Molecular phylogenetics of Chaetodon and the Chaetodontidae (Teleostei : Perciformes) with reference to morphology

Butterflyfish are colourful, pan-tropical coastal fish that are important and distinctive members of coral reef communities. A successful systematic scheme and a robust phylogeny is considered essential in understanding further their biogeography and ecology, although recent cladistic treatments of butterflyfish phylogeny, based on soft tissue and bone morphology and coded at the generic and subgeneric levels, differ in character coding and subsequently tree topology. This study provides an independent test of the morphologically based hypotheses, using molecular systematic data from two partial mitochondrial gene fragments, cytochrome b (cytb) and small subunit rRNA (rrnS), for 52 ingroup chaetodontids and seven pomacanthids used to root the molecular trees. Individual gene trees were largely compatible and a combined molecular phylogeny, inferred from Bayesian analysis, was used to test alternative hypotheses suggested by morphological analyses. The tree was also used to map the latest morphological matrix in order to evaluate potential synapomorphies for various nodes defining butterflyfish interrelationships. A clade comprised of Chelmon and Coradion was sister group to other chaetodontids. Heniochus and Hemitaurichthys were each resolved as monophyletic groups, and as sister taxa Of the taxa sampled, Prognothodes was resolved as the sister genus to Chaeotodon. Of the ten Chaetodon subgenera sampled, all were monophyletic but their interrelationships differed significantly from that inferred from morphological characters. Lepidochaetodon was the most basal subgenus followed by Exornator and the remaining subgenera. Molecular data support the sister group relationship between Corallochaetodon and Citharoedus suggested by morphology, but major differences occur among the remaining more derived taxa. Chaetodon trifascialis and C. oligacanthus were resolved as sister taxa adding weight to the inclusion of the latter in C. Megaprotodon. Of those pairs of taxa known to hybridize and sampled with molecular data, all were closely related phylogenetically, except those hybrids known to occur in the Rabdophorus subgenus. Two base changes separated C. pelewensis from C. paucifasciatus which have been regarded previously as a single species. Cytb provided greater resolution than rrnS and will likely provide additional resolution with greater taxon sampling.

Molecular phylogenetics of Lentibulariaceae inferred from plastid rps16 Intron and trnL-F DNA sequences: implications for character evolution and biogeography

Phylogenetic relationships among 75 species of Lentibulariaceae, representing the three recognized genera, were assessed by cladistic analysis of DNA sequences from the plastid rps16 intron and the trnL-F region. Sequence data from the two loci were analyzed both separately and in combination. Consensus trees from all analyses are congruent, and parsimony jackknife results demonstrate strong support for relationships both between and within each of the three demonstrably monophyletic genera. The genus Pinguicula is sister to a Genlisea-Utricularia clade, the phylogenetic structure within this clade closely follows Taylor's recent sectional delimitations based on morphology. Three principal clades are shown within Utricularia, with the basal sections Polypoinpholyx and Pleiochasia together forming the sister lineage of the remaining Utricularia species. Of the fundamental morphological specializations, the stoloniferous growth form apparently arose independently within Genlisea and Utricularia three times, and within Utricularia itself, perhaps more than once. The epiphytic habit has evolved independently at least three times, in Pinguicula, in Utricularia section Phyllaria, and within the two sections Orchidioides and Iperua (in the latter as bromeliad tank-epiphytes). The suspended aquatic habit may have evolved independently within sections Utricularia and Vesiculina. Biogeographic optimization on the phylogeny demonstrates patterns commonly associated with the boreotropics hypothesis and limits the spatial origin of Lentibulariaceae to temperate Eurasia or tropical America.

Platyhelminth phylogenetics - a key to understanding parasitism?

The comparative method, the inference of biological processes from phylogenetic patterns, is founded on the reliability of the phylogenetic tree. In attempting to apply the comparative method to the understanding of the evolution of parasitism in the phylum Platyhelminthes, we have highlighted several points we consider to be of value along with many problems. We discuss four of these topics. Firstly, we view the group at a phylum level, in particular discussing the importance of establishing the sister taxon to the obligate parasite group, the Neodermata, for addressing such questions as the monophyly, parasitism or the endo or ectoparasitic nature of the early parasites. The variety of non-congruent phylogenetic trees presented so far, utilising either or both morphological and molecular data, gives rise to the suggestion that any evolutionary scenarios presented at this stage be treated as interesting hypotheses rather than well-supported theories. Our second point of discussion is the conflict between morphological and molecular estimates of monogenean evolution. The Monogenea presents several well-established morphological autapomorphies, such that morphology consistently estimates the group as monophyletic, whereas molecular sequence analyses indicate paraphyly, with different genes giving different topologies. We discuss the problem of reconciling gene and species trees. Thirdly, we use recent phylogenetic results on the tapeworms to interpret the evolution of strobilation, proglottization, segmentation and scolex structure. In relation to the latter, the results presented indicate that the higher cestodes are diphyletic, with one branch difossate and the other tetrafossate. Finally, we use a SSU rDNA phylogenetic tree of the Trematoda as a basis for the discussion of an aspect of the digenean life-cycle, namely the nature of the first intermediate host. Frequent episodes of host-switching, between gastropod and bivalve hosts or even into annelids, are indicated.

Sugarcane moth borers (Lepidoptera: Noctuidae and Pyraloidea): phylogenetics constructed using COII and 16S mitochondrial partial gene sequences

Sugarcane moth borers are a diverse group of species occurring in several genera, but predominately within the Noctuidae and Pyraloidea. They cause economic loss in sugarcane and other crops through damage to stems and stalks by larval boring. Partial sequence data from two mitochondrial genes, COII and 16S, were used to construct a molecular phylogeny based on 26 species from ten genera and six tribes. The Noctuidae were found to be monophyletic, providing molecular support for the taxonomy within this subfamily. However, the Pyraloidea are paraphyletic, with the noctuids splitting Galleriinae and Schoenobiinae from the Crambinae. This supports the separation of the Pyralidae and Crambinae, but does not support the concept of the incorporation of the Schoenobiinae in the Crambidae. Of the three crambine genera examined, Diatraea was monophyletic, Chilo paraphyletic, and Eoreuma was basal to the other two genera. Within the Noctuidae, Sesamia and Bathytricha were monophyletic, with Busseola basal to Bathytricha. Many species in this study (both noctuids and pyraloids) had different biotypes within collection localities and across their distribution; however the individual biotypes were not phylogenetically informative. These data highlight the need for taxonomic revisions at all taxon levels and provide a basis for the development of DNA-based diagnostics for rapidly identifying many species at any developmental stage. This ability is vital, as the species are an incursion threat to Australia and have the potential to cause significant losses to the sugar industry.

Molecular systematics of the Philippine malaria vector Anopheles flavirostris

Allozyme and molecular sequence data from the malaria vector Anopheles flavirostris (Ludlow) (Diptera: Culicidae) were analysed from 34 sites throughout the Philippines, including the type locality, to test the hypothesis that this taxon is a single panmictic species. A finer-scaled allozyme study, of mainly Luzon samples, revealed no fixed genetic differences in sympatric sites and only low levels of variation. We obtained data from partial sequences for the internal transcribed spacer 2 (ITS2) (483 bp), the third domain (D3) (330 bp) of the 28S ribosomal DNA subunit and cytochrome c oxidase subunit I (COI) of mitochondrial DNA (261 bp). No sequence variation was observed for ITS2, only a one base pair difference was observed between Philippine and Indonesian D3 sequences and An. flavirostris sequences were unique, confirming their diagnostic value for this taxon. Sixteen COI haplotypes were identified, giving 25 parsimony informative sites. Neighbour-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian phylogenetic analysis of COI sequences for An. flavirostris and outgroup taxa revealed strong branch support for the monophyly of An. flavirostris, thus confirming that Philippine populations of this taxon comprise a single separate species within the Minimus Subgroup of the Funestus Group. Variation in the behaviour of An. flavirostris is likely to be intraspecific rather than interspecific in origin. © 2006 The Royal Entomological Society.

