Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Extremophilic organisms are fascinating in that they thrive in physiologically demanding environments. Extreme habitats include subsurface caves and the deep sea, which share several qualities like low light and cold temperatures. Extremophiles have adapted bizarre characteristics that allow them to thrive in such harsh environments including eye and pigment loss (cavefishes) and development of a lure in anglerfishes. These traits are integral to the health and fitness of these organisms, yet the evolutionary history of these traits is unclear.

Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. I reconstructed evolutionary relationships using phylogenomics, estimated the ancestral histories of eye-state, and examined the impact of cave adaptation on body shape evolution in North American Amblyopsidae cavefishes. I found support for three independent subterranean colonization events and that cave-adaptive evolution does have an effect on body shape in fishes. My study highlights the importance of interdisciplinary examinations to infer cave-adaptive evolution.

Cave-obligate aquatic organisms are difficult to monitor for conservation needs due to cryptic diversity and unknown cave and water connectivity. I used population genomic analyses to examine genetic diversity of the Southern Cavefish species complex with respect to conservation concerns. I recovered five genetic clusters with no genetic exchange between clusters and low genetic divergence estimates, suggesting highly restricted ranges and little connectivity between groups; such results are greatly concerning for the conservation of these cavefishes.

Species of Lophiiformes are some of the most mysterious fishes, as they inhabit the darkest depths of the oceans and have a variety of unique traits including bioluminescent lures and parasitic males. Despite their captivating nature, evolutionary relationships among the Lophiiformes anglerfishes remain unclear. Utilizing phylogenomics, I recovered a novel topology for the order, finding non-monophyletic relationships of some anglerfish families. I clarified the relationships among the frogfishes, but the deep-sea anglerfishes remain a mystery. By studying extremophile evolution, we can expand areas beyond just evolutionary biology, including impacts of global climate change, human biotechnology, and medicine. We are just beginning to illuminate the macroevolutionary implications of darkness.



Committee Chair

Chakrabarty, Prosanta