- In this dissertation I study evolutionary patterns at genes encoding antimicrobial peptides (AMPs) in frogs. AMPs are short, amphipathic, cationic, secreted proteins that kill bacteria and other pathogens through a non-catalytic mechanism that involves
binding to and disrupting the microbial cell membrane. In many animal taxa, positive selection is much more common at AMP genes than at most other types of genes, making them an ideal model for the study of non-neutral molecular evolution, as well as potentially important sites of adaptive differences in disease resistance between individuals, populations, or species. There is growing interest in the use of AMPs or their analogs in therapeutic applications, since they are functionally quite different from conventional antibiotics. However, evolutionary studies on AMPs or other immune effector molecules have been relatively rare compared to similar studies on other immunity genes. My research, which consists of both bioinformatic analyses of preexisting data and the generation of the first intraspecific polymorphism data at AMP loci in non-human vertebrates (leopard frogs; Ranidae: Rana: Pantherana), has uncovered several main results. First, I confirm that positive selection is common at frog AMP loci, indicative of coevolution with pathogens. Second, I demonstrate that a previoulsy proposed hypothesis of coordinated evolution between the mature AMP and the propiece is not supported by the data. Third, I show that substitution at synonymous sites is enhanced in the portion of the gene encoding the mature AMP; both the absence of an enhanced transversion/transition ratio and the low intraspecies polymorphism at silent sites argue against an enhanced mutation rate as the explanation, and therefore selection on "silent" sites is probably responsible. Fourth, I demonstrate that AMP gene duplication has occurred many times in the evolution of leopard frog genomes, possibly because it has been favored by selection. Finally, I reveal a striking non-neutral pattern of either very low or very high intraspecific polymorphism at AMP loci in leopard frogs; the former is due to positive selective sweeps, and the latter occurs because several highly divergent alleles are maintained by balancing selection, which probably takes the form of fluctuating selection.