Using Next-Generation Sequencing of Environmental DNA to Assess Fish Assemblages in Alaskan National Parks

In expansive and remote Alaska, it is cost-prohibitive to conduct comprehensive fish sampling over large areas.  As a result, data on fish species richness and distribution in small lakes and rivers in National Parks in Alaska are scant. We are currently developing field and laboratory methods for the simultaneous identification of multiple fish species in lakes and rivers in Alaskan National Parks, using environmental DNA (eDNA) extracted from water samples. Recent developments in the identification of species using eDNA recovered from environmental samples and classical genetic technologies, such as DNA barcoding, offer potentially powerful new approaches for fish monitoring, or for any research that relies on data regarding fish species richness or distribution. Nevertheless, eDNA approaches that apply a classical genetic approach generally target a single or few species, and the development of multiple-species detection methods is difficult and not cost-effective. Shotgun or amplicon-based next-generation (NG) sequencing approaches can overcome a number of the obstacles inherent in applying classical genetic technologies to eDNA studies that target assemblages, rather than single or few species.  Here we present an experimental amplicon approach, which targets subunits of both the 16S mitochondrial and 18S nuclear ribosomal genes, and discuss issues surrounding eDNA technologies in general. We also present results from our initial attempt to apply these NG-eDNA methods for detecting the presence of multiple fish species at a landscape scale, using water samples collected from both fish-bearing and fishless streams in Wrangell-St. Elias National Park and Preserve and Denali National Park and Preserve, and from lakes in the Bering Land Bridge National Preserve.