Date of Award


Publication Type


Degree Name



Biological Sciences


diet determination;Great Lakes fishes;high-throughput nanofluidic qRT-PCR;scDNA;stomach content DNA;targeted detection


Daniel Heath


Yingming Zhao



Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.


Stomach content DNA (scDNA) analyses provide important insights into feeding ecology, trophic interactions, and diet composition of predator fishes. However, previous scDNA analyses have focused on investigating a small number of predator and prey fishes using binary presence/absence data. Here, I describe the development and validation of a panel of single-species quantitative real-time PCR (qRT-PCR) assays targeting the polymorphic mitochondrial cytochrome oxidase subunit 1 (CO1) region of 28 Great Lakes prey fishes. The assay panel will significantly increase the number of targeted prey species available for predator diet assessment, while at the same time improving detection sensitivity and through-put. I validated all 28 assays and developed a nanofluidic OpenArray® chip, thus producing a novel and useful trophic ecology tool. I then utilized the OpenArray® chip to investigate the effects of feeding ecology, specifically two predator traits (predator species and predator size) and two ecological variables (capture basin and sampling year), on the feeding relationships of five common predator fishes in Lake Erie (Sander vitreus, Morone americana, Morone chrysops, Perca flavescens, Aplodinotus grunniens). I identified 9 prey species and showed that predator species, predator size, capture basin, and sampling year all significantly affected both the predators’ prey (all species) capture probability and individual prey species’ detection probabilities. I also used the quantitative aspect of qRT-PCR to estimate prey scDNA concentrations for three common prey species. This quantitative approach contextualizes the predator-prey interactions and helps determine predator preference for the selected prey fishes. Ultimately, targeted scDNA analyses identify important prey items for predator species, determine trophic linkages across aquatic food-webs, and measure predator and prey performance in their natural habitats, which are all crucial for fisheries management, conservation efforts, and monitoring freshwater ecosystem health.

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