Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Biotechnology Science and Engineering

Committee Chair

Matthew L. Niemiller

Committee Member

Zachary Culumber

Committee Member

Karen Ober

Committee Member

Megan L. Porter

Committee Member

Paul Wolf


Crangonyctidae--Phylogeny, Carabus--Phylogeny, Biospeleology, Comparative genomics


Cave organisms with their unusual morphologies including loss of eyes, lack of body pigmentation, and the compensatory improvement of nonvisual sensory systems have long intrigued and fascinated biologists. Due to their restricted distributions and life history traits, many troglomorphic (subterranean-adapted) species are considered imperiled and are high priority targets for protective management. With increasing anthropogenic threats to cave ecosystems, it is important to study cave-dwelling organisms, so that informed management decisions can be made on a regular basis. Detailed information on the genetics, taxonomy, distribution, and colonization history of cavernicoles are necessary to make rigorous ecological inference and develop respective recommendations for monitoring and protecting cave organisms. The inference of phylogenetic relationships among subterranean fauna can be challenging because of morphological homoplasy due to certain requirements of cave life. To overcome this, molecular data are needed to test morphology-based hypotheses regarding the systematic and biogeographic relationships of terrestrial and aquatic subterranean life. While recent genetic and phylogeographic analyses have greatly improved our understanding of evolutionary and biogeographic history of cave organisms, many questions either remain unanswered or poorly investigated. In this dissertation I examined the current state of knowledge on cave ecology and molecular evolution and also discuss the advantages and possibilities that biospeleological investigations at the genomic level or “speleogenomics” provide to the understanding of these fascinating systems – with special emphasis in the areas of systematics, selection pressures, mt genome evolution, and phylogeography. Particularly, I investigated several evolutionary and biogeographic questions in two model organisms, the eastern North American crangonyctid amphipods and cave trechine beetles. I described the complete mitogenomes of four species of groundwater amphipods as well as a surface spring-dwelling species belonging to the family Crangonyctidae. I compared the base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, examined evolutionary signals imprinted on mitogenome of surface-adapted amphipods and compared to their subterranean counterparts to show evidence of adaptive evolution. In addition, I elucidated the colonization history, biogeography, and systematics of cave trechine beetles distributed primarily in the Appalachians (APP), Interior Low Plateau (ILP), and Ozarks (OZK) karst regions of central and eastern North America using UCE phylogenomics to estimate divergence times and ancestral range distribution.



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