Date of Award


Degree Type


Degree Name

Doctor of Philosophy in Biological and Environmental Sciences


Ecology and Ecosystem Sciences


Fisheries, Animal and Veterinary Science

First Advisor

Austin Humphries


Coral reefs contain a disproportionately high amount of marine biodiversity and support millions of people worldwide by providing food security and livelihoods. This coupled relationship between reefs and people is increasingly threatened globally by climate change and globalization, as well as locally by overfishing, habitat destruction, and nutrient pollution. Biomonitoring the varied ecological outcomes of these threats and estimating how conservation and management interventions mitigate them are crucial scientific endeavors for understanding the socio-ecological complexity of coral reef dynamics. Common ecological indicators of reef health, however, are theoretically and taxonomically limited when used alone, thus a combination of modeling and methodological approaches is needed for comprehensive assessments of coral reef patterns and processes. In addition, there are under-discussed power dynamics and equity implications of biomonitoring, especially when novel technologies are employed. Here, we address these research gaps with field data collected from coral reefs in Indonesia using visual surveys of fishes and corals and environmental DNA (eDNA) surveys of coral reef animals more broadly. We also evaluate potential equity outcomes of eDNA frameworks and implementations using critical discourse analysis. Engaging with multiple disciplinary paradigms, the aims of this dissertation are to understand the biophysical and human-mediated pathways shaping coral reef fish and habitat assemblages, evaluate the utility of eDNA for uncovering spatial patterns in coral reef biodiversity, and critically examine how the discourses and practices of the eDNA field may lead to inequitable outcomes.

Chapter 1 contextualizes the results presented in Chapters 2, 3, and 4. It outlines the global magnitude of coral reef biodiversity and its threats, describes the common bioindicators used to evaluate management practices and ecosystem processes, gives rationale for using an eDNA approach, and establishes the importance of scrutinizing eDNA’s social dimensions. Key information about Indonesia’s coral reefs is also summarized.

In Chapter 2, we used structural equation models (SEMs) to evaluate the relative influences of biophysical and human-mediated pathways affecting coral reef fishes and habitats. SEMs are a form of path analysis that allows multiple competing hypotheses about a system to be evaluated within the same theoretical and statistical framework. SEMs allows for understanding coral reef processes because they organize field data from reefs in terms of their causal proximity to each other. In our SEMs, we used visual survey data collected on coral reef fishes and habitat conditions across four regions of Indonesia that vary in their management designations. We also incorporated additional socio-environmental data from global databases to further characterize our system. We first quantified a large gradient in fish biomass, coral cover, and structural complexity across our study regions, as well as regionally distinct reef fish communities. Then, our SEM results indicated that direct pathways of local human population consistently had significant effects on reef fish biomass and diversity, though with varying magnitudes and directions. Multi-use MPAs only partially mediated these effects, delivering biomass gains for carnivores, but not herbivores, local alpha diversity, or hard coral. Our results showed that the ecological outcomes of management can manifest through multiple and varied socio-ecological processes, suggesting that there may be trade-offs in zoning areas for fisheries management, biodiversity, and/or habitat restoration goals.

In Chapter 3, we evaluated the utility of eDNA surveys in uncovering spatial patterns of coral reef biodiversity in three regions of Indonesia. eDNA added taxonomic breadth to our evaluation of coral reef assemblages as a genetically-based and passive sampling method of enumerating coral reef biodiversity that is not reliant on the visual identification of reef species. We collected water and sediment samples for eDNA and amplified sequences using a general COI primer targeting metazoans (multicellular eukaryotes). We found that most of the sequences were assigned as unidentified Eukaryotes and represented organisms that have yet to be described by science and/or under-represented in regional genetic databases. Nevertheless, we detected a wide range of taxa from both metazoan and non-metazoan groups, including fish and coral taxa that we could confirm with our concomitant visual surveys and/or with other eDNA studies from the region. We also found differences in community compositions among regions and sample types, suggesting that the high heterogeneity of eDNA samples needs to be further evaluated with more rigorous sampling. Our results demonstrate the many opportunities and challenges to sampling eDNA in this hyper-diverse context.

In Chapter 4, we critically assessed the eDNA field more broadly by using the discourses within its peer-reviewed scientific literature and eDNA websites from public or private institutions as source materials. We employed critical discourse analysis and a process-based approach, drawing from the interdisciplinary fields of feminist science and technology studies and political ecology. We first make the argument that science is an important knowledge-making arena by which representations of humans and non-humans emerge. We then show how the scientific rhetoric, implementation, and future proposals of eDNA produce inequitable representations through interlinked neoliberal discourses of conservation, molecular-genetic reductionism, and technological solutionism. We cite key discursive examples from the eDNA field to show how values of efficiency, neutrality, and objectivity are communicated as justifications for eDNA research, which beneficially represents eDNA scientists as apolitical and neutral biodiversity experts. This framing positions other practitioners of biodiversity knowledge as traditional, biased, and inefficient, which may diminish forms of local participation and knowledge in science, conservation, and management. Our results are a call-to-action for the eDNA field to explicitly consider its social dimensions, rather than ignoring them in favor of continued methodological refinement.

Chapter 5 synthesizes the findings from Chapters 2, 3, and 4. It specifically highlights how coral reef biomonitoring has complex management, taxonomic, and social trade-offs. It discusses limitations and caveats for each of the studies, followed by suggestions for future research directions. I also write a final reflection about engaging in a multidisciplinary and reflexive research praxis.

Creative Commons License

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

Available for download on Thursday, May 08, 2025