Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae

Publication Type:Journal Article
Year of Publication:2007
Authors:Biffin, E, Harrington, MG, Crisp, MD, Craven, LA, Gadek, PA
Journal:Mol Phylogenet EvolMol Phylogenet EvolMol Phylogenet Evol
Volume:43
Pagination:124-39
Date Published:Apr
Type of Article:Comparative StudyResearch Support, Non-U.S. Gov't
ISBN Number:1055-7903 (Print)1055-7903 (Linking)
Accession Number:17070713
Keywords:*Evolution, Molecular, *Models, Genetic, *Phylogeny, Base Pairing, Base Sequence, Bayes Theorem, Computational Biology, DNA, Ribosomal Spacer/*genetics, Eugenia/*genetics, Likelihood Functions, Molecular Sequence Data, RNA, Ribosomal/*genetics, Selection, Genetic, Sequence Alignment, Sequence Analysis, DNA, Species Specificity
Abstract:

The internal transcribed spacers (ITS) of nuclear ribosomal DNA are widely used for phylogenetic inference. Several characteristics, including the influence of RNA secondary structure on the mutational dynamics of ITS, may impact on the accuracy of phylogenies estimated from these regions. Here, we develop RNA secondary structure predictions for representatives of the angiosperm family Myrtaceae. On this basis, we assess the utility of structural (stem vs. loop) partitioning, and RNA-specific (paired-sites) models for a 76 taxon Syzygium alignment, and for a broader, family-wide Myrtaceae ITS data set. We use a permutation approach to demonstrate that structural partitioning significantly improves the likelihood of the data. Similarly, models that account for the non-independence of stem-pairs in RNA structure have a higher likelihood than those that do not. The best-fit RNA models for ITS are those that exclude simultaneous double substitutions in stem-pairs, which suggests an absence of strong selection against non-canonical (G.U/U.G) base-pairs at a high proportion of stem-paired sites. We apply the RNA-specific models to the phylogeny of Syzygium and Myrtaceae and contrast these with hypotheses derived using standard 4-state models. There is little practical difference amongst relationships inferred for Syzygium although for Myrtaceae, there are several differences. The RNA-specific approach finds topologies that are less resolved but are more consistent with conventional views of myrtaceous relationships, compared with the 4-state models.

Short Title:Molecular phylogenetics and evolutionMolecular phylogenetics and evolution
Alternate Journal:Molecular phylogenetics and evolution
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith