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

Persistent Link:
http://hdl.handle.net/10150/223349
Title:
Systematic Revision within the Pleosporaceae and Identification of Processes that Occlude Phylogenetic Reconstruction
Author:
Lawrence, Daniel
Issue Date:
2012
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
Keywords:
Phylogenetics; Sections; Substitution saturation; Systematics; Plant Pathology; Alternaria; Horizontal gene transfer
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Plant Pathology
Degree Grantor:
University of Arizona
Advisor:
Pryor, Barry M.

Full metadata record

DC FieldValue Language
dc.language.isoenen_US
dc.titleSystematic Revision within the Pleosporaceae and Identification of Processes that Occlude Phylogenetic Reconstructionen_US
dc.creatorLawrence, Danielen_US
dc.contributor.authorLawrence, Danielen_US
dc.date.issued2012-
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © 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.en_US
dc.description.releaseRelease after 23-Oct-2012en_US
dc.description.abstractThe 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.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectPhylogeneticsen_US
dc.subjectSectionsen_US
dc.subjectSubstitution saturationen_US
dc.subjectSystematicsen_US
dc.subjectPlant Pathologyen_US
dc.subjectAlternariaen_US
dc.subjectHorizontal gene transferen_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplinePlant Pathologyen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorPryor, Barry M.en_US
dc.contributor.committeememberArnold, Anne Elizabethen_US
dc.contributor.committeememberVanEtten, Hansen_US
dc.contributor.committeememberHackett, Jeremiahen_US
dc.contributor.committeememberPryor, Barry M.en_US
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