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Type: Journal article
Title: Comparative study of the evolution of nuclear ribosomal spacers incorporating secondary structure analyzes within Dodonaeoideae, Hippocastanoideae and Xanthoceroideae (Sapindaceae)
Author: Harrington, M.
Biffin, E.
Gadek, P.
Citation: Molecular Phylogenetics and Evolution, 2009; 50(2):364-375
Publisher: Academic Press Inc Elsevier Science
Issue Date: 2009
ISSN: 1055-7903
Statement of
Mark G. Harrington, Ed Biffin and Paul A. Gadek
Abstract: Ribosomal DNA internal transcribed spacers (ITS) and partial external transcribed spacers (ETSf) are popularly used to infer evolutionary hypotheses. However, there is generally little consideration given to the secondary structures of these small RNA molecules and their potential effects on sequence alignment and phylogenetic analyzes. Intergeneric relationships amongst three of the four major lineages in the Sapindaceae, the Dodonaeoideae, Hippcastanoideae and Xanthoceroideae were assessed by firstly, generating secondary structure predictions for ITS and partial ETSf sequences, and then these predictions were used to assist alignment of the sequences. Secondly, the alignment was analyzed using RNA specific models of sequence evolution that account for the variation in nucleotide evolution in the independent loops and covariating stems regions of the ribosomal spacers. These models and phylogeny drawn from these analyzes were compared with that from analyzes using 'traditional' 4-state models and previous plastid analyzes. These analyzes identified that paired-site models developed to deal specifically with stem structures in RNA encoding sequences more appropriately account for the evolutionary history of the sequences than traditional 4-state substitution models.
Keywords: Sapindaceae; DNA, Ribosomal Spacer; RNA, Plant; Sequence Alignment; Sequence Analysis, RNA; Evolution, Molecular; Phylogeny; Nucleic Acid Conformation; Models, Genetic
RMID: 0020090123
DOI: 10.1016/j.ympev.2008.11.010
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Appears in Collections:Earth and Environmental Sciences publications
Environment Institute publications

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