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- Title
- The role of evolutionary history and niche differentiation in structuring species co-occurrence in New Zealand Pittosporum (Pittosporaceae)
- Creator
- Nolting, Kristen Marie
- Date
- 2014
- Collection
- Electronic Theses & Dissertations
- Description
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Understanding the processes that shape the spatial distribution of species, and their co-existence in communities, remains one of the biggest challenges that ecologists face today. Investigations of co-existence typically treat species as independent entities, thereby ignoring their shared evolutionary history, niche preferences and functional similarity. This limits the ability of ecologists to make strong inferences regarding co-existence mechanisms. It is more useful to employ a...
Show moreUnderstanding the processes that shape the spatial distribution of species, and their co-existence in communities, remains one of the biggest challenges that ecologists face today. Investigations of co-existence typically treat species as independent entities, thereby ignoring their shared evolutionary history, niche preferences and functional similarity. This limits the ability of ecologists to make strong inferences regarding co-existence mechanisms. It is more useful to employ a pluralistic approach that integrates phylogenetic information and species-specific environmental and trait associations. In this study I evaluated the role of evolutionary history and environmental and functional trait differentiation in predicting species co-occurrence in the New Zealand plant genus Pittosporum. I hypothesized that co-occurring species would be more distantly related than non co-occurring species, given that closely related species are likely to be more ecologically similar as a result of their shared ancestry, and thus competitive interactions would preclude them from co-occurring. Similarly, I predicted that co-occurring species would be more divergent in their functional traits to enable co-existence. I found that co-occurring species were no different than non co-occurring species with respect to their phylogenetic dissimilarity, that co-occurring species had higher environmental niche overlap than non co-occurring species, and that for most traits measured there was no difference in trait dissimilarity among co-occurring and non co-occurring species. Approximate maximum vessel length and leaf nitrogen content, however, showed convergence among co-occurring species.
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- Title
- Genome-wide association study reveals genes associated with mite recruitment phenotypes in the domesticated grapevine (vitis vinifera
- Creator
- LaPlante, Erika R.
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
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Plants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and...
Show morePlants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and could lead to breeding domesticated Vitis vinifera L. varieties that are naturally defended against pathogens. Little is known about the genetics underlying mite recruitment phenotypes in Vitis. We conducted a GWAS to determine the genetic architecture of mite recruitment traits in V. vinifera using 399 cultivars from a common garden diversity panel. We investigated eight traits previously established in the literature associated with an increase in beneficial mite abundance. We found single nucleotide polymorphisms (SNPs) significantly associated with each mite recruitment trait investigated. Corresponding gene annotations of SNP genetic coordinates revealed notable gene associations, including a trichome development gene, and a physiological defense response gene, suggesting these genetic regions may have a large impact on mediating mite-plant interactions in this species. Our findings are among the first to investigate which genes underly ecologically important mutualisms between plants and beneficial mites and suggest promising candidate genes for breeding and genetic editing to increase naturally occurring predator-based defenses in grapes.
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- Title
- Increasing student comprehension of evolution through laboratory investigations and simulations
- Creator
- McClintock, Steven W.
- Date
- 2008
- Collection
- Electronic Theses & Dissertations
- Title
- Evolutionary dynamics of 3D digital constructs
- Creator
- Stredwick, Jason Michael
- Date
- 2005
- Collection
- Electronic Theses & Dissertations
- Title
- A differential evolution approach to feature selection in genomic prediction
- Creator
- Whalen, Ian
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
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The use of genetic markers has become widespread for prediction of genetic merit in agricultural applications and is a beginning to show promise for estimating propensity to disease in human medicine. This process is known as genomic prediction and attempts to model the mapping between an organism's genotype and phenotype. In practice, this process presents a challenging problem. Sequencing and recording phenotypic traits are often expensive and time consuming. This leads to datasets often...
Show moreThe use of genetic markers has become widespread for prediction of genetic merit in agricultural applications and is a beginning to show promise for estimating propensity to disease in human medicine. This process is known as genomic prediction and attempts to model the mapping between an organism's genotype and phenotype. In practice, this process presents a challenging problem. Sequencing and recording phenotypic traits are often expensive and time consuming. This leads to datasets often having many more features than samples. Common models for genomic prediction often fall victim to overfitting due to the curse of dimensionality. In this domain, only a fraction of the markers that are present significantly affect a particular trait. Models that fit to non-informative markers are in effect fitting to statistical noise, leading to a decrease in predictive performance. Therefore, feature selection is desirable to remove markers that do not appear to have a significant effect on the trait being predicted. The method presented here uses differential evolution based search for feature selection. This study will characterize differential evolution's efficacy in feature selection for genomic prediction and present several extensions to the base search algorithm in an attempt to apply domain knowledge to guide the search toward better solutions.
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- Title
- Do latex and resin canals spur plant diversification? : re-examining a classic example of escape and radiate coevolution
- Creator
- Foisy, Michael
- Date
- 2020
- Collection
- Electronic Theses & Dissertations
- Description
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The association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven's 'escape-and-radiate' hypothesis of co-evolution. However, it has been nearly three decades since these plant defenses have been examined as key innovations, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. I gathered data on...
