Comparative study of the evolution of nuclear ribosomal spacers incorporating secondary structure analyzes within Dodonaeoideae, Hippocastanoideae and Xanthoceroideae (Sapindaceae)

Harrington, Mark G., Biffen, Ed, and Gadek, Paul A. (2009) Comparative study of the evolution of nuclear ribosomal spacers incorporating secondary structure analyzes within Dodonaeoideae, Hippocastanoideae and Xanthoceroideae (Sapindaceae). Molecular Phylogenetics and Evolution, 50 (2). pp. 364-375.

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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.

Item ID: 5529
Item Type: Article (Refereed Research - C1)
Keywords: secondary structure, ITS, ETS, Sapindaceae, RNA models, Bayesian analyzes, plant sciences
ISSN: 1095-9513
Date Deposited: 09 Nov 2009 04:41
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060409 Molecular Evolution @ 70%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060302 Biogeography and Phylogeography @ 30%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960805 Flora, Fauna and Biodiversity at Regional or Larger Scales @ 50%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 50%
Citation Count from Web of Science Web of Science 7
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