Abstract
Identifying species and population genetic compositions of biological invasions at early life stages and/or from environmental (e)DNA using targeted high‐throughput sequencing (HTS) metabarcode assays offers powerful and cost‐effective means for early detection, analysis of spread patterns, and evaluating population changes. The present study develops, tests, and applies this method with a targeted sequence assay designed to simultaneously identify and distinguish between the closely related invasive Eurasian zebra and quagga mussels (Dreissena polymorpha and D. rostriformis) and their relatives and discern their respective population genetic patterns. Invasions of these dreissenid mussel species have markedly changed freshwater ecosystems throughout North America and Europe, exerting severe ecological and economic damage. Their planktonic early life stages (eggs and larvae) are morphologically indistinguishable, yet each species exerts differential ecological effects, with the quagga often outcompeting the zebra mussel as adults. Our targeted assay analyzes genetic variation from a diagnostic sequence region of the mitochondrial (mt)DNA cytochrome oxidase I (COI) gene, to assess temporal and spatial inter‐ and intra‐specific genetic variability. The assay facilitates analysis of environmental (e)DNA from water, early life stages from thousands of individuals, and simultaneous analysis of 50–100 tagged field‐collected samples. Experiments evaluated its accuracy and performance using: (a) mock laboratory communities containing known DNA quantities per taxon, (b) aquaria with mixed‐species/haplotype compositions of adults, and (c) field‐collected water and plankton versus traditional sampling of adult communities. Results delineated species compositions, relative abundances, and population‐level diversity differences among ecosystems, habitats, time series, and life stages from two allopatric concurrent invasions in the Great Lakes (Lake Erie) and the Hudson River, which had separate founding histories. Findings demonstrate application of this targeted assay and our approach to accurately and simultaneously discern species‐ and population‐level differences across spatial and temporal scales, facilitating early detection and ecological understanding of biological invasions.
Highlights
The growing global prevalence of invasive species profoundly shapes contemporary ecosystems (Pimentel, 2014; Simberloff, 2013) and negatively affects commerce (Keller, Lodge, Lewis, & Shogren, 2009; Pimentel, Zuniga, & Morrison, 2005)
We focused on testing the two markers on zebra and quagga mussels, which were designed to each distinguish different single nucleotide polymorphisms (SNPs)
This study developed and tested a new high‐throughput sequencing (HTS) metabarcoding assay that simultaneously differentiated among dreissenid species and their intraspecific haplotypes from single samples containing DNA from thousands of individuals
Summary
The growing global prevalence of invasive species profoundly shapes contemporary ecosystems (Pimentel, 2014; Simberloff, 2013) and negatively affects commerce (Keller, Lodge, Lewis, & Shogren, 2009; Pimentel, Zuniga, & Morrison, 2005). The zebra mussel was discerned from eDNA in the Red River off Lake Winnipeg, Canada, in 2014, a year before the first adult was located (Gingera, Bajno, Docker, & Reist, 2017) Those studies detected dreissenids (De Ventura et al, 2017; Egan et al, 2015; Gingera et al, 2017; Ram et al, 2011), their methodology was unable to differentiate between zebra and quagga mussel species using a single assay and could not address population‐level variation (e.g., haplotypes). The research objective was to develop, test, and apply a new targeted HTS metabarcode assay that simultaneously identifies and differentiates among all six Dreissena species (see Stepien et al, 2013; Marshall & Stepien, 2019), including zebra and quagga mussels, and discerns their respective population‐level variability (i.e., haplotype representation and relative abundances) at all life stages. Accurate identification of dreissenids to species and assessment of their population genetic variability are projected to facilitate understanding their relative reproductive outputs, spread patterns, ecological interactions, successes, and adaptations over temporal and spatial scales
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