Abstract

Environmental DNA (eDNA) sampling is a new sampling technique that allows for non-invasive sampling of target species or the characterization of entire communities based on barcoding genes. The goal of this study was to sequence common barcoding genes such as 28S rRNA and Cytochrome C Oxidase I (COI), and then develop species-specific primers for eight macroinvertebrates listed as Species of Greatest Conservation Need (SGCN) in Texas. After sampling for the target species, five were not found, all of which were in the Order Trichoptera (caddisflies). A sixth target species, Isoperla sagittata, was found to have only one gap and four differences in nucleotides across the entire 28S gene region (~1950 nucleotides) in comparison to the most closely related (based on phylogenetic analyses) 28S stonefly sequences on NCBI. In contrast, a novel species-specific primer for the 28S gene was developed for both target mayfly species (seventh and eighth species), Tricorythodes curvatus and Sparbarus coushatta, (TCf/TCr & SCf/SCr primers). In vitro lab testing of these mayfly primers was promising; however, when testing these novel primers against eDNA samples from the field, they were unable to detect the presence of the target species leading to false negatives. The reason for the false negatives may relate to the fact that these are rare species with likely low abundances coupled with the fact that we do not know how fast eDNA degrades in the lentic Texas water bodies or the rate at which these macroinvertebrate species shed eDNA.

Date of publication

2024

Document Type

Thesis

Language

english

Persistent identifier

http://hdl.handle.net/10950/4735

Committee members

Dr. Greenwold, Dr. Kellner, Dr. Williams

Degree

Master of Biology

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