@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 {22,
	title = {Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae},
	journal = {Mol Phylogenet EvolMol Phylogenet EvolMol Phylogenet Evol},
	volume = {63},
	number = {1},
	year = {2012},
	note = {Thornhill, Andrew HPopple, Lindsay WCarter, Richard JHo, Simon Y WCrisp, Michael DMol Phylogenet Evol. 2012 Apr;63(1):15-27. Epub 2011 Dec 14.},
	month = {Apr},
	pages = {15-27},
	edition = {2011/12/27},
	abstract = {The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.},
	isbn = {1095-9513 (Electronic)1055-7903 (Linking)},
	author = {Thornhill, A. H. and Popple, L. W. and Carter, R. J. and Ho, S. Y. and Crisp, M. D.}
}
@article {23,
	title = {Phylogenetic relationships in Myrceugenia (Myrtaceae) based on plastid and nuclear DNA sequences},
	journal = {Mol Phylogenet EvolMol Phylogenet EvolMol Phylogenet Evol},
	volume = {62},
	number = {2},
	year = {2012},
	note = {Murillo-A, JoseRuiz-P, EduardoLandrum, Leslie RStuessy, Tod FBarfuss, Michael H JMol Phylogenet Evol. 2012 Feb;62(2):764-76. Epub 2011 Dec 3.},
	month = {Feb},
	pages = {764-76},
	type = {Research Support, Non-U.S. Gov{\textquoteright}t},
	edition = {2011/12/14},
	abstract = {Myrceugenia is a genus endemic to South America with a disjunct distribution: 12 species occurring mainly in central Chile and approximately 25 in southeastern Brazil. Relationships are reconstructed within Myrceugenia from four plastid markers (partial trnK-matK, rpl32-trnL, trnQ-5{\textquoteright}rps16 and rpl16) and two ribosomal nuclear regions (ETS and ITS) using maximum parsimony and Bayesian analyses. Relationships inferred previously from morphological data are not completely consistent with those from molecular data. All molecular analyses support the hypothesis that Myrceugenia is monophyletic, except for M. fernadeziana that falls outside the genus. Chilean species and Brazilian species form two separate lineages. Chilean species form three early diverging clades, whereas Brazilian species are a strongly supported monophyletic group in a terminal position. Least average evolutionary divergence, low resolution, short branches, and high species diversity found in the Brazilian clade suggest rapid radiation. Geographical distributions and phylogenetic reconstructions suggest that extant Myrceugenia species arose in northern Chile followed by colonization southward and finally to the Juan Fernandez Islands and southeastern Brazil.},
	isbn = {1095-9513 (Electronic)1055-7903 (Linking)},
	author = {Murillo, A. J. and Ruiz, P. E. and Landrum, L. R. and Stuessy, T. F. and Barfuss, M. H.}
}
