Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels

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.

Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection

“…Our targeted metabarcoding HTS assay could be applied en masse to analyzing eDNA from water or entire plankton samples from net tows (i.e., discerning early life stages of eggs and larvae) to detect new occurrences and dispersal patterns by managers. A targeted assay designed by our laboratory to be specific for the two species of invasive dreissenid mussels, distinguishing between them and many of their haplotypes, has been successfully deployed to simultaneously analyze tens of thousands of veliger larvae to species and population levels from net tows, as well as eDNA water samples [129].…”

“…The ruffe exhibited limited genetic diversity and some population divergence across its 30 year history in the upper Great Lakes, revealing founder effect attributable to a single European source area; it has declined in effective population size and numbers in recent years [6]. In comparison, the zebra mussel’s genetic composition has changed over its three decades in the Hudson River, experiencing several population turn-overs and recolonizations [15, 16], yet has remained consistent in Lake Erie throughout [15, 129]. Some invasions possessed little population genetic structure across their ranges; for example, colonization by Virginia’s warbler Oreothlypis virginiae (Baird, 1860) of the Black Hills in South Dakota showed no differentiation, implicating high gene flow and dispersal [130].…”

A practical guide to DNA metabarcoding for entomological ecologists

“…For example, early detection of mosquito vectors using water sample eDNA presented a comparable or higher detection probability to traditional surveys (Schneider et al ., ; Boerlijst et al ., ). There have also been some attempts at using DNA metabarcoding to conduct population genetics studies (Elbrecht et al ., ; Marshall & Stepien, ). However, metabarcoding‐based genotyping shows at least as many experimental biases as DNA metabarcoding for species identification, and is prone to the recovery of erroneous haplotypes (Elbrecht et al ., ).…”

Population‐level inferences from environmental DNA—Current status and future perspectives

“…Baker et al () applied droplet digital PCR, also targeting the D‐loop region, to distinguish between different ecotypes of Orcinus orca (Linnaeus, ) (killer whale) (Table ), and found that eDNA results were consistent with hydrophone recordings and visual observations. Most recently, Stepien et al () applied a marker in the mtDNA cytochrome b (Cyt b ) gene to distinguish between specific haplotypes of the invasive Hypophthalmichthys molitrix (Valenciennes, ) (silver carp), while Marshall and Stepien () used a region of the mtDNA cytochrome c oxidase I (COI) gene to distinguish between different haplotypes within the invasive mussel species Dreissena polymorpha (Pallas ()) (European zebra mussel) and D. rostriformis (Deshayes, ) (quagga mussel) (Table ). Stat et al () obtained information on intraspecific diversity within fish species of the genus Lethrinus through metabarcoding of the mitochondrial large ribosomal subunit (16S) gene of fishes (Table ).…”