i Dissertation Abstract Experiencing a novel environment is a common driver of evolutionary change. This change can be promoted by a variety of mechanisms and outcomes, such as novel selection, decreases in genetic variation due to founder effects, drift effects, and genetic admixture. Equally important are forces that impede or prevent change, including lack of suitable mutations, genetic correlations, developmental constraints, or antagonistic selection. A valuable system for studying

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... s related to evolutionary change following colonization of a novel habitat is the cave habitat, which has induced dramatic adaptive changes in many species that inhabit caves as a result of both adaptive and neutral forces. I studied the evolution of cave-dwelling salamanders, and in particular in the cave salamander, Eurycea lucifuga. Eurycea lucifuga is an evolutionary puzzle, inhabiting caves while having maintained brilliant coloration more typical of ancestral, surface dwelling ancestors. I first compared body shape among salamanders within Eurycea to examine the prediction from many previous studies that cave-dwellers are elongated relative to noncave-dwellers. I found that terrestrial species were larger than aquatic species, and also that cave species had shorter tails relative to their body size than non-cave species. These results contrast with trends generally discussed in the cave literature, and reflect a need for explicit testing of how habitat impacts morphology in salamanders. I next investigated the phylogeographic history of Eurycea lucifuga and found that divergence among major lineages happened millions of years ago, with more recent expansion within each clade. This is similar to other cave-dwellers that show extreme morphological specialization to the subterranean climate. Our results do not support the idea that a lack ii of time underground acts as a constraint on adaptive evolution in this species. Lastly, I compared phenotypic differentiation in color traits with neutral genetic differentiation. The findings indicated that at small scales there is evidence of local differentiation in color relative to the neutral expectation. However, the spatial structuring of differentiation differs between the color phenotype and genotype. Population genetic analyses within a cave system indicated that migration likely occurs by surface corridors, suggesting that coloration may be maintained by a more substantial reliance on non-cave habitats than has been documented for this species. I concluded from these results that the phenotype of the cave salamander, Eurycea lucifuga, is greatly impacted by a relatively minor aspect of its ecology, and hypothesize that its non-cave morphology is selectively maintained by use of surface habitats. In general, this work emphasizes the need to examine trait change in a broad context, considering phylogenetics, ecology, and neutral processes. iii Acknowledgements Though it is impossible to name all of the people who have contributed to the completion of this dissertation, there are a few who require special recognition. First and foremost, I am deeply grateful to my advisor, Doug Taylor, who has contributed overwhelmingly to any professional and personal growth I experienced during my time in his lab. From my first semester in the department, Doug put a great deal of energy into helping me identify my proximate and ultimate goals, and then supporting my pursuit of them wholeheartedly. His enthusiasm for unraveling scientific puzzles and the care he has put into mentoring me are examples I hope to follow someday in my own lab. I am also indebted to my committee members, Bob Cox, Butch Brodie, Laura Galloway, and Dave Carr. Their guidance and support, as well as their critical evaluation of the design, execution, and presentation of these projects, have been invaluable, and I could not have asked for a better group of mentors. Bob Cox in particular has been an incredibly conscientious first reader, and consistently went above and beyond to ensure that I was on track, both scientifically and administratively. I greatly appreciate his patience and keen insight. There exists a group of people who, like the Cave Salamander, display an overwhelming preference for the subterranean habitat. None of the research I have conducted would have been possible if not for the assistance of cavers across the country, who gave up their time to assist me in accessing caves and collecting samples. Though I will never attain their level of enthusiasm for caving, being deep underground with these fine folks has made me acutely aware of how incredible the natural world is, and what a small part of it I inhabit.