Graduate Thesis Or Dissertation
 

Inferring Patterns and Processes of Emergence in Clonal Phytophthora Epidemics using Population Genomic Approaches

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  • Oomycete and fungal pathogens threaten food, fiber, and forests around the world. With climate change, these pathogens are expected to emerge more frequently. Evolution can facilitate their emergence through mechanisms such as mutations that change or expand host range. Characterizing evolutionary mechanisms in plant pathogens will contribute to our ability to predict how or when a pathogen might emerge. This dissertation used population and comparative genomic approaches to characterize patterns of emergence in two species of plant pathogenic oomycetes. The focus of this dissertation is on Phytophthora ramorum, the causal agent of sudden oak death and a threat to forests in the Western US and in Europe. Many oomycetes and fungi including P. ramorum have mixed mating systems, allowing them to reproduce sexually and asexually. Divergent lineages of P. ramorum have survived millions of years primarily clonally, and lineages have repeatedly re- emerged, making this a useful study system to understand how the costs of asexuality can be overcome. Describing pathways in which pathogens move into and within ecosystems is important to reduce disease outbreaks. The nursery industry is an important component of the pathway in which pathogens are introduced to ecosystems. In chapter two we analyzed a collection of P. plurivora from Oregon nurseries to characterize genetic diversity. I show that the meta-population among four nurseries is dominated by one single clone, but there is additional cryptic diversity. In chapters three and four, I show that the clonal lineage EU1 was introduced only once in a four- year period after the outbreak was found. I also show that currently, there is more diversity in the population of the clonal lineage NA1 than in the population of the EU1 clonal lineage. This is consistent with population genetic theory, since the NA1 population has accumulated mutations over a longer period of time. This work also compares the two P. ramorum lineages during the initial period of establishment in Oregon. While the EU1 population had lower diversity, we found cryptic diversity in the NA1 population. This is contrary to population genetic theory, as both populations were expected to show a similar pattern of variation. I show that this variation can mostly be attributed to losses of heterozygosity (LOH), a chromosomal aberration resulting in the spontaneous loss of one allele or chromosomal region in the diploid genome. Plasticity can be an important factor in pathogen emergence. In chapter two, I show phenotypic plasticity in fungicide tolerance within a dominant clone of P. plurivora. In chapter four, I show genomic plasticity at a population-level is generated through LOH in an NA1 population of P. ramorum. In chapter five, I show plasticity of effector content among divergent lineages of P. ramorum. I do not attribute causality of pathogen emergence to the plasticity I characterize in this dissertation. However, this work proposes important contributions to a greater understanding of various roles plasticity could influence pathogen emergence. Despite international efforts to prevent the movement of pathogens, the inadvertent transportation of infected plants and plant materials continues to challenge and threaten natural ecosystems. Understanding of population genetic and evolutionary biology of emerging and reemerging pathogens will be indispensable in our ability to understand and, eventually, predict epidemics.
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  • Ongoing Research
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  • 2023-06-08 to 2024-01-11

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