A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data

The 16S rRNA gene (16S rDNA) is currently the most widely used gene for estimating the evolutionary history of prokaryotes, To date, there are more than 30 000 16S rDNA sequences available from the core databases, GenBank, EMBL and DDBJ, This great number may cause a dilemma when composing datasets for phylogenetic analysis, since the choice and number of reference organisms are known to affect the resulting tree topology. A group of sequences appearing monophyletic in one dataset may not be so in another. This can be especially problematic when establishing the relationships of distantly related sequences at the division (phylum) level. In this study, a multiple-outgroup approach to resolving division-level phylogenetic relationships is suggested using 16S rDNA data. The approach is illustrated by two case studies concerning the monophyly of two recently proposed bacterial divisions, OP9 and OP10.

A phylogenetic study of Lepidapedoides Yamaguti, 1970 (Digenea) with a key and descriptions of two new species from western Australia

Two new species of the genus Lepidapedoides are described from the aulopodid teleost Aulopus purpurissatus from south-western Australia. Both are distinguished from other Lepidapedoides spp. by their pedunculate ventral sucker. Lepidapedoides pistoris n. sp. and L. elongatrium n. sp. are distinguished by the possession of a narrow, elongate form, a long ventral sucker to ovary distance: the vitellarium reaching only to the posterior level of the cirrus-sac, the cirrus-sac length and the deep genital atrium with the metraterm entering distally to its base in L. elongatrium. A key to species of the genus is given. A character matrix is included for the genus. Poorly resolved phylogenetic trees indicate two main lineages in the genus. The two new species described here are resolved as sister taxa. The new combination Lepidapedoides freitasi (Kohn gr Fernandes, 1970) is formed for Acanthocolpoides freitasi.

Generic delimitation and phylogenetic uncertainty: An example from a group that has undergone an explosive radiation

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience. © CSIRO.

Reassessment of the phylogenetic position of Caulobacter subvibrioides

Determination of the 16S rRNA gene sequence of Caulobacter subvibrioides ATCC 15264(T) (T = type strain) confirmed that this species is a member of the alpha subclass of the Proteobacteria and showed that it is phylogenetically most closely related to the Caulobacter group comprising the species Caulobacter bacteroides, Caulobacter crescentus, and Brevandimonas (Pseudomonas) diminuta, for which 16S rRNA sequences of the type strains are currently available. The closest known relative of strain ATCC 15264(T) among these species is B. diminuta (level of direct pairwise sequence similarity, 95%). On the basis of its previously determined 16S rRNA sequence (accession number M83797), C. subvibrioides is most closely related to Sphingomonas adhaesiva in the alpha-4 subgroup (level of similarity, 97.7%). Analysis of the hydroxy fatty acids of C. subvibrioides ATCC 15264(T) showed that the 2-hydroxymyristic acid which is characteristic of the genus Sphingomonas was absent.

Phylogenetic relationships and uncertain taxonomy of Pedomicrobium species

The phylogenetic relationships among the species of the genus Pedomicrobium were studied by comparing their 16S rRNA sequences, The Pedomicrobium species form a coherent phylogenetic cluster within the genera of the hyphal budding bacteria in the alpha-Proteobacteria. The sequences of two strains of Pedomicrobium australicum were obtained from DNAs extracted from nonviable freeze-dried cells, which are the only source of material available, and were found to be almost identical (level of similarity, 99.9%), Overall, the Pedomicrobium species are closely related, with sequence similarities ranging from 96.2 to 99.9%, Pedomicrobium manganicum is phylogenetically the most distantly related species and exhibits the lowest similarity (96.2%) with Pedomicrobium americanum, Australian isolate Pedomicrobium sp, strain ACM 3067, P, americanum, and P, australicum are all very highly related, with similarities greater than 99%, Pedomicrobium sp, strain ACM 3067 is most closely related to P, australicum (level of similarity, 99.6%) and P, americanum (99.4%), These manganese-oxidizing species are more closely related to the iron-oxidizing species Pedomicrobium ferrugineum than to the other manganese-oxidizing species, P, manganicum. Taxonomic uncertainties resulting from the loss of the type culture of P, australicum are discussed.

