APPLICATION AND VALIDATION OF THE EDNA-METABARCODED MIFISH/MITOFISH PIPELINE FOR ASSESSMENT OF NATIVE AND NON-NATIVE FISH COMMUNITIES OF LAKE MICHIGAN
thesisposted on 08.05.2020 by Samantha Jurecki
In order to distinguish essays and pre-prints from academic theses, we have a separate category. These are often much longer text based documents than a paper.
Environmental DNA (eDNA) is being used increasingly for biomonitoring of communities (e.g., microbes, macroinvertebrates, fish species) across terrestrial and aquatic ecosystems. Developing methods that combine eDNA approaches with metagenomic barcoded amplicon sequencing (eDNA-metabarcoding) are now providing a powerful noninvasive and cost-effective means for comprehensively surveying biodiversity in a wide range of habitats. Invasive species have a substantial impact on the ecology and economics of the Great Lakes region, and eDNAmetabarcoding methods have recently been applied in monitoring non-native, as well as native, fish populations in the freshwater systems there. In this research, we validated an eDNAmetabarcoding approach that uses established platforms, the MiFish/MitoFish pipeline, for fish community monitoring on Lake Michigan. For validation, we compared survey results from our eDNA-metabarcoding approach to those obtained using traditional surveys (e.g., electrofishing and seining). We also sampled a closed 180,000-gallon freshwater fish tank system to see how well our methods characterized a known native fish population that resided in the tank. Finally, we applied the approach to monitoring invasive and native fish populations in southern Lake Michigan at a site that is currently undergoing restoration to improve the aquatic habitats.. We were able to reliably capture the fish community structure of the native fish tank as well as those of open waters on the lake using our methods. Diversity patterns detected at the restoration site using our eDNA-metabarcoding approach accurately reflected those of the historical record, which have taken many years to establish by conventional means. Overall, this study suggests eDNAmetabarcoding is an efficient, credible, and powerful approach to biomonitoring.