Novel Applications of Environmental DNA Analyses in the Tropical Eastern Pacific Ocean

Abstract

Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring and conservation biology by enabling the detection of species and genetic diversity from environmental samples. This dissertation addresses key improvements to the design, analysis, and interpretation of eDNA metabarcoding studies, applying these improved methods to studies of multitrophic ecology and blacktip shark genetic diversity in marine ecosystems in the Tropical Eastern Pacific Ocean. Key advancements include the development of the REGATTA bioinformatic method to reconcile taxonomic assignments with local species checklists, the application of Hill numbers to compare different facets of biodiversity, and the development of a non-invasive mitochondrial haplotyping assay for blacktip sharks. These novel analytical methods for assessing ecological interactions and spatiotemporal patterns of genetic diversity provide high-resolution insights into the conservation issues affecting scalloped hammerhead and blacktip sharks. The first study leverages these key advancements to the analysis of eDNA datasets to explore multitrophic biodiversity patterns in shark nursery bays of the Galápagos archipelago. By reconciling global and local taxonomic assignments and employing tools such as correlation analysis, co-occurrence networks, and predator effect analyses, this study provides detailed insights into the ecological drivers of fish and crustacean biodiversity and the influence of juvenile sharks on community composition in shark nursery bays. The second study introduces a novel mitochondrial haplotyping assay for blacktip sharks, demonstrating its efficacy in non-invasive monitoring of spatiotemporal patterns of intraspecific genetic diversity of this threatened top predator in coastal marine ecosystems. Together, these studies highlight innovative methodologies to enhance the specificity, sensitivity, and applicability of eDNA metabarcoding techniques in ecological and conservation research, providing robust tools to assess biodiversity at both intra- and interspecific levels. Ultimately, this work demonstrates the value of eDNA studies for generating comprehensive, non-invasive assessments of biodiversity and for informing ecosystem-based management and conservation efforts in complex marine systems.