Doctoral Dissertation Research: Kratovil: Phylogeographic analysis of introgressive gene flow among nuclear loci functionally linked to the mitochondrion

Overview: Our proposed research has a major aim: to test hypotheses of introgressive gene flow between diverging species using mitochondrial DNA (mtDNA) markers, randomly sampled nuclear markers, and nuclear markers that encode proteins that are functional within the mitochondrion. Specifically, we will use a salamander study system (Desmognathus fuscus and related species) with demonstrated patterns of mtDNA gene flow across species boundaries to test the hypothesis that nuclear-encoded mitochondrial genes (NEMGs) are more likely, on average, to introgress across species boundaries with patterns similar to those of mtDNA, relative to nuclear genes with non-mitochondrial function. This research will involve the development and sequencing of NEMG markers. These data will be paired with mtDNA and nuclear sequence data generated to test other complementary thesis objectives and collectively they will be implemented in comparative analyses at the phylogenetic and population level to test hypotheses concerning the co-evolution of the mitochondrial and nuclear genomes. This targeted project has the potential to address the following questions: 1) are patterns of divergence at NEMG loci and other nuclear loci similar at the genealogical level and at the population level?; 2) Is there evidence of introgression in NEMG loci between different Desmognathus species? or 3) between different D. fuscus populations? These questions cannot be adequately answered without robust sampling and analysis of NEMGs comparable at the depth examined in other samples of the nuclear genome. Intellectual Merit: Mito-nuclear discordance is a commonly observed phenomenon across many animal taxa. While there are many explanations for patterns of discordance at the population level, it's unlikely that NEMGs will reflect the same amount of discordance because of coevolutionary processes and interactions between genomes even in the face of recombination and gene-flow. Combining targeted parallel tagged amplicon sequencing of NEMGs with next-generation technologies, we have power to tease apart challenging problems that have persisted in systematics to inform species delimitation. To our knowledge, NEMGs have never been studied at the population level for the purpose of delimiting species boundaries or testing hypotheses of correlated patterns of gene flow with the mtDNA genome, and this proposed research will provide insight about the dynamic evolutionary histories of coevolving genomes. Broader Impacts: The proposed research will directly contribute to the improvement of my dissertation and will enhance my professional and academic development. This project will increase my aptitude in bioinformatics and data analysis that are essential in the age of genomics research. Our laboratory is fortunate to have many talented and dedicated undergraduates, and the proposed research is an excellent opportunity for me to lead a project to completion through the mentorship and training of undergraduate scholars, many of whom are members of historically underrepresented groups in science. For example, I currently mentor Jose Bocanegra, a UK Biology Ribble Scholar originally from , who has a strong interest in evolutionary and genomic research. The completion of this project will entail advancing scholarship through the preparation of materials for peer review and presentations at regional and national meetings. This research will also contribute to the broader understanding of molecular systematics and phylogenetics that are essential in investigations of heterogeneous evolutionary patterns across the genome, mito-nuclear discordance, introgression, and conservation. This research is of broad interest in plethodontid salamander research, as this is the largest and most diverse family of salamanders in the world; consequently, data from this study could contribute to many other projects.