Anurans (frogs) are spectacularly diverse in their life histories, evolutionary trajectories, and morphological features. Advancement of next-generation sequencing techniques has improved knowledge of anuran genetics, but the functional genomic underpinnings of adaptation in most frog species remains uncharacterized. Transcriptomic approaches are some of the most powerful tools available to understand the molecular workings of adaptation among lineages and species. Because anurans face a multitude of anthropogenic threats and are unique in their biphasic life history, a question of particular interest is how gene expression profiles relate to phenotypic variation within and among species. In this dissertation, I tackle this question at multiple biological scales ranging from individuals to populations to species. I investigate transcriptome expression profiles and sequence data across the anuran tree of life, with an emphasis on non-model frog species native to the Americas. My overarching aim is to provide novel insights into how transcriptome elements recapitulate phenotypic adaptation in anurans. In Chapter 1, I examined positive selection signals in adaptation genes related to high-elevation diversification in Pristimantis, a diverse frog complex with direct development. My findings revealed widespread relaxed purifying selection among single-copy genes, while duplicated genes experienced intensified positive selection, suggesting these genes are valuable targets for future studies on high-elevation adaptation and direct development. In Chapter 2 I conducted a fully factorial experiment with Rana pipiens tadpoles, assessing the impacts of environmental predator cues and the pathogenic fungus Batrachochytrium dendrobatidis (Bd) on morphology and gene expression. Pathogen introduction significantly affected tadpole mortality, but morphological changes due to Bd or predator cues were minimal. Negative Bd qPCR results at the end of the experiment suggest that tadpoles’ ability to clear the pathogen infection may can offset its effects on morphology during early development. In Chapter 3, I analyzed transcriptomic data from natural populations of Rana yavapaiensis with varying levels of tolerance or susceptibility to Bd infection. Tolerant populations showed stronger suppression of genes that negatively regulate transcriptional responses to chytrid infection compared to susceptible populations, with gene expression related to steroid hormone production and transposable element activity potentially influencing pathogen susceptibility. Overall, my dissertation integrates genomic insights into species evolution, environmental challenges, and pathogen responses, illustrating the dynamic resilience of frogs in a changing world.
Nicholas Christodoulides
Advisor: Dr. Anna Savage
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