. fluminea from the seven lakes without known populations. Further, the distribution of eDNA detections within Lake Tahoe generally matched the known, restricted distribution of C. fluminea in this large lake. We conclude from this successful field validation that our eDNA assay for C. fluminea will be useful for researchers and managers seeking to detect new introductions and potentially monitor population trends of this major freshwater invader and other closely related members of its genus

Performance of Genetic Distance Metrics in Gravity and General Mixed Effects Models

There are many causes for the genetic patterns that arise among populations across a landscape. Effective population size, natal site preference, geographic distance, or barriers to gene flow associated with landscape composition may work in opposition or in concert resulting in varying degrees of population differentiation. Here, we simulate 40 populations under 3 different ecological hypotheses of individual dispersal with random mating for 1500 generations, with scenarios: 1) dispersal and mating is dependent on habitat between populations, 2) dispersal and mating is dependent on individuals finding habitat similar to their natal habitat, and 3) dispersal and mating is dependent on habitat between populations but population size is dependent on surrounding habitat quality. We estimate the efficacy of generalized linear mixed-effect models (GLMMs) and gravity models to identify each of the 3 scenarios. Additionally, we tested the ability of 5 different genetic metrics (Dps, Fst, PCA, Nei’s D, and Cavalli-Sforza Dkf) to identify gene flow across ecological drivers, landscape composition, and time. We predict that more heterogeneous landscapes will influence genetic structure more quickly than more homogeneous landscapes and will be detected sooner by allele frequency approaches. Management of organisms in fragmented habitats, particularly those at risk, requires a knowledge of habitat effect and population genetic structure that can be informed by these types of simulations

A Decision Tree Analysis of Nonindigenous Species Risk from Ballast Water to the Lower Columbia River and Oregon coast, USA

Hazard characterization and risk assessment are commonly used to prioritize vectors of nonindigenous species (NIS) for inspection or other prevention opportunities. Commercial shipping vessels are a target of such vector-based management since ballast water has been known to transport NIS between aquatic ecosystems globally. Here we used a risk-based screening protocol to prioritize vessels discharging ballast water to the lower Columbia River and Oregon coast. We began by adapting established methods of assessing risk factors that influence the initial stages of the invasion process (arrival and survival). We created relative risk scales for each factor using data collected from vessels that discharged ballast water in three unique zones within our study area. We then organized a decision tree based on the confidence level of the proxies used for each risk factor to create a tool that prioritizes vessels with high risk ballast water for attention from regulatory personnel. In order of consideration, decision tree factors included: intent to discharge ballast water, reported adherence to required management practices, environmental distance between source and discharge locations (habitat suitability), ballast water discharge volume (propagule pressure number and frequency), and ballast water age (organism viability). As a result, vessels were prioritized on a scale of low, medium, medium-high, or high. We applied the decision tree to a 2016 dataset of vessel arrivals and found that 173 of 1,592 arrivals were deemed high priority, with most occurring at ports in the freshwater zone of the Columbia River (158), followed by fewer in the estuarine zone of the Columbia River (4) and in Coos Bay (11). The decision tree is transferable to NIS prevention and regulatory efforts in other port systems. The vessel prioritizations are adaptable for managers using risk assessment strategies to allocate limited regulatory program resources for vector screening

Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances

1. Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types. 2. We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus and to reflect patterns of its relative abundance, in upper Midwest, USA, inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates and also tested the relationship between eDNA copy number and O. rusticus relative abundance. 3. We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well predicted by relative abundance of this species and lake water clarity. However, there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. 4. Synthesis and applications. Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperiled crayfishes and other benthic arthropods

Environmental DNA (eDNA) Detects the Invasive Crayfishes Orconectes rusticus and Pacifastacus leniusculus in Large Lakes of North America

We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to recent sampling for presence/absence and relative abundance of P. leniusculus in California and Nevada via overnight sets of baited traps. We successfully detected O. rusticus eDNA at six sites from the Great Lakes and P. leniusculus from six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats

Environmental DNA Detection of Aquatic Invasive Plants in Lab Mesocosm and Natural Field Conditions

Aquatic invasive plant species cause negative impacts to economies and ecosystems worldwide. Traditional survey methods, while necessary, often do not result in timely detections of aquatic invaders, which can be cryptic, difficult to identify, and exhibit very rapid growth and reproduction rates. Environmental DNA (eDNA) is a relatively new method that has been used to detect multiple types of animals in freshwater and marine ecosystems through tissues naturally shed from the organism into the water column or sediment. While eDNA detection has proven highly effective in the detection of aquatic animals, we know less about the efficacy of eDNA as an effective surveillance tool for aquatic plants. To address this disparity, we designed mesocosm experiments with Elodea species to determine the ability to detect accumulation and degradation of the DNA signal for aquatic plants, followed by field surveillance of the highly invasive Hydrilla verticillata in freshwaters across several U.S. geographic regions. In both lab and field experiments, we designed a high sensitivity quantitative PCR assay to detect the aquatic plant species. In both experiments, plant eDNA detection was successful; we saw accumulation of DNA when plants were introduced to tanks and a decrease in DNA over time after plants were removed. We detected eDNA in the field in areas of known Hydrilla distribution. Employing eDNA detection for aquatic plants will strengthen efforts for early detection and rapid response of invaders in global freshwater ecosystems

Water Flow and Biofilm Cover Influence Environmental DNA Detection in Recirculating Streams

The increasing use of environmental DNA (eDNA) for determination of species presence in aquatic ecosystems is an invaluable technique for both ecology as a field and for the management of aquatic ecosystems. We examined the degradation dynamics of fish eDNA using an experimental array of recirculating streams, also using a “nested” primer assay to estimate degradation among eDNA fragment sizes. We introduced eDNA into streams with a range of water velocities (0.1–0.8 m s–1) and substrate biofilm coverage (0–100%) and monitored eDNA concentrations over time (∼10 d) to assess how biophysical conditions influence eDNA persistence. We found that the presence of biofilm significantly increased initial decay rates relative to previous studies conducted in nonflowing microcosms, suggesting important differences in detection and persistence in lentic vs lotic systems. Lastly, by using a nested primer assay that targeted different size eDNA fragments, we found that fragment size altered both the estimated rate constant coefficients, as well as eDNA detectability over time. Larger fragments (\u3e600 bp) were quickly degraded, while shorter fragments (\u3c100 \u3ebp) remained detectable for the entirety of the experiment. When using eDNA as a stream monitoring tool, understanding environmental factors controlling eDNA degradation will be critical for optimizing eDNA sampling strategies

Data from: Environmental DNA (eDNA) detects the invasive rusty crayfish (Orconectes rusticus) at low abundances

Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types. We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus, and to reflect patterns of its relative abundance, in upper Midwest, USA inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates, and also tested the relationship between eDNA copy number and O. rusticus relative abundance. We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well-predicted by relative abundance of this species and lake water clarity. However there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. Synthesis and applications. Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperilled crayfishes and other benthic arthropods