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

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.

Evolution and biogeography of Alectryon (Sapindaceae).

Phylogenetic analysis of nucleotide sequences from four plastid loci (matK, partial trnK-matK introns, rps16 intron) and one nuclear locus (the internal transcribed spacer of rDNA; ITS-1) was conducted for 14 species of Alectryon and five related genera in Sapindaceae. Both matK and rps16 intron provide few informative characters within Alectryon, whereas ITS-1 provides the largest number of parsimony-informative characters and has the greatest sequence divergence between taxa. Support for branches in cladograms produced in PAUP increased markedly upon inclusion of ITS-1 data to matK and rps16 intron data. Analyses of each region alone or combined produced congruent results, suggesting that the regions are complementary. Phylogenetic analysis indicates that there are two main lineages within Alectryon, with A. subcinereus sister to the remaining sampled Alectryon taxa. Two morphological characters, presence/absence of petals and aril patterning, are congruent with the molecular phylogeny. One robustly supported clade is characterized by smooth arils and petals, in contrast to the taxa in the other major clade which have patterned arils and an absence of petals. These analyses also support a number of revised subgeneric groupings for Alectryon. The decision to submerge Heterodendrum in Alectryon is supported, although taxa belonging to Heterodendrum do not form a clade. The majority of the Australian Alectryon appear to belong to the tropical monsoonal/arid flora with species from both lineages being found in representative vine thickets across northern Australia. It appears that the seasonally dry rainforest communities comprise a number of elements that do not share common evolutionary histories within this genus.

Myrtaceae revisited: a reassessment of infrafamilial groups.

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.

Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach.

Parsimony analysis of matK and rbcL sequence data, together with a nonmolecular database, yielded a well-resolved phylogeny of Cupressaceae sensu lato. Monophyly of Cupressaceae sensu stricto is well supported, and separate northern and southern hemisphere subclades are resolved, with Tetraclinis within the northern subclade; there is no support for any of the tribes sensu Li. Taxodiaceae comprise five separate lineages. Chamaecyparis nootkatensis falls within Cupressus, clustering with a robust clade of New World species. Libocedrus Florin is paraphyletic and should incorporate Pilgerodendron. Evolution of several characters of wood and leaf anatomy and chemistry is discussed in light of this estimate of the phylogeny; numerous parallelisms are apparent. A new infrafamilial classification is proposed in which seven subfamilies are recognized: Callitroideae Saxton, Athrotaxidoideae Quinn, Cunninghamioideae (Sieb. & Zucc.) Quinn, Cupressoideae Rich. ex Sweet, Sequoioideae (Luerss.) Quinn, Taiwanioideae (Hayata) Quinn, Taxodioideae Endl. ex K. Koch. The rbcL sequence for Taxodium distichum is corrected, and the implications for a previously published estimate of the minimum rate of divergence of the gene since the Miocene are highlighted.

Rosid affinities of Surianaceae: molecular evidence.

Nucleotide sequences of the chloroplast gene, rbcL, were obtained for Suriana maritima, Cadellia pentastylis, Guilfoylia monostylis, Stylobasium australe, Quassia amara, Brucea mollis, Cupaniopsis anacardioides, Mangifera indica, Connarus conchocarpus, and Comesperma ericinum. Phylogenetic analyses of these, along with published sequences of representatives of rosid families, support the monophyly of the Surianaceae sensu Cronquist and provide evidence of an affinity with the Polygalaceae and Fabaceae. These conclusions are discussed in the light of available morphological data.