Dissertations, Theses, and Capstone Projects

Date of Degree

6-2026

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy

Program

Biology

Advisor

Jessica Ware

Committee Members

David Lohman

Phillip Staniczenko

John Abbott

Christopher Beatty

Subject Categories

Biodiversity | Bioinformatics | Entomology | Evolution | Genetics | Molecular Biology | Terrestrial and Aquatic Ecology

Keywords

Phylogenomics, Anchored Hybrid Enrichment, eDNA, Macromiidae, Idaho

Abstract

Dragonflies and damselflies (Insecta: Odonata) are globally distributed freshwater insects with extensive museum representation, established genomic resources, and documented sensitivity to environmental change. Leveraging this, my dissertation combines targeted enrichment sequencing of museum odonate specimens, phylogenetic reconstruction, and environmental DNA surveys of urban waterways to study odonate diversity across evolutionary and ecological scales. My first chapter evaluates the performance of Anchored Hybrid Enrichment on historical Odonata specimens spanning more than 100 years of collection. Locus recovery ranged from as few as 4 to as many as 1,000 loci per sample. Neither specimen age nor size predicted locus capture success, whereas museum origin had a significant effect, consistent with differences in preservation history. Within a reconstructed phylogeny, samples with low locus recovery clustered within ambiguous regions, indicating that reduced locus capture can contribute to localized topological uncertainty. Despite this variation, recovered loci were sufficient to reconstruct established higher-level odonate relationships, demonstrating that target enrichment data from museum specimens retain phylogenetic signal even with heterogeneous DNA quality. These results reaffirm that museum collections can support genome-scale studies while highlighting preservation practices as a key determinant of data completeness. In my second chapter, I present the most densely sampled phylogenomic framework to date for Macromiidae, a family of riverine dragonflies. Using Anchored Hybrid Enrichment data from 62 species representing all four genera, I recover three major lineages and show that Didymops is nested within Macromia, challenging previous generic boundaries. Ancestral state reconstruction of male genitalic characters identified diagnostic synapomorphies that independently support the major lineages. Fossil-calibrated divergence estimation places the crown origin of Macromiidae in the late Oligocene, with major radiations concentrated in the Miocene. Historical biogeographic reconstructions support Afrotropical origins for Phyllomacromia, Indo-Malayan ancestry for Epophthalmia, and a complex multi-regional history for Macromia. Ancestral habitat reconstructions favor lentic origins, while diversification analyses indicate that habitat association alone does not explain rate heterogeneity. In my final chapter, I integrate eDNA metabarcoding with community science observations to assess urban Odonata diversity across southwest Idaho. Results reveal strong spatial heterogeneity in assemblages and complementary detection biases between methods: eDNA excels at identifying rare or elusive taxa, while community science provides broader temporal coverage and finer taxonomic resolution. Together, this chapter shows that these approaches offer a complementary, robust, and scalable framework for monitoring aquatic insects in rapidly changing landscapes.

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