rdf-syntax-grammar
mods:
  schema location: http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
  title info:
    title: Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules
  name:
    name part: Gillespie, Joseph James
    name part: 1974-
    role:
      role term: creator
  name:
    name part: Cognato, Anthony I.
    role:
      role term: thesis advisor.
  type of resource: text
  genre: bibliography
  origin info:
    place:
      place term: txu
    date issued: 2005
    issuance: monographic
  language:
    language term: eng
  physical description:
    form: remote
    extent: 1 online resource.
  abstract: Ribosomal RNA (rRNA) molecules form highly conserved secondary and tertiary structures via rRNA-rRNA and rRNA-protein interactions that collectively comprise the macromolecule that is the ribosome. Because of their cellular universality, rRNA molecules are commonly used for phylogeny estimations spanning all divergences of life. In this dissertation, I elucidate the structure of several rRNAs by analyzing multiply aligned sequences for basepair covariation and conserved higher order structural motifs. Specifically, I predict novel structures for expansion segments D2 and D3 of the nuclear large subunit rRNA (28S) and variable regions V4-V9 of the nuclear small subunit rRNA (18S) from from 249 galerucine leaf beetles (Coleoptera: Chrysomelidae). I describe a novel means for characterizing regions of alignment ambiguity that improves methods for retaining phylogenetic information without violating nucleotide positional homology. In the program PHASE, I explore a variety of RNA maximum likelihood models using the 28S rRNA dataset and discuss the utitilty of these models in light oftheir performance under Bayesian analysis. I conclude that seven-state models are likely the best models to use for phylogenetic estimation, although I cannot determine with confidence which of the two seven-state models (7A or 7D) is better. Evaluation of the unpaired sites within both rRNAs in Modeltest provided a similar model of evolution for these non-pairing regions (TrN+ I+G). In addition, a sequenced region of the mitochondrial cytochrome oxidase I gene (COI) from the galerucines was evaluated in Modeltest, with each codon position modeled separately (GTR+I+G for positions 1 and 2, GTR+G for position 3). The combined galerucine dataset (28S+18S rRNA helices,28S+18S rRNA unpaired sites, COI 1st, 2nd and 3rd positions) provided for two mixed- model Bayesian analysis of five discretely-modeled partitions (using 7A and 7D). The results of these analyses are compared with those obtained fr…
  note: by Joseph James Gillespie.
  note: "Major Subject: Entomology"
  note: Title from author supplied metadata (automated record created on Nov. , 09:45:50.)
  note: Vita.
  note: Abstract.
  note: Electronic resource.
  note: System requirements: Adobe Acrobat Reader.
  note: Ph. D. Texas A&M University 2005.
  note: Includes bibliographical references.
  note: Text (Dissertation).
  subject:
    topic: Major entomology
  subject:
    topic: secondary structure
  subject:
    topic: ribosomal RNA
  subject:
    topic: molecular evolution
  subject:
    topic: phylogeny
  identifier: http://hdl.handle.net/1969.1/2580
  record info:
    record content source: TXA
    record creation date: 061121
    record change date: 20151104085744.0
    record identifier: in00002200740