@article {32,
	title = {Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae},
	journal = {Ann BotAnn BotAnn Bot},
	volume = {106},
	number = {1},
	year = {2010},
	note = {Biffin, EdLucas, Eve JCraven, Lyn ARibeiro da Costa, ItayguaraHarrington, Mark GCrisp, Michael DEnglandAnn Bot. 2010 Jul;106(1):79-93. Epub 2010 May 11.},
	month = {Jul},
	pages = {79-93},
	type = {Research Support, Non-U.S. Gov{\textquoteright}t},
	edition = {2010/05/14},
	abstract = {BACKGROUND AND AIMS: The angiosperm family Myrtaceae comprises 17 tribes with more than half of the estimated 5500 species being referred to the fleshy-fruited and predominantly rainforest associated Syzygieae and Myrteae. Previous studies suggest that fleshy fruits have evolved separately in these lineages, whereas generally shifts in fruit morphology have been variously implicated in diversification rate shifts among angiosperms. A phylogenetic hypothesis and estimate divergence times for Myrtaceae is developed as a basis to explore the evidence for, and drivers of, elevated diversification rates among the fleshy-fruited tribes of Myrtaceae. METHODS: Bayesian phylogenetic analyses of plastid and nuclear DNA sequences were used to estimate intertribal relationships and lineage divergence times in Myrtaceae. Focusing on the fleshy-fruited tribes, a variety of statistical approaches were used to assess diversification rates and diversification rate shifts across the family. KEY RESULTS: Analyses of the sequence data provide a strongly supported phylogenetic hypothesis for Myrtaceae. Relative to previous studies, substantially younger ages for many of the clades are reported, and it is argued that the use of flexible calibrations to incorporate fossil data provides more realistic divergence estimates than the use of errorless point calibrations. It is found that Syzygieae and Myrteae have experienced elevated diversification rates relative to other lineages of Myrtaceae. Positive shifts in diversification rate have occurred separately in each lineage, associated with a shift from dry to fleshy fruit. CONCLUSIONS: Fleshy fruits have evolved independently in Syzygieae and Myrteae, and this is accompanied by exceptional diversification rate shifts in both instances, suggesting that the evolution of fleshy fruits is a key innovation for rainforest Myrtaceae. Noting the scale dependency of this hypothesis, more complex explanations may be required to explain diversification rate shifts occurring within the fleshy-fruited tribes, and the suggested phylogenetic hypothesis provides an appropriate framework for this undertaking.},
	keywords = {*Evolution, Molecular, Bayes Theorem, Fruit/genetics, Myrtaceae/*classification/*genetics, Phylogeny, Plasmids/genetics},
	isbn = {1095-8290 (Electronic)0305-7364 (Linking)},
	author = {Biffin, E. and Lucas, E. J. and Craven, L. A. and Ribeiro da Costa, I. and Harrington, M. G. and Crisp, M. D.}
}
@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.}
}