Molecular sieve silica membranes for H2/CO separation

Efficient separation of fuel gas (H2) from other gases in reformed gas mixtures is becoming increasingly important in the development of alternative energy systems. A highly efficient and new technology available for these separations is molecular sieve silica (MSS) membranes derived from tetraethyl-orthosilicate (TEOS). A permeation model is developed from an analogous electronic system and compared to transport theory to determine permeation, selectivity and apparent activation of energy based on experimental values. Experimental results for high quality membranes show single gas permselectivity peaking at 57 for H2/CO at 150°C with a H2 permeation of 5.14 x 10^-8 mol.m^-2.s^-1.Pa^-1. Higher permeance was also achieved, but at the expense of selectivity. This is the case for low quality membranes with peak H2 permeation at 1.78 x 10-7 mol.m-2.s-1.Pa-1 at 22°C and H2/CO permselectivity of 4.5. High quality membranes are characterised with positive apparent activation energy while the low quality membranes have negative values. The model had a good fit of r-squared of 0.99-1.00 using the experimental data.

Molecular Sieve Silica (MSS) Membranes for Gas Separation and Reaction Processes

Weakly branched silica films formed by the two-step sol-gel process allow for the formation of high selectivity membranes for gas separation. 29Si NMR and gas permeation showed that reduced crosslinking leads to He/CH4 selectivity improvement from 300 to 1000. Applied in membrane reactor for cyclohexane conversion to benzene, conversions were achieved at 14 fold higher than a conventional reactor at 250°C. Hydrothermal stability studies showed that carbon templating of silica is required for hydrothermally stable membranes. From our work it was shown that with correct application of chemistry, practical membrane systems can be built to suit gas separation (e. g. hydrogen fuel) and reactor systems.

Hydrothermal stable templated molecular sieve silica (TMSS) membranes for gas separation

In this work we compare the hydrothermal stability performance of a Templated Molecular Sieve Silica (TMSS) membrane against a standard, non-templated Molecular Sieve Silica (MSS) membrane. The tests were carried under dry and wet (steam) conditions for single gas (He, H2, CO and CO2) at 1-2 atm membrane pressure drop at 200oC. Single gas TMSS membrane H2, permeance and H2/CO permselectivity was found to be 2.05 x 10-8 mols.m-2.s-1.Pa-1 and 15, respectively. The MSS membrane showed similar selectivity, but increased overall flux. He permeance through membranes decayed at a rate of 4-5 x 10-10 mols.m-2.s-1.Pa-1 per day regardless of membrane ambience (dry or wet). Although H2/CO permselectivity of the TMSS membrane slightly improved from 15 to 18 after steam testing, the MSS membrane resulted in significant reduction from 16 to 8.3. In addition, membrane regeneration after more than 50 days resulted in the TMSS membrane reverting to its original permeation levels while no significant improvements were observed for the MSS membra ne. Results showed that the TMSS membrane had enhanced hydrothermal stability and regeneration ability.

Hydrothermal Stability Analysis of Carbonised Template Molecular Sieve Silica Membranes

For fuel cell CO clean up application, the presence of water with silica membranes greatly reduces their selectivity to CO. We show results of a new functional carbonised template membrane of around 13nm thickness which offered hydrothermal stability with no compromise to the membrane’s H2/CO permselectivity of 16. Lost permeance was also regenerated.

Hydrostability and Scaling Up Molecular Sieve Silica (MSS) Membranes for H2/CO Separation in Fuel Cell Systems

MSS membranes are a good candidate for CO cleanup in fuel cell fuel processing systems due to their ability to selectively permeate H2 over CO via molecular sieving. Successfully scaled up tubular membranes were stable under dry conditions to 400°C with H2 permeance as high as 2 x 10-6 mol.m-2.s^-1.Pa^-1 at 200 degrees C and H2/CO selectivity up to 6.4, indicating molecular sieving was the dominant mechanism. A novel carbonised template molecular sieve silica (CTMSS) technology gave the scaled up membranes resilience in hydrothermal conditions up to 400 degrees C in 34% steam and synthetic reformate, which is required for use in fuel cell CO cleanup systems.

A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.