Phylogenetic revision of Agapophytinae subf.n. (Diptera : Therevidae) based on molecular and morphological evidence

Agapophytinae subf.n. is a highly diverse lineage of Australasian Therevidae, comprising eight described and two new genera: Agapophytus Guerin-Meneville, Acupalpa Krober, Acraspisa Krober, Belonalys Krober, Bonjeania Irwin & Lyneborg, Parapsilocephala Krober, Acatopygia Krober, Laxotela Winterton & Irwin, Pipinnipons gen.n. and Patanothrix gen.n. A genus-level cladistic analysis of the subfamily was undertaken using sixty-eight adult morphological characters and c. 1000 base pairs of the elongation factor-1 alpha (EF-1 alpha) protein coding gene. The morphological data partition produced three most parsimonious cladograms, whereas the molecular data partition gave a single most parsimonious cladogram, which did not match any of the cladograms found in the morphological analysis. The level of congruence between the data partitions was determined using the partition homogeneity test (HTF) and Wilcoxon signed ranks rest. Despite being significantly incongruent in at least one of the incongruence tests, the partitions were combined in a simultaneous analysis. The combined data yielded a single cladogram that was better supported than that of the individual partitions analysed separately. The relative contributions of the data partitions to support for individual nodes on the combined cladogram were investigated using Partitioned Bremer Support. The level of support for many nodes on the combined cladogram was non-additive and often greater than the sum of support for the respective nodes on individual partitions. This synergistic interaction between incongruent data partitions indicates a common phylogenetic signal in both partitions. It also suggests that criteria for partition combination based solely on incongruence may be misleading. The phylogenetic relationships of the genera are discussed using the combined data. A key to genera of Agapophytinae is presented, with genera diagnosed and figured. Two new genera are described: Patanothrix with a new species (Pat. skevingtoni) and Pat. wilsoni (Mann) transferred from Parapsilocephala, and Pipinnipons with a new species (Pip. kroeberi). Pipinnipons fascipennis (Krober) is transferred from Squamopygin Krober and Pip. imitans (Mann) is transferred from Agapophytus. Agapophytus bicolor (Krober) is transferred from Parapsilocephala. Agapophytus varipennis Mann is synonymised with Aga, queenslandi Krober and Aga. flavicornis Mann is synonymised with Aga. pallidicornis (Krober).

The adult ventral nerve cord as a phylogenetic character in brachyceran Diptera

Insect ganglia are often composed of fused segmental units or neuromeres. We estimated the evolution of the ventral nerve cord (VNC) in higher Diptera by comparing the patterns of neuromere fusion among 33 families of the Brachycera. Variation within families is uncommon, and VNC architecture does not appear to be influenced by body shape. The outgroup pattern, seen in lower Diptera, is fusion of neuromeres belonging to thoracic segments 1 and 2 (T1 and T2), and fusion of neuromeres derived from T3 and abdominal segment 1 (A1). In the abdomen, neuromeres A7-10 are fused into the terminal abdominal ganglion (TAG). Increased neuromere fusion is a feature of the Brachycera. No brachyceran shows less fusion than the outgroups. We established six pattern elements; (1) fusion of T1 and T2, (2) fusion of T3 and A1, (3) fusion of the T1/T2 andT3/A1 ganglia, (4) increase in the number of neuromeres comprising the TAG, (5) anteriorward fusion of abdominal neuromeres, and (6) the complete fusion of thoracic and abdominal neuromeres into a synganglion. States 1 and 2 are present in the outgroup lower Diptera, and state 3 in the Xylophagomorpha, Stratiomyomorpha, Tabanomorpha and Cyclorrhapha. State 4 is a feature of all Eremoneura. State 5 is present in Cyclorrhapha only, and state 6, fusion into a synganglion, has evolved at least 4 times in the Eremoneura. Synapomorphies are provided for the Cyclorrhapha and Muscoidea, and a grouping of three basal brachyceran infraorders Xylophagomorpha, Stratiomyomorpha and Tabanomorpha. The patterns of fusion suggest that VNC architecture has evolved irreversibly, in accordance with Dollo's law.

