Data from: Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries

The extraction and characterization of DNA from aquatic environmental
samples offers an alternative, non-invasive approach for the detection of
rare species. Environmental DNA, coupled with PCR and next-generation
sequencing (“metabarcoding”), has proven to be very sensitive for the
detection of rare aquatic species. Our study used a custom designed
group-specific primer set and next-generation sequencing for the detection
of three species at risk; (Eastern Sand Darter, Ammocrypta pellucida;
Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis
photogenis), one invasive species (Round Goby, Neogobius melanostomus) and
an additional 78 native species from two large Great Lakes tributary
rivers in southern Ontario, Canada; the Grand River and the Sydenham
River. Out of 82 fish species detected in both rivers using capture-based
and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish
species in the Grand River and the Sydenham River, respectively, which
included our four target species. Our analyses also identified significant
positive and negative species co-occurrence patterns between our target
species and other identified species. Our results demonstrate that eDNA
metabarcoding that targets the fish community as well as individual
species of interest provides a better understanding of factors affecting
the target species spatial distribution in an ecosystem than possible with
only target species data. Additionally, eDNA is easily implemented as an
initial survey tool, or alongside capture-based methods, for improved
mapping of species distribution patterns.