Sex and meiosis are ubiquitous in eukaryotes as the primary mode of reproduction. This suggests that despite the theoretical energetic advantages of asexual reproduction, organisms capable of sexual reproduction are at a much greater long-term evolutionary advantage. Rotifers, a group of microinvertebrates, offer unique opportunities to examine the evolution of sex due to their extensive proliferation, successful adaptation to a wide variety of ecological niches, and the diversity of reproductive modes represented in the group. The cyclically parthenogenetic monogonont rotifers have overcome constraints on the loss of sexual reproduction in order to frequently transition between sexual and asexual generations, making them a powerful system with which to address the maintenance of sex in animals. Obligately asexual bdelloid rotifers appear to have thrived without sex for tens of millions of years, a period of time much longer than expected given the hypothesized advantages of sexual reproduction. However, the molecular nature of sex and parthenogenesis is poorly understood in any rotifer species. To expand our knowledge of the molecular mechanisms of monogonont reproduction, we sequenced genomes of two distantly related species, Brachionus calyciflorus and Brachionus manjavacas and identified over 80 homologs for genes involved in meiotic processes. Several of these genes have undergone duplication events specific to the monogonont lineage, including genes with known roles in regulation of cell cycle transitions during meiosis. In addition, global gene expression patterns were determined using obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of B. calyciflorus. Quantitative comparison of expression between these strains revealed differentially expressed genes specific to sexual and asexual reproduction in this species, including genes related to dormancy/resting egg formation, meiosis, and hormone signaling pathways that are thought to be involved in the induction of sexual reproduction in monogononts. Finally, we analyzed gene expression in bdelloid rotifers for evidence of sexual reproduction or the utilization of meiotic genes under conditions inducing high levels of recombination. Through this work, we have established molecular markers for sexuality and asexuality in monogonont rotifers, and used these markers to evaluate reproduction in bdelloids. The data generated specifically allows for more informed analyses of the evolution of cyclical parthenogenesis and rotifer reproduction. Furthermore, this work extends the use of monogononts as a model system for addressing broader questions regarding the evolution of sexual reproduction.

Stress can be a driving force for new evolutionary changes leading to local adaptation, or may be responded to with pre-existing, ancestral tolerance mechanisms. Using brachionid rotifers (microzooplankton) as a study system, I demonstrate roles of both conserved physiological mechanisms (heat shock protein induction) and rapid evolution of traits in response to ecologically relevant stressors such as temperature and hydroperiod. Rapid evolution of higher levels of sex and dormancy in cultures mimicking temporary waters represents an eco-evolutionary dynamic, with trait evolution feeding back into effects on ecology (i.e., reduced population growth). I also reveal that prolonged culture in a benign laboratory environment leads to evolution of increased lifespan and fecundity, perhaps due to reduction of extrinsic mortality factors. Potential mechanisms (e.g., hormonal signals) are suggested that may control evolvability of facets of the stress response. Due to prior studies suggesting a role of progesterone signaling in rotifer sex and dormancy, the membrane associated progesterone receptor is assayed as a candidate gene that could show positive selection indicating rapid divergence. Despite some sequence variation that may contribute to functional differences among species, results indicate this hormone receptor is under purifying selection. Detailed analyses of multiple stress responses and their evolution as performed here will be imperative to understanding current patterns of local adaptation and trait-environment correlations. Such research also is key to predicting persistence of species upon introduction to novel habitats and exposure to new stressors (e.g., warming due to climate change). Perhaps one of the most intriguing results of this dissertation is the rapid, adaptive change in levels of sex and dormancy in a metazoan through new mutations or re-arrangements of the genetic material. This suggests species may be able to rapidly evolve tolerance of new stressors, even if standing genetic variation does not currently encompass the suite of alleles necessary for survival.