Dissertations, Theses, and Capstone Projects

Date of Degree


Document Type


Degree Name





Elizabeth Alter


John Waldman

Committee Members

Stephen Gosnell

Mark Stoeckle

Tom Noji

Subject Categories

Aquaculture and Fisheries | Biodiversity | Other Genetics and Genomics | Terrestrial and Aquatic Ecology


Fisheries, biomonitoring, conservation, eDNA, metabarcoding


Mounting an effective response to the threats faced by freshwater fish may require expansions to aquatic biomonitoring in excess of what is feasible using the capture-based survey techniques currently relied upon by natural resource managers. Methods for analyzing environmental DNA (eDNA) are emerging as a minimally invasive and cost-effective approach for surveying fish and other organisms. By detecting taxon-specific DNA sequences recovered from environmental samples (e.g. water, sediment), eDNA methods are able to infer species presence from samples that can be collected rapidly with simple equipment. In many cases, eDNA detection rates of fish species have been shown to meet or exceed those of capture surveys, while exhibiting lower rates of false negatives, but empirical validation of any eDNA approach remains necessary both to assess concordance of the resolved fish assemblage with prior observations, where such records exist, and to establish a baseline of molecular observations.

In this dissertation, I provide eDNA observations of fishes for the Bronx River and 11 tributaries to the Hudson River over three studies, each varying in spatial and taxonomic scale. First, I explore the potential for eDNA to serve as a quantitative indicator of fish abundance by testing for a relationship between the density of American Eels (Anguilla rostrata) in the Bronx River and qPCR measurements of the concentration of their DNA in water samples. I then demonstrate the capacity of eDNA methods to bridge gaps in fish monitoring by conducting a watershed scale survey of the fish biodiversity of tributaries to the lower Hudson River using eDNA metabarcoding. In the final chapter, I return to the Bronx River, employing metabarcoding as a survey of fish diversity along its freshwater extent and comparing the resolved assemblages to those of an intensive capture survey.