Browsing by Author "Renshaw, Mark A."

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    Development and field validation of an environmental DNA (eDNA) assay for invasive clams of the genus Corbicula
    (REABIC, 2018) Cowart, Dominique A.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Egan, Scott P.; Lodge, David M.; Larson, Eric R.
    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.
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    Diversity Metrics Are Robust to Differences in Sampling Location and Depth for Environmental DNA of Plants in Small Temperate Lakes
    (Frontiers Media S.A., 2021) Drummond, Jennifer A.; Larson, Eric R.; Li, Yiyuan; Lodge, David M.; Gantz, Crysta A.; Pfrender, Michael E.; Renshaw, Mark A.; Correa, Adrienne M.S.; Egan, Scott P.
    Environmental DNA (eDNA) analysis methods permit broad yet detailed biodiversity sampling to be performed with minimal field effort. However, considerable uncertainty remains regarding the spatial resolution necessary for effective sampling, especially in aquatic environments. Also, contemporary plant communities are under-investigated with eDNA methods relative to animals and microbes. We analyzed eDNA samples from six small temperate lakes to elucidate spatial patterns in the distributions of algae and aquatic and terrestrial plants, using metabarcoding of the Internal Transcribed Spacer-1 (ITS1) genomic region. Sampling locations were varied across horizontal and vertical space: sites in each lake included a mixture of nearshore and offshore positions, each of which was stratified into surface (shallow) and benthic (deep) samples. We detected the expected community variation (beta diversity) from lake to lake, but only small effects of offshore distance and sampling depth. Taxon richness (alpha diversity) was slightly elevated in nearshore samples, but displayed no other significant spatial effects. These diversity metrics imply that plant eDNA is more evenly distributed than its generating organisms in these small lake environments. Read abundances were heavily weighted toward aquatic macrophytes, though taxon richness was greatest in the algae and other nonvascular plants. We also identified representatives of many phylogenetically and ecologically varied plant taxa, including terrestrial species from surrounding areas. We conclude that freshwater plant eDNA surveys successfully capture differences among lake communities, and that easily-accessible, shore-based sampling may be a reliable technique for informing research and management in similar ecosystems.
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    Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America
    (Springer, 2017) Larson, Eric R.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Lodge, David M.; Egan, Scott P.
    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.
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    Environmental DNA (eDNA) detects the invasive crayfishesﾠOrconectes rusticusﾠandﾠPacifastacus leniusculusﾠin large lakes of North America
    (Springer, 2017) Larson, Eric R.; Renshaw, Mark A.; Gantz, Crysta A.; Umek, John; Chandra, Sudeep; Lodge, David M.; Egan, Scott P.
    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 crayfishﾠPacifastacus leniusculusﾠ(Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfishﾠOrconectes rusticusﾠ(Girard, 1852), as well as for the invasion ofﾠO. rusticusﾠinto large lakes of California and Nevada, US known to be invaded byﾠP. leniusculus.ﾠWe compared eDNA detections to historic localities forﾠO. rusticusﾠwithin the Great Lakes, and to recent sampling for presence/absence and relative abundance ofﾠP. leniusculusﾠin California and Nevada via overnight sets of baited traps. We successfully detectedﾠO. rusticusﾠeDNA at six sites from the Great Lakes andﾠP. leniusculusﾠfrom 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.
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    Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances
    (Wiley, 2016) Dougherty, Matthew M.; Larson, Eric R.; Renshaw, Mark A.; Gantz, Crysta A.; Egan, Scott P.; Erickson, Daniel M.; Lodge, David M.
    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.