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    Systematic Revision within the Pleosporaceae and Identification of Processes that Occlude Phylogenetic Reconstruction

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    Author
    Lawrence, Daniel
    Issue Date
    2012
    Keywords
    Phylogenetics
    Sections
    Substitution saturation
    Systematics
    Plant Pathology
    Alternaria
    Horizontal gene transfer
    Advisor
    Pryor, Barry M.
    
    Metadata
    Show full item record
    Publisher
    The University of Arizona.
    Rights
    Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
    Embargo
    Release after 23-Oct-2012
    Abstract
    The hypothesis of horizontal gene transfer of a hybrid gene from bacteria to the filamentous Ascomycota was tested using constrained phylogenetic analyses and tests of topological congruence. Results suggest that the hybrid gene was acquired from bacteria by a single transfer before the radiation of the Leotiomyceta. The phylogenetic relationship among Nimbya and Embellisia was investigated using both morphological and molecular data. Examination of conidia morphology revealed that Nimbya and Embellisia comprise two and four distinct morphological groups, respectively. Molecular analyses support all morphological groups of Nimbya and Embellisia and reveal that both genera are polyphyletic. Results suggest the circumscription of these genera is based upon convergent morphological characters. To further understand the evolutionary relationship among Alternaria and closely related genera, ten protein-coding genes were sequenced across 176 species. Three genes possessed significant substitution saturation and two other genes did not possess sufficient phylogenetic signal to assess relationships among the asexual Alternaria. The remaining five loci revealed strong support for asexual Alternaria and the order of divergence among eight asexual Alternaria species-groups. The current polyphyly of Alternaria was resolved using morphological and molecular data. Morphological examination revealed that most members of the infectoria clade (sexual Alternaria) produce diagnostic colony characters on dichloran rose bengal yeast extract sucrose agar (DRYES) and weak potato dextrose agar (WPDA) that are fundamentally different as compared to other small-spored Alternaria species. These data also revealed that all members of the infectoria clade produce arachnoid vegetative hyphae with multiple primary conidiophores, whereas other small-spored Alternaria species do not. Phylogenetic analyses revealed that the sexual infectoria clade clusters with other sexual genera phylogenetically distant to the asexual Alternaria. Lastly, the validity of taxonomy and the phylogenetic relationship among three small-spored Alternaria species was examined. Total ortholog comparisons and whole-genome comparisons revealed that the DNA sequence of A. alternata ATCC 11680 has a higher percent similarity to A. tenuissima EGS 34-015 than to A. alternata EGS 34-016. This suggests that these two isolates share a more recent common ancestor and A. alternata EGS 34-016 is more distantly related.
    Type
    text
    Electronic Dissertation
    Degree Name
    Ph.D.
    Degree Level
    doctoral
    Degree Program
    Graduate College
    Plant Pathology
    Degree Grantor
    University of Arizona
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