A preliminary phylogenetic analysis of the Capsalidae (Platyhelminthes : Monogenea : Monopisthocotylea) inferred from large subunit rDNA sequences

Phylogenetic relationships within the Capsalidae (Monogenea) were examined Using large subunit ribosomal DNA sequences from 17 capsalid species (representing 7 genera, 5 subfamilies), 2 outgroup taxa (Monocotylidae) plus Udonella caligorum (Udonellidae). Trees were constructed using maximum likelihood, minimum evolution and maximum parsimony algorithms. An initial tree, generated from sequences 315 bases long, Suggests that Capsalinae, Encotyllabinae, Entobdellinae and Trochopodinae are monophyletic, but that Benedeniinae is paraphyletic. Analyses indicate that Neobenedenia, currently in the Benedeniinae, should perhaps be placed in 2 separate subfamily. An additional analysis was made which omitted 3 capsalid taxa (for which only short sequences were available) and all outgroup taxa because of alignment difficulties. Sequence length increased to 693 bases and good branch support was achieved. The Benedeniinae was again paraphyletic. Higher-level classification of the Capsalidae, evolution of the Entobdellinae and issues of species identity in Neobenedenia are discussed.

Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity

The diversity of the culturable microbial communities was examined in two sponge species-Pseudoceratina clavata and Rhabdastrella globostellata. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis. The bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both Firmicutes and Alphaproteobacteria. The majority of the Alphaproteobacteria isolates were most closely related to isolates from other sponge species including alpha proteobacterium NW001 sp. and alpha proteobacterium MBIC3368. Members of the low %G + C gram-positive (phylum Firmicutes), high %G + C gram-positive (phylum Actinobacteria), and Cytophaga-Flavobacterium-Bacteroides (phylum Bacteroidetes) phyla of domain Bacteria were also represented in both sponges. In terms of culturable organisms, taxonomic diversity of the microbial community in the two sponge species displays similar structure at phylum level. Within phyla, isolates often belonged to the same genus-level monophyletic group. Community structure and taxonomic composition in the two sponge species P. clavata and Rha. globostellata share significant features with those of other sponge species including those from widely separated geographical and climatic regions of the sea.

Upper level, C House, Coorparoo, Brisbane

View along North-West elevation upper level.

Lower level interior, C House, Coorparoo, Brisbane

View to landcape beyond from lower level interior.

High-level and phonological awareness abilities of children following management for supratentorial tumour: Part II

Background. Limited information is available regarding the impact of childhood tumour on the cerebral hemispheres and supratentorial cranial fossa. However, a recent study found that children managed for a tumour located in this region may demonstrate reduced general language abilities. However, the indirect or direct impact of a tumour in this region on higher-level language abilities in childhood is at present largely unknown. Materials and methods. The present study examined the higher language and phonological awareness abilities of five children treated for supratentorial tumour ranging in age from seven to fourteen years in age. Assessments included measures of receptive and expressive semantic abilities, inferencing, figurative language, and problem solving, as well as a comprehensive pre-literacy test. Results. As a group, reductions were evident in problem solving, and in the ability to receive and decode content of high-level language when compared to a group of age- and gender-matched peers. At an individual level, only two of five children managed for supratentorial tumour demonstrated language deficits. These two cases were noted to be the same children previously identified as also having general language deficits. More widespread findings were noted in phonological awareness, with four of the five children previously managed for supratentorial tumour demonstrating weaknesses in one or more areas. Conclusions. Findings demonstrated that weaknesses in general language ability in children managed for supratentorial tumour may indicate higher-level language difficulties. Language abilities beyond general measures of language should be monitored, as well as long-term consideration of phonological awareness abilities in this population.

Stairs to upper level, Brannigan House, St Lucia, Brisbane

Stairs to upper bedroom/studio spaces. Kitchen and central deck on left.

Lower level floor plan, Brannigan House, St Lucia, Brisbane

Hand-drawn floor plan.

Towards realistic simulations of lava dome growth using the level set method

The level set method has been implemented in a computational volcanology context. New techniques are presented to solve the advection equation and the reinitialisation equation. These techniques are based upon an algorithm developed in the finite difference context, but are modified to take advantage of the robustness of the finite element method. The resulting algorithm is tested on a well documented Rayleigh–Taylor instability benchmark [19], and on an axisymmetric problem where the analytical solution is known. Finally, the algorithm is applied to a basic study of lava dome growth.