Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera)

Background The gene composition, gene order and structure of the mitochondrial genome are remarkably stable across bilaterian animals. Lice (Insecta: Phthiraptera) are a major exception to this genomic stability in that the canonical single chromosome with 37 genes found in almost all other bilaterians has been lost in multiple lineages in favour of multiple, minicircular chromosomes with less than 37 genes on each chromosome. Results Minicircular mt genomes are found in six of the ten louse species examined to date and three types of minicircles were identified: heteroplasmic minicircles which coexist with full sized mt genomes (type 1); multigene chromosomes with short, simple control regions, we infer that the genome consists of several such chromosomes (type 2); and multiple, single to three gene chromosomes with large, complex control regions (type 3). Mapping minicircle types onto a phylogenetic tree of lice fails to show a pattern of their occurrence consistent with an evolutionary series of minicircle types. Analysis of the nuclear-encoded, mitochondrially-targetted genes inferred from the body louse, Pediculus, suggests that the loss of mitochondrial single-stranded binding protein (mtSSB) may be responsible for the presence of minicircles in at least species with the most derived type 3 minicircles (Pediculus, Damalinia). Conclusions Minicircular mt genomes are common in lice and appear to have arisen multiple times within the group. Life history adaptive explanations which attribute minicircular mt genomes in lice to the adoption of blood-feeding in the Anoplura are not supported by this expanded data set as minicircles are found in multiple non-blood feeding louse groups but are not found in the blood-feeding genus Heterodoxus. In contrast, a mechanist explanation based on the loss of mtSSB suggests that minicircles may be selectively favoured due to the incapacity of the mt replisome to synthesize long replicative products without mtSSB and thus the loss of this gene lead to the formation of minicircles in lice.

Molecular characterisation of environmental enterococci derived from water samples and assessment of associated public health hazards

Enterococci are versatile Gram-positive bacteria that can survive under extreme conditions. Most enterococci are non-virulent and found in the gastrointestinal tract of humans and animals. Other strains are opportunistic pathogens that contribute to a large number of nosocomial infections globally. Epidemiological studies demonstrated a direct relationship between the density of enterococci in surface waters and the risk of swimmer-associated gastroenteritis. The distribution of infectious enterococcal strains from the hospital environment or other sources to environmental water bodies through sewage discharge or other means, could increase the prevalence of these strains in the human population. Environmental water quality studies may benefit from focusing on a subset of Enterococcus spp. that are consistently associated with sources of faecal pollution such as domestic sewage, rather than testing for the entire genus. E. faecalis and E. faecium are potentially good focal species for such studies, as they have been consistently identified as the dominant Enterococcus spp. in human faeces and sewage. On the other hand enterococcal infections are predominantly caused by E. faecalis and E. faecium. The characterisation of E. faecalis and E. faecium is important in studying their population structures, particularly in environmental samples. In developing and implementing rapid, robust molecular genotyping techniques, it is possible to more accurately establish the relationship between human and environmental enterococci. Of particular importance, is to determine the distribution of high risk enterococcal clonal complexes, such as E. faecium clonal complex 17 and E. faecalis clonal complexes 2 and 9 in recreational waters. These clonal complexes are recognized as particularly pathogenic enterococcal genotypes that cause severe disease in humans globally. The Pimpama-Coomera watershed is located in South East Queensland, Australia and was investigated in this study mainly because it is used intensively for agriculture and recreational purposes and has a strong anthropogenic impact. The primary aim of this study was to develop novel, universally applicable, robust, rapid and cost effective genotyping methods which are likely to yield more definitive results for the routine monitoring of E. faecalis and E. faecium, particularly in environmental water sources. To fullfill this aim, new genotyping methods were developed based on the interrogation of highly informative single nucleotide polymorphisms (SNPs) located in housekeeping genes of both E. faecalis and E. faecium. SNP genotyping was successfully applied in field investigations of the Coomera watershed, South-East Queensland, Australia. E. faecalis and E. faecium isolates were grouped into 29 and 23 SNP profiles respectively. This study showed the high longitudinal diversity of E. faecalis and E. faecium over a period of two years, and both human-related and human-specific SNP profiles were identified. Furthermore, 4.25% of E. faecium strains isolated from water was found to correspond to the important clonal complex-17 (CC17). Strains that belong to CC17 cause the majority of hospital outbreaks and clinical infections globally. Of the six sampling sites of the Coomera River, Paradise Point had the highest number of human-related and human-specific E. faecalis and E. faecium SNP profiles. The secondary aim of this study was to determine the antibiotic-resistance profiles and virulence traits associated with environmental E. faecalis and E. faecium isolates compared to human pathogenic E. faecalis and E. faecium isolates. This was performed to predict the potential health risks associated with coming into contact with these strains in the Coomera watershed. In general, clinical isolates were found to be more resistant to all the antibiotics tested compared to water isolates and they harbored more virulence traits. Multi-drug resistance was more prevalent in clinical isolates (71.18% of E. faecalis and 70.3 % of E. faecium) compared to water isolates (only 5.66 % E. faecium). However, tetracycline, gentamicin, ciprofloxacin and ampicillin resistance was observed in water isolates. The virulence gene esp was the most prevalent virulence determinant observed in clinical isolates (67.79% of E. faecalis and 70.37 % of E. faecium), and this gene has been described as a human-specific marker used for microbial source tracking (MST). The presence of esp in water isolates (16.36% of E. faecalis and 19.14% of E. faecium) could be indicative of human faecal contamination in these waterways. Finally, in order to compare overall gene expression between environmental and clinical strains of E. faecalis, a comparative gene hybridization study was performed. The results of this investigation clearly demonstrated the up-regulation of genes associated with pathogenicity in E. faecalis isolated from water. The expression study was performed at physiological temperatures relative to ambient temperatures. The up-regulation of virulence genes demonstrates that environmental strains of E. faecalis can pose an increased health risk which can lead to serious disease, particularly if these strains belong to the virulent CC17 group. The genotyping techniques developed in this study not only provide a rapid, robust and highly discriminatory tool to characterize E. faecalis and E. faecium, but also enables the efficient identification of virulent enterococci that are distributed in environmental water sources.

