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.

Paralogy and orthology in the MALVACEAE rpb2 gene family: investigation of gene duplication in hibiscus.

A sample of the second largest subunit of low-copy nuclear RNA polymerase II (rpb2) sequences from Malvaceae subfamily Malvoideae suggests that rpb2 has been duplicated early in the subfamily's history. Hibiscus and related taxa possess two rpb2 genes, both of which produce congruent phylogenetic patterns that are largely concordant with cpDNA topologies. No evidence of functional divergence or disruption was found among duplicated copies, suggesting that long-term maintenance of duplicated copies of rpb2 is usual in this lineage. Therefore, this gene may be suitable for the potential diagnosis of relatively old polyploid events. One probable pseudogene was found in Radyera farragei and a single chimeric sequence was recovered from Howittia trilocularis, suggesting that the rpb2 locus is not as prone to evolutionary processes that can confound phylogenetic inferences based on nDNA sequences. The pattern of relationships among rpb2 sequences, coupled with chromosome number information and Southern hybridization data, suggests that an early polyploid event was not the cause of the duplication, despite independent evidence of paleopolyploidy in some members of Malvoideae. Rpb2 exons and introns together are suitable for phylogenetic analysis, producing well-resolved and well-supported results that were robust to model permutation and congruent with previous studies of subfamily Malvoideae using cpDNA characters.