Browsing by Author "Pfrender, Michael E."

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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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    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.