Ecological and Population Genetic Assessments of Entire Fish Communities Using Environmental DNA and Next-Generation Sequencing: Case Studies in the Great Lakes

Biological community assessments depend on accurate species identification, their relative abundances, and population genetic/genomic variation and adaptations. However, sampling rare and/or endangered species may harm them and their habitats, elusive species often avoid collection gear, and new invasive species may be overlooked at low abundances, especially during early life history. Environmental (e)DNA coupled with next-generation sequencing (NGS) and population genetics and bioinformatic tools, can be used to assess the species identities, relative numbers, and genetic composition of entire communities. We have developed a new eDNA/NGS assay to collect these data simultaneously for all fish species from water samples, targeted for all Great Lakes and Mississippi River fish species, as well as all high-risk potential invasive fish species. Our assay amplifies and sequences targeted diagnostic regions of various lengths from the cytochrome b and COI mitochondrial DNA genes, and we are adding a nuclear gene, yielding a redundant and accurate system. Experiments employing varying concentrations of DNA from known fish communities yielded results highly correlated to expected relative species abundances, confirming our assay’s performance. We have ground-truthed our results from water samples with aquarium experiments of captive fish communities, as well as wild fish communities in field sampling (netting and electroshocking).