Key innovation or adaptive change? A test of leaf traits using Triodiinae in Australia.

The evolution of novel traits ("key innovations") allows some lineages to move into new environments or adapt to changing climates, whereas other lineages may track suitable habitat or go extinct. We test whether, and how, trait shifts are linked to environmental change using Triodiinae, C4 grasses that form the dominant understory over about 30% of Australia. Using phylogenetic and relaxed molecular clock estimates, we assess the Australian biogeographic origins of Triodiinae and reconstruct the evolution of stomatal and vascular bundle positioning. Triodiinae diversified from the mid-Miocene, coincident with the aridification of Australia. Subsequent niche shifts have been mostly from the Eremaean biome to the savannah, coincident with the expansion of the latter. Biome shifts are correlated with changes in leaf anatomy and radiations within Triodiinae are largely regional. Symplectrodia and Monodia are nested within Triodia. Rather than enabling biome shifts, convergent changes in leaf anatomy have probably occurred after taxa moved into the savannah biome-they are likely to have been subsequent adaptions rather than key innovations. Our study highlights the importance of testing the timing and origin of traits assumed to be phenotypic innovations that enabled ecological shifts.

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.

Frequency modulation and transient effects in the resonant propagation of coherent light pulses.

A theoretical analysis of the propagation of near resonant and linearly chirped light pulses through a resonant medium is presented under the restriction that the pulses are far enough off resonance or weak enough so that they do not significantly alter the atomic populations. If the pulses are of duration comparable to or less than the phase memory time T(2) of the atoms, it is found that the transient response of the medium gives rise to amplitude-and phase-modulating effects. Analytic solutions are presented to describe the propagation of an off-resonant pulse which is very short compared with T(2) and an off-resonant rectangular pulse. The evolution of a Gaussian pulse having a positive linear chirp is studied numerically.

Laser induced surface damage.

A summary of recent investigations of surface damage of transparent dielectrics is presented. Damage threshold measurements made on Owens-Illinois ED-2 laser glass at normal incidence and at Brewster's angle are reported. For 30-nsec pulses at normal incidence, exit surface damage thresholds are typically 100 J/cm(2) for ED-2 glass. The observed ratio between entrance and exit damage thresholds for the two geometries can be explained by considering the electric field strengths at the surfaces and including interference between incident and reflected light waves. A similar analysis is applied to surface damage that occurs during total internal reflection. Finally the morphology of surface damage of ED-2 laser glass is described, and a model based upon reflections from the laser induced plasma is proposed to explain the observations.

A molecular phylogeny of the endemic Australian genus Gastrolobium (Fabaceae: Mirbelieae) and allied genera using chloroplast and nuclear markers.

Gastrolobium (Fabaceae: Mirbelieae) is an endemic Australian genus that produces toxic sodium monofluoroacetate. A phylogenetic reconstruction of Gastrolobium and the related genera Brachysema, Callistachys, Jansonia, Nemcia, Oxylobium, and Podolobium is presented, using sequence data from three regions-the psbA-trnH intergenic spacer and the trnK 5' intron from chloroplast DNA and the 3' end of the external transcribed spacer (ETS) from nuclear ribosomal DNA. Gastrolobium is shown to be paraphyletic, with Brachysema, Jansonia, Nemcia, and Oxylobium lineare nesting within it, and Nemcia is shown to be polyphyletic within Gastrolobium. Past key morphological characters, such as fluoroacetate content and characters associated with pollination syndrome, are shown to be homoplastic, with fluoroacetate possibly a plesiomorphic condition lost in more derived species. Podolobium is also shown to be polyphyletic, with the P. ilicifolium group sister to Gastrolobium and the P. alpestre group sister to Callistachys, a member of the Oxylobium group. It is recommended that Gastrolobium be expanded to include Brachysema, Jansonia, Nemcia, and Oxylobium lineare, while further work is required to test the sister-group relationship between Podolobium s.s. (sensu stricto) and Gastrolobium.

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.