Browsing by Subject "Adaptive evolution"
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Item Determination of the genetic basis of seed oil composition and melting point—adaptive quantitative traits—and their fitness effects in Arabidopsis thaliana(2013-12) Pelc, Sandra Elaine; Linder, C. RandalEvidence indicates seed oil melting point is likely an adaptive quantitative trait in many flowering plant species. An adaptive hypothesis suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The predicted differences in relative fitness under different temperatures have not yet been tested and little is known about the genetic basis of differences in oil composition. I used Arabidopsis thaliana to: (1) assess the fitness consequences of high and low melting point seeds germinating at different temperatures, (2) assess what genes underlie natural variation in seed oil composition, and (3) consider how these genes may be used to create oils with particular characteristics. To assess the effects of seed oil melting point on timing of seedling emergence and fitness, I competed high and low melting point lines of A. thaliana under cold and warm temperatures. Emergence timing between these lines was not significantly different at either temperature, which comported with warm temperature predictions but not cold temperature predictions. Under all conditions, plants competing against high melting point lines had lower fitness relative to those against low melting point lines, which matched expectations for undifferentiated emergence times. To assess the genetic basis of naturally occurring variation in seed oil melting point, the seed oil compositions of 391 accessions of A. thaliana were used in a genome-wide association study. Twelve genes were tightly linked with SNPs significantly associated with seed oil melting point variation. Seven encoded lipid synthesis enzymes or regulatory products. The remaining 5 encoded products with no clear relation to seed oil melting point. Results suggest selection can alter quantitative trait variation in response to local conditions through a small set of genes. 268 seed-expressed, candidate genes were linked to 103 SNPs associated with A. thaliana seed oil fatty acids. Eight genes were involved in lipid metabolism, and thirty-four encoded regulatory products. I discuss how knowledge of these genes can be used to breed and engineer desirable oil compositions for industry and nutrition.Item Emerging epizootic diseases of amphibians and fish : approaches to understanding Ranavirus emergence and spread(2013-12) Abrams McLean, Audrey Jeanine; Cannatella, David C.; Hillis, David M., 1958-Ranaviruses are large dsDNA viruses that are considered emerging pathogens, and they are known to cause mortality events in amphibian and fish populations. This research utilizes experimental and genomic data to elucidate the mechanisms driving the evolution and spread of ranaviruses, with a focus on host switching within the genus. In Chapter 1, we utilize virus challenge assays to examine potential transfer of ranaviruses between cultured juvenile largemouth bass (M. salmoides) and bullfrog tadpoles (Rana catesbeiana). Additionally, a commonly used antiparasitic treatment containing malachite green and formalin (MGF) was utilized to suppress the immune system of largemouth bass to assess the susceptibility of immunocompromised fish to ranaviruses. The results indicate that tadpoles are not susceptible to Largemouth Bass Virus (LMBV), but that bass are susceptible to ranaviruses isolated from amphibians. Furthermore, immunocompromised fish were more susceptible to both LMBV and FV3 infections than immunocompetent fish. In Chapter 2, we used eight sequenced ranavirus genomes and two selection-detection methods (site-based and branch-based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which are newly-acquired genes unique to ranavirus genomes. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching. In Chapter 3, we annotated and analyzed the nearly complete genomic sequence of LMBV to determine its taxonomic classification. The available genomic content and phylogenetic evidence suggests that LMBV is more closely related to amphibian-like ranaviruses (ALRVs) than grouper ranaviruses, and this is further supported by greater genomic collinearity between LMBV and ALRVs. This data suggests that the classification of LMBV as a ranavirus is warranted. The results presented here will help to clarify the taxonomic relationships of ranaviruses, and will also be useful in developing management strategies to limit interspecific and intraspecific viral spread. The information garnered from this research will have far-reaching implications in studies of amphibian conservation, disease evolution, and virology.