The fate of any lineage is contingent on the rate at which its genome changes over time. Genome dynamics are influenced by patterns of mutation and recombination. Mutations as the raw force of variation can be acted on independently during exchanges of homologous genetic regions via meiotic recombination. While molecular evolution in sexual lineages is impacted by both mutation and recombination, asexual lineage fate is primarily influenced by the mutation rate; recombination is often altered or absent in asexuals. Although multiple studies show accelerated mutation accumulation in asexual lineages that have lost recombination, virtually nothing is known about rate patterns when meiosis is retained. Here, I use parasitic wasps in genus Diachasma to investigate genome evolution in a recently-derived asexual lineage. I provide evidence that asexual Diachasma possess a canonical set of meiosis genes as well as high levels of genomic homozygosity. Taken together, these observations support an active, albeit modified, form of meiosis in this asexual lineage. In addition, I present the first documentation of accelerated mutation accumulation in the nuclear genome of a naturally-occurring, meiotically- reproducing organism. If harmful, these mutations could impede asexual lineage persistence and contribute strong support for the long-term benefits of sex.

Phytophagous (plant-feeding) insects are extremely species-rich and typically display tight host associations (meeting and mating on or near their host plant) with one or a small number of hosts. This specialized lifestyle can promote diversification through assortative mating, ultimately leading to genetically differentiated host races (host associated differentiation; HAD). It has been shown that HAD can cascade up to the parasitic wasps (parasitoids) that utilize the phytophagous insects as hosts. Cascading HAD occurs when there is genetic differentiation among parasitoids as a result of differential host plant use by their host insects. Thus, host switching can promote parasitoid diversification as well. Here, I present three studies designed to help understand aspects of parasitoid shifts to novel hosts and environments. All of the studies in this dissertation utilize the Rhagoletis complex of flies and their associated parasitoids. Specifically, I address i) the role of subtle trait variation and environmental context in predicting successful parasitoid host shifts; ii) whether parasitoid host discrimination (a trait that can influence host shifts) is an innate or learned behavior; and iii) whether contemporary patterns of host shifts among parasitoids are echoed by historical host shifts in cophylogenetic analyses of host and parasitoid genera? Towards my first aim, I present a phenomenological model developed to predict successful host shifts by parasitoids. The simulations of the model explore how environmentally mediated traits can affect successful parasitoid colonization of a new host. For my second aim, I hypothesize that behaviors impacting parasitoid host plant preferences host shifts will be genetically based rather than a learned behavior. Shifting to a new host plant has been shown to cause reproductive isolation in phytophagous insects because of strong fidelity with their host plant. Parasitoids, however, have no direct contact with the host plant as they develop entirely within the host insect. The differences in life history traits could result parasitoid host shifts being driven by random changes in host preferences. I present preliminary results suggesting that parasitoids preferentially respond to their ancestral host plant’s olfactory cues, suggesting that host preferences have a genetic basis. Finally, I present a cophylogenetic analysis of Rhagoletis hosts and their parasitoids. I find that cospeciation is the most common coevolutionary event, although there is evidence of recent host shifting that contributes to current parasitoid species diversity. The results of these studies can help us understand how host shifts can act as a potential mechanism driving diversification in parasitoids.