Show moreThe association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven's 'escape-and-radiate' hypothesis of co-evolution. However, it has been nearly three decades since these plant defenses have been examined as key innovations, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. I gathered data on latex and resin canals across 345 families and 986 genera of vascular plants and conducted a multi-scale test of the association between these traits and lineage diversification rates. At a broad scale (across clades), I used sister-clade comparisons to test whether 28 canal-bearing clades had higher net diversification rates than their canal-lacking sister clades. At a finer scale (within clades), I used ancestral state reconstructions and phylogenetic models of lineage diversification rates to examine the relationship between trait evolution and the timing of diversification rate shifts in two better-characterized clades - Araceae and Papaveraceae. At both scales of analyses, I found poor support for the predicted relationship between diversification and the evolution of latex and resin canals. This re-examination reveals that there is no longer strong evidence for latex or resin canals as general, consistently replicable drivers of species diversity across plants. However, I could not rule out a relationship in all groups, and therefore argue that theoretical and empirical work aimed at understanding ecological factors that condition 'escape-and-radiate' dynamics will allow for more nuanced tests of the hypothesis in the future.
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- Title
- Phylogeny of Astylopsis Casey (Coleoptera : Cerambycidae) species and patterns of host use
- Creator
- Camerato, Ellen M.
- Date
- 2021
- Collection
- Electronic Theses & Dissertations
- Description
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Cerambycid (longhorn) beetles are diverse in their morphology and life history traits, but all share the common trait of being larval plant-borers. The larvae bore into and develop inside various plant tissues thus they can potentially cause significant economic and ecological damage, especially when transported to non-native localities. There is little empirical data on cerambycid life history traits that are essential in understanding their ecological and economic effects. Astylopsis Casey ...
Show moreCerambycid (longhorn) beetles are diverse in their morphology and life history traits, but all share the common trait of being larval plant-borers. The larvae bore into and develop inside various plant tissues thus they can potentially cause significant economic and ecological damage, especially when transported to non-native localities. There is little empirical data on cerambycid life history traits that are essential in understanding their ecological and economic effects. Astylopsis Casey (Lamiinae: Acanthocinini) is an eastern North American genus of six species. Host preference varies greatly among the species, including both angiosperms and gymnosperms. I used morphological characters and molecular data to reconstruct phylogenies of Astylopsis to test the hypothesis that host plant use among Astylopsis species is conserved. I constructed phylogenies using partial COI and CAD DNA sequences from Astylopsis species and outgroups using parsimony methods. Astylopsis collaris, A. macula, A. sexguttata, and A. arcuata were monophyletic in both COI and combined gene phylogenies, with the genus also exhibiting monophyly in the combined gene tree. Evidence of host shift from angiosperms to gymnosperms in some species was also observed. These results confirm current taxonomic separations among the four species and their outgroups and provide important host use information. No conclusions could be drawn regarding DNA variation in association with geographic locality. These findings will inform future studies expanding the molecular dataset for Astylopsis with additional genes (arginine kinase, 28S, and EF1-α) and species (Astylopsis perplexa and A. fascipennis).
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- Title
- Oceanic salt spray and herbivore pressure contribute to local adaptation of coastal perennial and inland annual ecotypes of the Seep Monkeyflower (Mimulus guttatus)
- Creator
- Popovic, Damian
- Date
- 2018
- Collection
- Electronic Theses & Dissertations
- Description
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In this study, we used the emergent model system Mimulus guttatus to explore the agents of selection that drive local adaptation across California’s coast-inland moisture gradient. We implemented a field reciprocal transplant experiment within agrofabric exclosures at sites in coastal and inland Sonoma County, California – minimizing the effects of aboveground stressors in an effort to elucidate their role in the evolution of local adaptation in this system. ASTER life-history modeling and...
Show moreIn this study, we used the emergent model system Mimulus guttatus to explore the agents of selection that drive local adaptation across California’s coast-inland moisture gradient. We implemented a field reciprocal transplant experiment within agrofabric exclosures at sites in coastal and inland Sonoma County, California – minimizing the effects of aboveground stressors in an effort to elucidate their role in the evolution of local adaptation in this system. ASTER life-history modeling and generalized linear mixed modeling approaches were used to analyze survival and dry aboveground biomass as fitness proxies. Despite altering no edaphic conditions, we found that among coastal exclosures, inland replicates were significantly more fit than their control counterparts, essentially rescuing inland fitness outside of their native range. Exclosures provided no fitness advantage for either ecotype at the inland site, aside from a moderate but statistically significant increase in biomass among exclosed coastal replicates. While it is unlikely to know all the agents of selection limited by our exclosures, we found that the number of replicates that experienced herbivory were significantly lower across all exclosures at the coast site. An elemental analysis of Sodium (Na) using salt traps installed at each site also demonstrated a reduction in salt exposure within exclosures. It is likely that some combination of aboveground stressors, likely driven primarily by herbivory and/or salt stress, plays a continuing role in the evolution of coastal M. guttatus populations, thus providing a new understanding of how local adaptation is maintained in this model system.
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