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.

Habitat use, diet and body size of Heard Island weevils

Habitat use, diet and body-size variation are examined in weevils from Heard Island. with specific attention being given to the Ectemnorhinus viridis species complex. E. viridis shows marked altitudinal variation in body size and vestiture, but there are no consistent associations between body size and diet. nor are there consistent among-individual differences in conventional taxonomic characters. Thus, the status of E. viridis as a single, variable species is maintained. This species occurs from sea level to 600 rn and it feeds on vascular plants and bryophytes. Canonopsis sericeus also feeds on bryophytes and vascular plants and occurs over a narrower altitudinal range. Palirhoeus eatoni is restricted to the surpralittoral zone where it feeds on marine algae and lichens. Bothrometopus brei,is and B. gracilipes both feed on cryptogams, with the former species occurring from sea level to 450 m. and the latter from 50 to 550 m above sea level. In all species, males are smaller than females and there is a size cline such that populations from higher elevations are smaller than those at lower altitudes. This cline is the reverse of that found on the Prince Edward Islands which, unlike Heard Island, lie to the north of the Antarctic Polar Frontal Zone. This difference in body-size clines between weevils on the two island groups is ascribed to the shorter growing season on the colder Heard Island. The information presented here supports previous ideas regarding the evolution of the Ectemnorhinus-group of weevils on the South Indian Ocean Province Islands, although it suggests that subsequent tests of these hypotheses would profit from the inclusion of molecular systematic work.

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).

Resolution of natural groups using iterative assignment tests: an example from two species of Australian native rats (Rattus)

Sympatric individuals of Rattus fuscipes and Rattus leucopus, two Australian native rats from the tropical wet forests of north Queensland, are difficult to distinguish morphologically and are often confused in the field. When we started a study on fine-scale movements of these species, using microsatellite markers, we found that the species as identified in the field did not form coherent genetic groups. In this study, we examined the potential of an iterative process of genetic assignment to separate specimens from distinct (e.g. species, populations) natural groups. Five loci with extensive overlap in allele distributions between species were used for the iterative process. Samples were randomly distributed into two starting groups of equal size and then subjected to the test. At each iteration, misassigned samples switched groups, and the output groups from a given round of assignment formed the input groups for the next round. All samples were assigned correctly on the 10th iteration, in which two genetic groups were clearly separated. Mitochondrial DNA sequences were obtained from samples from each genetic group identified by assignment, together with those of museum voucher specimens, to assess which species corresponded to which genetic group. The iterative procedure was also used to resolve groups within species, adequately separating the genetically identified R. leucopus from our two sampling sites. These results show that the iterative assignment process can correctly differentiate samples into their appropriate natural groups when diagnostic genetic markers are not available, which allowed us to resolve accurately the two R. leucopus and R. fuscipes species. Our approach provides an analytical tool that may be applicable to a broad variety of situations where genetic groups need to be resolved.

Effect of leucaena supplementation level, and provision of urea, on utilisation by sheep of Rhodes grass hay

Tarramba leucaena (Leucaena leucocephala cv. Tarramba) foliage had per kilogram dry matter, 169 g protein and 29.8 g condensed tannins. Its value as a supplement, given either with or without urea, to sheep given a low-quality Callide Rhodes grass (Chloris gayana cv. Callide) hay was studied. Six rumen fistulated sheep (mean +/- s.d. liveweight, 34 +/- 1.4 kg) were used to compare 6 dietary treatments in an incomplete latin square design. Rhodes grass hay was given ad libitum either alone, or with urea 7 g/day (U), or with leucaena 150 g/day (L150), or leucaena with urea (L150U), or leucaena 300 g/day (L300), or leucaena with urea (L300U). Digestible organic matter intake was increased significantly by leucaena supplementation although digestibility of the whole diet did not alter. Rumen fluid ammonia-N was not altered by leucaena supplementation, but was increased by urea. This suggests that Tarramba foliage protein has some resistance to ruminal degradation. Liquid and solids passage rates were not affected by the treatments. Microbial nitrogen supply to the intestine (g/day), and the efficiency of microbial nitrogen synthesis (g/kg organic matter apparently digested in the rumen), were increased by leucaena supplementation (P

Quantifying stresses and support requirements in the undercut and production level drifts of block and panel caving mines

