Browsing by Author "Lodge, David M."

Now showing 1 - 7 of 7
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    Environment and shipping drive environmental DNA beta-diversity among commercial ports
    (Wiley, 2023) Andrés, Jose; Czechowski, Paul; Grey, Erin; Saebi, Mandana; Andres, Kara; Brown, Christopher; Chawla, Nitesh; Corbett, James J.; Brys, Rein; Cassey, Phillip; Correa, Nancy; Deveney, Marty R.; Egan, Scott P.; Fisher, Joshua P.; vanden Hooff, Rian; Knapp, Charles R.; Leong, Sandric Chee Yew; Neilson, Brian J.; Paolucci, Esteban M.; Pfrender, Michael E.; Pochardt, Meredith R.; Prowse, Thomas A. A.; Rumrill, Steven S.; Scianni, Chris; Sylvester, Francisco; Tamburri, Mario N.; Therriault, Thomas W.; Yeo, Darren C. J.; Lodge, David M.
    The spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographical patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship-borne species spread homogenizes port communities. We first collected and metabarcoded water samples from ports in Europe, Asia, Australia and the Americas. We then calculated community dissimilarities between port pairs and tested for effects of environmental dissimilarity, biogeographical region and four alternative measures of ship-borne species transport risk. We predicted that higher shipping between ports would decrease community dissimilarity, that the effect of shipping would be small compared to that of environment dissimilarity and shared biogeography, and that more complex shipping risk metrics (which account for ballast water and stepping-stone spread) would perform better. Consistent with our hypotheses, community dissimilarities increased significantly with environmental dissimilarity and, to a lesser extent, decreased with ship-borne species transport risks, particularly if the ports had similar environments and stepping-stone risks were considered. Unexpectedly, we found no clear effect of shared biogeography, and that risk metrics incorporating estimates of ballast discharge did not offer more explanatory power than simpler traffic-based risks. Overall, we found that shipping homogenizes eukaryotic communities between ports in predictable ways, which could inform improvements in invasive species policy and management. We demonstrated the usefulness of eDNA metabarcoding and dissimilarity regression for disentangling the drivers of large-scale biodiversity patterns. We conclude by outlining logistical considerations and recommendations for future studies using this approach.
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    Rapid Molecular Detection of Invasive Species in Ballast and Harbor Water by Integrating Environmental DNA and Light Transmission Spectroscopy
    (American Chemical Society, 2015) Egan, Scott P.; Grey, Erin K.; Olds, Brett; Feder, Jeffrey L.; Ruggiero, Steven T.; Tanner, Carol E.; Lodge, David M.
    Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial shipﾒs 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assayﾒs detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.