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Evolution and Adaptation in Caves: Freshwater Crayfish Phylogenetics, Diversification and Gene Expression Evolution Open Access

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Obligate cave-dwelling animals have long interested biologists due to the unique morphologies they develop in aphotic subterranean environments, including the reduction and loss of eyes and pigmentation. Comparative studies of these organisms can provide critical insights into the processes of adaptation to extreme environments, parallel evolution and trait loss. The goal of this dissertation is to explore the macroevolutionary consequences of cave adaptation using the freshwater crayfish, a group with approximately 45 described cave-dwelling species, as a study system. First, I develop a phylogenetic hypothesis for the ~650 species of freshwater crayfish using molecular sequence data and a phylogenetic synthesis approach combining results of several studies of smaller scale. I assess the state of phylogenetic knowledge for the group as well as the geographic and phylogenetic distributions of extinction risk. Second, I test the evolutionary dead-end hypothesis for cave-dwelling crayfish, which predicts that cave animals may be doomed to go extinct before they can diversify or transition to a more evolutionarily stable state. I find that crayfish have evolved to live in caves multiple times throughout their history and although they tend to have restricted geographic ranges and have a very low probability of transitioning back to the surface, they are able to maintain a stable diversity of lineages through time, meaning that caves are not evolutionary dead-ends. Finally, I assess the role of gen expression evolution underlying the loss of vision in blind cave crayfish. Using RNA-seq data from the eyes of eight blind and six sighted species, I find no significant convergence in gene expression patterns across vision loss events and a pervasive signature of increased variation in expression levels among and within species across the transcriptomes of blind lineages. This suggests that an absence of selective constraint maintaining gene expression levels allows genetic drift to drive vision loss in cave crayfish.

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