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dc.contributor.advisorEdwards, Scott
dc.contributor.authorShultz, Allison Jane
dc.date.accessioned2019-08-09T09:28:18Z
dash.embargo.terms2019-05-01
dc.date.created2017-05
dc.date.issued2017-05-11
dc.date.submitted2017
dc.identifier.citationShultz, Allison Jane. 2017. Comparative and Population Genomics of Host-Pathogen Co-Evolution in Birds. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:41142072*
dc.description.abstractInfectious disease produces some of the strongest selective forces on natural populations across the tree of life. The signatures of pathogen-mediated evolution on host genomes have been described for several traditional model organisms, but few studies of more diverse organisms have detected such signatures beyond candidate immune loci. In my dissertation, I combine population and comparative genomics to study the dynamics of pathogen-mediated selection at two evolutionary timescales in wild bird populations. In Chapters 1 and 2, I integrate geographic and temporal sampling to compare the impacts on genomic variability of recent founder events and an epizootic on the House Finch (Haeomorhous mexicanus). House Finches, native to the western US and Mexico, were introduced to the Hawaiian Islands in 1870 and separately to the eastern US in 1940. In 1994, Mycoplasma gallisepticum (MG), previously associated with poultry, jumped to House Finches and caused severe declines. In Chapter 1, I genotype ~2,000 loci in samples collected before and 10 years after the epizootic. I demonstrate that demographic shifts brought about by the founder events have much more profound genomic impacts than pathogen-mediated natural selection. In Chapter 2, I use whole-genome resequencing data in six House Finch populations from three time points. I show that the expansion of the western US population following the last glacial maximum had the largest impact on patterns of genomic variation, followed by the eastern founder event. This genome-wide dataset also enables me to detect a decrease in genetic diversity immediately following the epizootic. Additionally, the lack of temporal differentiation at individual SNPs suggests that House Finches evolved resistance through polygenic selection. As a complement to these population-level analyses, in Chapter 3, I use over 11,000 well-annotated genes from 39 bird genomes to I show that immune genes encoding proteins that interact directly with pathogens consistently show evidence of positive selection. Using a dataset comprised of all genes regardless of function, I also show that immune system functional pathways are enriched for signatures of positive selection. Taken together, I demonstrate that host-pathogen interactions play an important role in shaping the bird genome over long evolutionary timescales.
dc.description.sponsorshipBiology, Organismic and Evolutionary
dc.format.mimetypeapplication/pdf
dc.language.isoen
dash.licenseLAA
dc.subjectgenomics
dc.subjecthost-pathogen co-evolution
dc.subjectbirds
dc.subjectaves
dc.subjecthouse finch
dc.subjectmycoplasma
dc.subjectnatural selection
dc.subjectpolygenic selection
dc.subjectpositive selection
dc.titleComparative and Population Genomics of Host-Pathogen Co-Evolution in Birds
dc.typeThesis or Dissertation
dash.depositing.authorShultz, Allison Jane
dash.embargo.until2019-05-01
dc.date.available2019-08-09T09:28:18Z
thesis.degree.date2017
thesis.degree.grantorGraduate School of Arts & Sciences
thesis.degree.grantorGraduate School of Arts & Sciences
thesis.degree.levelDoctoral
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy
thesis.degree.nameDoctor of Philosophy
dc.contributor.committeeMemberHoekstra, Hopi
dc.contributor.committeeMemberWakeley, John
dc.type.materialtext
thesis.degree.departmentBiology, Organismic and Evolutionary
thesis.degree.departmentBiology, Organismic and Evolutionary
dash.identifier.vireo
dc.identifier.orcid0000-0002-2089-4086
dash.author.emailallisonjshultz@gmail.com


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