DISSERTATION RESEARCH: Phylogenetic analysis of vision loss and gene expression in cave and surface adapted crayfish

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The repeated loss of pigmentation, eyes and vision in cave-dwelling animals presents biologists with an excellent opportunity to understand the genetic changes that have resulted in the convergent evolution of similar morphological changes in unrelated organisms. Freshwater crayfish have evolved to live in caves on at least seven occasions throughout their history, repeatedly losing vision. This project will use a well-supported evolutionary framework of freshwater crayfish to understand the role of gene regulation in producing iconic cave morphologies. This research will promote training of undergraduate and high school students in field, laboratory, and computational work. Data and analysis pipelines will be made available to the public and will contribute to invertebrate genomics research efforts. Ultimately, this research will advance our knowledge of how organisms adapt to novel habitats and contribute to the growing body of research in vision genomics.While the genetics of vision loss has been studied in single species systems such as the Mexican blind cave fish (Astyanax mexicanus), comparative studies across multiple species aimed at revealing statistically significant and biologically meaningful correlations have been lacking. The multiple transitions to cave habitats by freshwater crayfish and the subsequent loss of vision in each case make the group an ideal model to test hypotheses concerning the loss of complex traits in response to a common selective pressure. These evolutionarily independent replicates provide statistical power as well as the potential to uncover biologically meaningful correlations. Researchers will use comparative transcriptomics to develop a set of candidate genes related to vision loss and cave adaptation in this system. Gene expression levels will be measured across a set of these genes from multiple individuals of 14 species, both cave and surface, and modeled as an evolving trait on the phylogeny. These data and methods will be used to test if regulatory changes associated with vision loss show a signature of adaptive evolution and if the transcriptome evolves in a predictable way in vision loss events. This project will help to elucidate the role of gene regulation in producing these iconic cave phenotypes, using a unique framework, new technologies, and newly developed evolutionary models.