Wetland fragments in Illinois support over 100 bird species, 15 of which are threatened and endangered in Illinois. Wetland birds are of particular concern under the Illinois State Wildlife Action Plan due to their poorly known population sizes and distributions; small body sizes, infrequent vocalizations, and the unique habitat requirements of multiple species cause traditional methods to largely fall short of elucidating cryptic wetland bird occupancy. Since we cannot conserve species unless we know where they occur, harnessing environmental DNA methods may bolster traditional survey occupancy data. Environmental DNA approaches have been used successfully in freshwater habitats to track species invasion, such as Asian Carp invading the Great Lakes, and to find rare species, such as Eastern Hellbender salamanders in Indiana and Missouri. In this study, we investigated the utility of environmental DNA for detecting and monitoring secretive wetland birds in fragmented wetlands. We collected water samples from wetlands in Fulton, Champaign, and Vermillion Counties in Illinois in early November, 2016. We filtered water samples and extracted eDNA from filters using a Qiagen DNeasy kit. We quantified extracts on a Qubit 3.0 fluorometer, and amplified a short fragment of the mitochondrial cytochrome oxidase subunit 1 locus with PCR, using newly designed degenerated primers. We hypothesized that environmental DNA sampling can be used to identify individual cryptic wetland bird occurrences in wetland fragments. We also hypothesized that taking environmental DNA samples over time will allow us to track cryptic wetland bird migration in Illinois.
We positively detected environmental DNA in our samples; environmental DNA concentrations assessed using Qubit fluorometric quantitation ranged from 1.30 ng/ml to 80.3 ng/ml. As expected, negative controls collected in the field yielded no environmental DNA or contamination. Degenerate primers positively detected heron DNA from laboratory specimen control samples. Unexpectedly and despite strong evidence of wetland bird occurrences at collection sites, our preliminary results indicate wetland bird DNA concentrations may be too low to be detected in environmental DNA samples obtained in early November. Results are pending from temporal environmental DNA replicated collected in the spring, when we expect to discover relatively higher bird DNA concentrations in wetland habitats due to higher bird densities, increased molting, and increases in breeding activities following spring migration.