A numerical modelling strategy has been developed in order to quantify the magnitude of induced stresses at the boundaries of production level and undercut level drifts for various in situ stress environments and undercut scenarios. The results of the stress modelling were in line with qualitative experiential guidelines and a limited number of induced stress measurements documented from caving sites. A number of stress charts were developed which quantify the maximum boundary stresses in drift roofs for varying in situ stress regimes, depths and undercut scenarios. This enabled many of the experiential guidelines to be quantified and bounded. A limited number of case histories of support and support performance in cave mine drifts were compared to support recommendations using the NGI classification system, The stress charts were used to estimate the Stress Reduction Factor for this system. The back-analyses suggested that the NGI classification system might be able to give preliminary estimates of support requirements in caving mines with modifications relating to rock bolt length and the support of production level intersections. (C) 2002 Elsevier Science Ltd. All rights reserved.

Auditor independence and fee dependence

This study investigates whether fee dependence within the audit firms' offices jeopardises auditor independence. Fee dependence is examined at both the national audit firm level as well as the local office level and in a setting where public disclosure of fees is mandatory. We focus our tests on audit fee dependence and at the same time we control for the effects of non-audit service fee dependence post the 1989 mergers. We operationalise the exercise of independent judgement in auditing by the propensity to issue qualified audit opinions. If fee dependence affects auditors' independent judgement, then auditors are less likely to qualify the accounts. The study's results show that the level of auditor fee dependence does not affect auditor propensity to issue unqualified audit opinions. The findings remain robust to a number of sensitivity tests including the analyses controlling for the effects of non-audit service fee dependence and other settings in which there is heightened pressure on auditors to confront the effects of fee dependence on exercising independent audit judgement. (C) 2002 Elsevier Science B.V. All rights reserved.

Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) revelas a high level of colinearity between the two genomes

A genetic linkage map of mungbean (Vigna radiata, 2n = 2x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an intersubspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' (V radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab (Lablab purpureus, 2n = 2x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.

Bayesian feedback versus Markovian feedback in a two-level atom

We compare two different approaches to the control of the dynamics of a continuously monitored open quantum system. The first is Markovian feedback, as introduced in quantum optics by Wiseman and Milburn [Phys. Rev. Lett. 70, 548 (1993)]. The second is feedback based on an estimate of the system state, developed recently by Doherty and Jacobs [Phys. Rev. A 60, 2700 (1999)]. Here we choose to call it, for brevity, Bayesian feedback. For systems with nonlinear dynamics, we expect these two methods of feedback control to give markedly different results. The simplest possible nonlinear system is a driven and damped two-level atom, so we choose this as our model system. The monitoring is taken to be homodyne detection of the atomic fluorescence, and the control is by modulating the driving. The aim of the feedback in both cases is to stabilize the internal state of the atom as close as possible to an arbitrarily chosen pure state, in the presence of inefficient detection and other forms of decoherence. Our results (obtained without recourse to stochastic simulations) prove that Bayesian feedback is never inferior, and is usually superior, to Markovian feedback. However, it would be far more difficult to implement than Markovian feedback and it loses its superiority when obvious simplifying approximations are made. It is thus not clear which form of feedback would be better in the face of inevitable experimental imperfections.

Combined hydraulic and biological modelling and full-scale validation of SBR process

The biological reactions during the settling and decant periods of Sequencing Batch Reactors (SBRs) are generally ignored as they are not easily measured or described by modelling approaches. However, important processes are taking place, and in particular when the influent is fed into the bottom of the reactor at the same time (one of the main features of the UniFed process), the inclusion of these stages is crucial for accurate process predictions. Due to the vertical stratification of both liquid and solid components, a one-dimensional hydraulic model is combined with a modified ASM2d biological model to allow the prediction of settling velocity, sludge concentration, soluble components and biological processes during the non-mixed periods of the SBR. The model is calibrated on a full-scale UniFed SBR system with tracer breakthrough tests, depth profiles of particulate and soluble compounds and measurements of the key components during the mixed aerobic period. This model is then validated against results from an independent experimental period with considerably different operating parameters. In both cases, the model is able to accurately predict the stratification and most of the biological reactions occurring in the sludge blanket and the supernatant during the non-mixed periods. Together with a correct description of the mixed aerobic period, a good prediction of the overall SBR performance can be achieved.