It’s always a pleasure : exploring productivity and pleasure in a writing group for early career academics

The professional development needs of early career academics (ECAs) are increasingly subject to scrutiny. The literature notes writing groups can be successful in increasing research outputs and improving research track records – a core concern for ECAs. However, the pressure on ECAs to publish takes the pleasure out of writing for many. We argue writing groups, created by and for ECAs, can provide an environment for ECAs to (re)produce pleasure in writing and participation in the processes of academic review and debate. In addition, our experience of a writing group was that it provided a platform of social and emotional support contributing to our personal well-being and professional development.

A molecular phylogeny for the Tribe Dacini (Diptera: Tephritidae) : systematic and biogeographic implications

With well over 700 species, the Tribe Dacini is one of the most species-rich clades within the dipteran family Tephritidae, the true fruit flies. Nearly all Dacini belong to one of two very large genera, Dacus Fabricius and Bactrocera Macquart. The distribution of the genera overlap in or around the Indian subcontinent, but the greatest diversity of Dacus is in Africa and the greatest diversity of Bactrocera is in south-east Asia and the Pacific. The monophyly of these two genera has not been rigorously established, with previous phylogenies only including a small number of species and always heavily biased to one genus over the other. Moreover, the subgeneric taxonomy within both genera is complex and the monophyly of many subgenera has not been explicitly tested. Previous hypotheses about the biogeography of the Dacini based on morphological reviews and current distributions of taxa have invoked an out-of-India hypothesis; however this has not been tested in a phylogenetic framework. We attempted to resolve these issues with a dated, molecular phylogeny of 125 Dacini species generated using 16S, COI, COII and white eye genes. The phylogeny shows that Bactrocera is not monophyletic, but rather consists of two major clades: Bactrocera s.s. and the ‘Zeugodacus group of subgenera’ (a recognised, but informal taxonomic grouping of 15 Bactrocera subgenera). This ‘Zeugodacus’ clade is the sister group to Dacus, not Bactrocera and, based on current distributions, split from Dacus before that genus moved into Africa. We recommend that taxonomic consideration be given to raising Zeugodacus to genus level. Supportive of predictions following from the out-of-India hypothesis, the first common ancestor of the Dacini arose in the mid-Cretaceous approximately 80 mya. Major divergence events occurred during the Indian rafting period and diversification of Bactrocera apparently did not begin until after India docked with Eurasia (50–35 mya). In contrast, diversification in Dacus, at approximately 65 mya, apparently began much earlier than predicted by the out-of-India hypothesis, suggesting that, if the Dacini arose on the Indian plate, then ancestral Dacus may have left the plate in the mid to late Cretaceous via the well documented India–Madagascar–Africa migration route. We conclude that the phylogeny does not disprove the predictions of an out-of-India hypothesis for the Dacini, although modification of the original hypothesis is required.

