@article {36,
	title = {Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae},
	journal = {Mol Phylogenet EvolMol Phylogenet EvolMol Phylogenet Evol},
	volume = {43},
	number = {1},
	year = {2007},
	note = {Biffin, EHarrington, M GCrisp, M DCraven, L AGadek, P AMol Phylogenet Evol. 2007 Apr;43(1):124-39. Epub 2006 Aug 22.},
	month = {Apr},
	pages = {124-39},
	type = {Comparative StudyResearch Support, Non-U.S. Gov{\textquoteright}t},
	edition = {2006/10/31},
	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.},
	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},
	isbn = {1055-7903 (Print)1055-7903 (Linking)},
	author = {Biffin, E. and Harrington, M. G. and Crisp, M. D. and Craven, L. A. and Gadek, P. A.}
}
@article {50,
	title = {Myrtaceae revisited: a reassessment of infrafamilial groups},
	journal = {Am J BotAm J BotAm J Bot},
	volume = {88},
	number = {11},
	year = {2001},
	note = {Wilson, P GO{\textquoteright}Brien, M MGadek, P AQuinn, C JAm J Bot. 2001 Nov;88(11):2013-25.},
	month = {Nov},
	pages = {2013-25},
	edition = {2001/11/01},
	abstract = {Cladistic analyses are presented of matK sequence data as well as a nonmolecular database for an identical set of exemplar species chosen to represent the core genera or groups of genera in Myrtaceae. Eleven robust clades are recognized on the molecular data. Polyphyly of the previously recognized Metrosideros and Leptospermum alliances is confirmed, and several smaller informal taxonomic groupings are recognized from among the members of the former alliance, i.e., the Tristania, Tristaniopsis, Metrosideros, and Lophostemon groups. The nonmolecular analysis provides only limited resolution of relationships. A degree of congruence exists between the two analyses in that two separate fleshy-fruited clades, the Acmena and Myrtoid groups, are identified, as are the Eucalypt and Tristania groups, and Psiloxylon and Heteropyxis are the first lineages to diverge in both analyses. A combined analysis recognized all 11 clades that received strong support from the molecular data. A high level of homoplasy is revealed in many of the nonmolecular characters when they are examined against the combined estimate of phylogeny.},
	isbn = {0002-9122 (Print)0002-9122 (Linking)},
	author = {Wilson, P. G. and O{\textquoteright}Brien, M. M. and Gadek, P. A. and Quinn, C. J.}
}
