This dissertation utilizes maximum likelihood optimization of morphological and molecular characters onto molecular phylogenies of snail-kiling flies and freshwater mussels to study character evolution. The larvae of snail-killing flies (Diptera: Sciomyzidae) display a wide range of feeding behaviors, being predators, parasitoids, or saprophages of a wide variety of gastropod mollusks. The genus Tetanocera is particularly interesting because its species occupy five distinct larval feeding behavioral groups with each species’ larvae living in one of two general habitat types (aquatic or terrestrial). Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics. Evidence is provided that phylogenetic niche conservatism was responsible for the maintenance of aquatic-associated larval morphological character states, and concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. Maximum likelihood optimization of larval feeding behavioral groups estimated that the ancestor to Tetanocera was an aquatic predator of non-operculate pulmonate snails, and that Tetanocera lineages made at least eight feeding group transitions during their phylogenesis. As a consequence, Tetanocera lineages transitioned from aquatic to terrestrial habitats at least six times independently.
Freshwater unionoidean bivalves have distinct maternal (F) and paternal (M) mtDNA genomes. Male unionoidean bivalves have a ~550bp 3' coding extension to the cox2 gene (Mcox2e) that is apparently absent from all other metazoans. Molecular sequence analyses indicate that this region is unique to unionoidean bivalves, is functional and likely the result of a single >65 MY old insertion event, has relatively high rates of evolution in its primary and secondary structures including variability in transmembrane helix (TMH) number, shows instances of site-specific positive selection, shows an overall pattern of purifying selection that leads to the preservation of the TMH and hydrophilic C-terminus tail sub-regions with variation in pedicted TMH number stemming from substitution-based processes, and has a more conserved C-terminus tail that is likely biologically active because it contains functional motifs. These results provide supporting evidence that MCOX2e has a novel reproductive function within unionoidean bivalves and indicate that unionoidean bivalve MCOX2 is a chimeric animal mtDNA-encoded protein.