Genome evolution, morphological homoplasy, and the phylogeny of plethodontid salamanders

This dissertation examines the mitochondrial and nuclear genomes of plethodontid salamanders. Chapter One reports 24 new complete mitochondrial genome sequences representing the major clades of plethodontid salamanders. These sequences, plus three published previously, were analyzed using maximum parsimony, maximum likelihood, and partitioned and unpartitioned Bayesian phylogenetic analyses. Model-based analyses yielded congruent topologies, which strongly conflict with the morphological phylogenetic hypothesis reflected in current taxonomy. Consequently, novel scenarios were constructed for the evolution of projectile tongues, reduction in number of toes, and transition between a biphasic and direct-developing life-history strategy.; Chapter Two describes the molecular mechanisms yielding gene rearrangements in six plethodontid mitochondrial genomes. In each case, genomic evidence consistent with the duplication-random loss model of gene rearrangement remains in the genome in the form of pseudogenes and/or additional, presumably functional copies of tRNA genes and regulatory regions. Hypotheses for elevated rates of gene rearrangement in Plethodontidae based on nuclear genome size, metabolic rate, and mitochondrial genome effective population size are presented.; Chapter Three reports divergence dates for nodes in the plethodontid phylogeny and rates of molecular evolution for each mitochondrial gene. Phylogenetic performances of mitochondrial genes were assessed against the complete mitochondrial genome phylogeny. Multiple regression of phylogenetic performance onto gene length, rate of evolution, and among-site rate heterogeneity was also performed. rrnL and nad4 showed the best phylogenetic performance, and gene length and rate of molecular evolution were correlated with such performance.; Chapter Four presents a description of enucleated red blood cells in the genus Batrachoseps and an analysis of the relationship between nuclear genome size and red blood cell morphology. Genome and cell sizes, percentages of enucleated red blood cells, and a phylogenetic hypothesis with divergence dates for the main clades are presented. The range of genome sizes within Batrachoseps is narrow; the expected relationship between genome and cell size, if present, is therefore unrecoverable. However, cell sizes in Batrachoseps are smaller than those of other salamanders with comparable genome sizes, a likely result of enucleation, which may result from a rheological constraint on blood circulation imposed by effects of miniaturization on the microcirculatory system.