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Item Natural enemy abundance and biological control in Bt maize using simulations of predator-prey interactions(Montana State University - Bozeman, College of Agriculture, 2017) Brown, Christopher Regan; Chairperson, Graduate Committee: Robert K. D. Peterson; Laura A. Burkle, Daniel Salinas Duron, Adam Schapaugh, Christopher K. Sehy, Paul C. Stoy, David K. Weaver, Jeffrey D. Wolt and Robert K. D. Peterson were co-authors of the article, 'Simulating interactions between natural enemies and pests in maize to assess the influence of alternative food, cannibalism, and intraguild predation' which is contained within this thesis.; Laura A. Burkle, Daniel Salinas Duron, Adam Schapaugh, Christopher K. Sehy, Paul C. Stoy, David K. Weaver, Jeffrey D. Wolt and Robert K. D. Peterson were co-authors of the article, 'Simulating interactions between natural enemies and prey in Bt and conventional maize' which is contained within this thesis.The potential effects of genetically modified maize expressing insect-resistant proteins from Bacillus thuringiensis (Bt) on natural enemies represent an active area of research highlighting considerable interest in understanding even subtle perturbations in agroecosystems. In the case of Bt maize, indirect effects on natural enemies may occur due to a reduced prey base caused by the desired effect of pest control by the Bt plant. Although these indirect effects may be subtle and difficult to study in the field, a modeling approach offers an alternative, allowing factors related to these subtle effects to be easily explored. In this effort, simulations of interactions between maize, two pests (the European corn borer (ECB) and an aphid), and two natural enemies (a lady beetle and green lacewing) were made using a modified TrophicLink model. TrophicLink is an individual-based model that uses functional ecology and food web network theory to simulate the trophic interactions of individuals and the resulting flow of energy. The individual-based model approach emphasizes the unique experiences of individuals and their trophic interactions leading to system level effects. Pollen utilization, cannibalism, and intraguild predation by natural enemies were simulated to explore the influence of these factors and to test the model. The model performed well in terms of reasonable representation of trophic functional types and interactions between them. The natural enemies were able to reduce a lepidopteran pest population and partially protect yield. The presence of pollen was influential in natural enemy population sizes and the biological control they provide. Cannibalism and intraguild predation caused notable reductions in natural enemy populations, but only small differences in biological control levels. In a second set of simulations involving Bt maize, prey-reduced scenarios included a short-term Bt maize scenario with ECB eggs and young larvae, and a second scenario without any ECB representing regional suppression of ECB by wide adoption of the Bt maize. Lady beetle and green lacewing population mass were similar across scenarios indicating resiliency of the generalist natural enemies to prey removal in the scenarios simulated. These findings are consistent with field study data that have not found consistent effects of Bt maize on natural enemies.Item Population genetics of Synehococcus species inhabiting the Mushroom Spring microbial mat, Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2010) Melendrez, Melanie Crystal; Chairperson, Graduate Committee: David M. Ward; Frederick M. Cohan (co-chair)The species concept in microbiology is under considerable debate. Some scientists believe that traditional approaches are adequate, while others search for more natural concepts. The ecotype concept (ecological species concept) was evaluated in this work. Two temperature sites of a well-studied microbial mat system in Yellowstone National Park were investigated. Previous molecular analyses with 16S rRNA and the adjacent internal transcribed spacer (ITS) suggested the dominance of two putative ecotypes (PEs) of cyanobacteria in these sites, Synechococcus genotypes A and B'. Higher resolution molecular approaches were developed to address the hypotheses that (i) there are more Synechococcus PEs than those discerned by 16S rRNA/ITS sequence variation, (ii) these PEs exhibit distinct ecological distribution patterns and (iii) recombination has been less important than mutation in shaping the evolution of these Synechococcus populations. Analysis of single protein-encoding loci revealed more sample-specific PEs than previously detected, but didn't account for recombination. Bacterial artificial chromosome (BAC) libraries were constructed to sample multiple loci near 16S rRNA genes for multi-locus sequence analyses (MLSA). Analysis of BAC clone end sequences revealed that 16S rRNA regions of the genomes of Synechococcus A- and B'-like populations have undergone rearrangement. Multiple BAC loci were analyzed using two population genetics algorithms; Evolutionary Simulation (ES) and eBURST. ES of concatenated MLSA sequences, but not eBURST analysis, suggested a much greater number of PEs than were detected by 16S rRNA and ITS and provided stronger evidence of sample-specificity. Recombination, suggested by phylogenetic incongruency among loci, multiple recombination tests and polymorphism patterns, appears to have been more frequent than mutation, but not to have erased ecotype structure. Many PEs predicted by ES contained a dominant variant surrounded by rare variants. eBURST predicted some clonal complexes with the same dominant variant, but different rare variants. ES appears to miss phylogenetically distant variants that differ at one locus, whereas eBURST appears to miss phylogenetically similar variants that differ at >1 locus. True ecotype populations in nature may contain both types of variants, but this must be evaluated by examining the distribution of all variants relative to environmental gradients.