Complex language functions and subcortical mechanisms: evidence from Huntington's disease and patients with non-thalamic subcortical lesions

The neuropathological changes associated with Huntington's disease (HD) are most marked in the head of the caudate nucleus and, to a lesser extent, in the putamen and globus pallidus, suggesting that at least part of the language impairments found in patients with HD may result from non-thalamic subcortical (NTS) pathology. The present study aimed to test the hypothesis that a signature profile of impaired language functions is found in patients who have sustained damage to the non-thalamic subcortex, either focally induced or resulting from neurodegenerative pathology. The language abilities of a group of patients with Huntington's disease (n=13) were compared with those of an age- and education-matched group of patients with chronic NTS lesions following stroke (n=13) and a non-neurologically impaired control group (n=13). The three groups were compared on language tasks that assessed both primary and more complex language abilities. The primary language battery consisted of The Western Aphasia Battery and The Boston Naming Test, whilst the more complex cognitive-linguistic battery employed selected subtests from The Test of Language Competence-Expanded, The Test of Word Knowledge and The Word Test-Revised. On many of the tests of primary language function from the Western Aphasia Battery, both the HD and NTS participants performed in a similar manner to the control participants. The language performances of the HD participants were significantly more impaired (p<0.05 using modified Bonferroni adjustments) than the control group, however, on various lexico-semantic tasks (e. g. the Boston Naming Test and providing definitions), on both single-word and sentence-level generative tasks (e. g. category fluency and formulating sentences), and on tasks which required interpretation of ambiguous, figurative and inferential meaning. The difficulties that patients with HD experienced with tasks assessing complex language abilities were strikingly similar, both qualitatively and quantitatively, to the language profile produced by NTS participants. The results provide evidence to suggest that a signature language profile is associated with damage to the non-thalamic subcortex resulting from either focal neurological insult or a degenerative disease.

Physiological and symptomatic responses to cycling and walking in intermittent claudication

To shed light on the potential efficacy of cycling as a resting modality in the treatment of intermittent claudication (IC), this study compared physiological and symptomatic responses to graded walking and cycling tests in claudicants. Sixteen subjects with peripheral arterial disease (resting ankle:brachial index (ABI) < 0.9) and IC completed a maximal graded treadmill walking (T) and cycle (C) Lest after three familiarization tests on each mode. During cacti test, symptoms, oxygen uptake (VO2), minute ventilation (V-E), (respiratory exchange ratio) (RER) and heart rate (HR) were measured, and for 10 min after each Lest the brachial and ankle systolic pressures were recorded, All but One subject experienced calf pain as the primary limiting symptom during T whereas the symptoms were more varied during C and included thigh pain, calf pain and dyspnoea, Although maximal exercise time was significantly longer on C than T (690 +/- 67 vs, 495 +/- 57 s), peak VO2, peak, V-E and peak heart rate during C and T were not different; whereas peak RER was higher during C. These responses during C and T were also positively 1, (P < 0.05) with each other, with the exception of RER. The postexercise systolic pressures were also not different between C and T. However, the peak decline ill ankle pressures from resting values after C and T were not correlated with each other. Thew data demonstrate that cycling and walking induce a similar level of metabolic and cardiovascular strain, but that the primary limiting symptoms and haemodynamic response in an individual's extremity, measured after exercise, can differ substantially between these two modes.

Genetic linkage analysis of the lesser grain borer Rhyzopertha dominica identifies two loci that confer high-level resistance to the fumigant phosphine

High levels of inheritable resistance to phosphine in Rhyzopertha dominica have recently, been detected in Australia and hi art effort to isolate the genes responsible For resistance we have used random amplified DNA fingerprinting (RAF) to produce a genetic linkage map of R. dominica. The map consists of 94 dominant DNA markers with art average distance between markers of 4.6 cM and defines nine linkage groups with a total recombination distance of 390.1 cM. We have identified two loci that are responsible for high-level resistance. One provides similar to50x resistance to phosphine while the other provides 12.5x resistance and in combination, the two genes act synergistically to provide a resistance level 250 x greater than that of fully susceptible beetles. The haploid genome size has been determined to be 4.76 x 10(8) bp, resulting in an average physical distance of 1.2 Mbp per map unit. No recombination has been observed between either of the two resistance loci and their adjacent DNA markers in a population of 44 fully resistant F-5 individuals, which indicates that the genes are likely to reside within 0.91 cM (1.1 Mbp) of the DNA markers.

Model specification tests in nonparametric stochastic regression models

In this paper, we consider testing for additivity in a class of nonparametric stochastic regression models. Two test statistics are constructed and their asymptotic distributions are established. We also conduct a small sample study for one of the test statistics through a simulated example. (C) 2002 Elsevier Science (USA).