Doctoral Dissertations

Date of Award


Degree Type


Degree Name

Doctor of Philosophy


Ecology and Evolutionary Biology

Major Professor

Benjamin M. Fitzpatrick

Committee Members

James A. Fordyce, Randall L. Small, Matthew J. Gray


Cave organisms are classic examples of regressive evolution, as many disparate taxa have evolved similar convergent phenotypes in subterranean environments. While recent phylogeographic and population genetic analyses have greatly improved our understanding of the evolutionary and biogeographic history of cave organisms, many questions remain unanswered or poorly investigated. I investigated several evolutionary and biogeographic questions in a model system for regressive evolution and studies of ecological and evolutionary mechanisms, amblyopsid cavefishes. In chapter I, I used recently developed methods to delimit species boundaries and relationships in a widely distributed cavefish, Typhlichthys. I show that species diversity in Typhlichthys is currently underestimated and that the view of a single, widely distributed species is not valid. Rather, several morphologically cryptic lineages comprise the diversity in this clade. In chapter II, I examined regressive evolution and potential re-evolution of an eyed, surface form in amblyopsid cavefishes. Whether evolution is truly irreversible, known as Dollo’s Law, has become a question of increasing interest, as several recent studies have made claims that complex structures can be recovered after loss. Phylogenetic and ancestral character state analyses of amblyopsid cavefishes are consistent with re-evolution of eyes and pigmentation and recolonization of surface habitats in the surface-dweller Forbesichthys, providing an opportunity to rigorously discriminate between re-evolution and parallel evolution of cave phenotypes. Despite strong support for re-evolution and contradiction of Dollo’s Law, eye histological evidence and analyses of molecular evolution in the eye gene rhodopsin are consistent with Dollo’s Law supporting at least three independent subterranean colonizations and eye degeneration. Phylogenetic reconstructions of character evolution can occasionally produce strongly supported yet misleading results. In chapter III, I examined the biogeography and speciation of Typhlichthys. Phylogenetic and divergence time analyses support monophyly of Typhlichthys with the majority of cladogenic events occurring in the late Pliocene to Pleistocene, implicating climate change as the primary mechanism driving diversification. Biogeographical analyses, examination of molecular variation in rhodopsin, and structuring of genetic variation with hydrological boundaries, support multiple colonization events by a broadly distributed surface ancestor that subsequently went extinct rather than a single colonization event followed by subterranean dispersal and vicariance.

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