DISSERTATION RESEARCH: Surviving habitat loss: Physiological and evolutionary basis underlying tolerance to deforestation

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Tropical deforestation reshapes biological communities, benefitting some species, while pushing others towards local extinction. This research will examine the ecological and evolutionary underpinnings of tolerance to deforestation by focusing on the genetics of two closely related Central American frog species. Along with climate change and disease, habitat loss is pushing numerous amphibian species towards extinction. Understanding the biochemical basis for thermal adaptation is a crucial area of research given the multifaceted ways that humans are heating local, regional, and global climates. This research will inform conservation outcomes by providing insight into the reasons that some species are capable of bucking this global trend. The project also will involve the training of a graduate student and undergraduates, including individuals from groups that are underrepresented in the sciences.The researchers will study two species in the genus Craugastor that differ in their tendency to live in forested and deforested areas. Their previous research identified thermal tolerance as the primary factor explaining whether a species can survive in warmer, deforested areas. They will subject both species to forest- or pasture-like temperature regimes, and then uses Illumina-based RNA sequencing to test whether interspecific differences in constitutive expression and capacity to upregulate thermal stress tolerance genes (e.g., heat shock proteins) correspond to habitat affinity. They can thus begin to assess how gene regulation facilitates survival in deforested habitats. While differential expression may facilitate survival, structural differences (i.e., in protein coding sequence) also likely play a role. They will compare sequence data between species to scan for signatures of adaptation by employing both conventional molecular evolutionary tests for positive selection (i.e., dN/dS), as well as developing a novel structure-based approach that examines how changes at the DNA level are expected to alter protein stability at warm temperatures. Using protein homology modeling and RNA sequence data, they will test the hypothesis that proteins in the deforestation-tolerant species exhibit increased thermal stability. Because conventional methods of testing for positive selection are prone to false negatives, the use of a structure based, hypothesis-testing framework will substantially increase the detection of thermal adaptation. This study will place ecological changes caused by human activity in a macroevolutionary context, and provide a specific structural hypothesis to detect thermal adaption in an increasingly warm, human-dominated biosphere.