Response to comments on "Productivity is a poor predictor of plant species richness"

Pan et al. claim that our results actually support a strong linear positive relationship between productivity and richness, whereas Fridley et al. contend that the data support a strong humped relationship. These responses illustrate how preoccupation with bivariate patterns distracts from a deeper understanding of the multivariate mechanisms that control these important ecosystem properties.

Population structure of Bactrocera dorsalis s.s., B. papayae and B. philippinensis (Diptera: Tephritidae) in southeast Asia: evidence for a single species hypothesis using mitochondrial DNA and wingshape data

Background Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status. Results Geometric morphometric results generated from 15 landmarks for wings of 169 flies revealed significant differences in wing shape between almost all sites following canonical variate analysis. For the combined data set there was a greater isolation-by-distance (IBD) effect under a ‘non-Euclidean’ scenario which used geographical distances within a biogeographical ‘Sundaland context’ (r2 = 0.772, P < 0.0001) as compared to a ‘Euclidean’ scenario for which direct geographic distances between sample sites was used (r2 = 0.217, P < 0.01). COI sequence data were obtained for 156 individuals and yielded 83 unique haplotypes with no correlation to current taxonomic designations via a minimum spanning network. BEAST analysis provided a root age and location of 540kya in northern Thailand, with migration of B. dorsalis s.l. into Malaysia 470kya and Sumatra 270kya. Two migration events into the Philippines are inferred. Sequence data revealed a weak but significant IBD effect under the ‘non-Euclidean’ scenario (r2 = 0.110, P < 0.05), with no historical migration evident between Taiwan and the Philippines. Results are consistent with those expected at the intra-specific level. Conclusions Bactrocera dorsalis s.s., B. papayae and B. philippinensis likely represent one species structured around the South China Sea, having migrated from northern Thailand into the southeast Asian archipelago and across into the Philippines. No migration is apparent between the Philippines and Taiwan. This information has implications for quarantine, trade and pest management.

Abundance of introduced species at home predicts abundance away in herbaceous communities

Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites – grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

A randomised controlled trial of an enhanced interdisciplinary community based group program for people with Parkinson’s disease: study rationale and protocol

Parkinson’s disease (PD) is a progressive, chronic neurodegenerative disorder for which there is no known cure. Physical exercise programs may be used to assist with the physical management of PD. Several studies have demonstrated that community based physical therapy programs are effective in reducing physical aspects of disability among people with PD. While multidisciplinary therapy interventions may have the potential to reduce disability and improve the quality of life of people with PD, there is very limited clinical trial evidence to support or refute the use of a community based multidisciplinary or interdisciplinary programs for people with PD. A two group randomized trial is being undertaken within a community rehabilitation service in Brisbane, Australia. Community dwelling adults with a diagnosis of Idiopathic Parkinson’s disease are being recruited. Eligible participants are randomly allocated to a standard exercise rehabilitation group program or an intervention group which incorporates physical, cognitive and speech activities in a multi-tasking framework. Outcomes will be measured at 6-week intervals for a period of six months. Primary outcome measures are the Montreal Cognitive Assessment (MoCA) and the Timed Up and Go (TUG) cognitive test. Secondary outcomes include changes in health related quality of life, communication, social participation, mobility, strength and balance, and carer burden measures. This study will determine the immediate and long-term effectiveness of a unique multifocal, interdisciplinary, dual-tasking approach to the management of PD as compared to an exercise only program. We anticipate that the results of this study will have implications for the development of cost effective evidence based best practice for the treatment of people with PD living in the community.

Unravelling the mechanisms behind the invasion of an introduced and now undesirable grass species

The introduction of Eragrostis curvula (African Lovegrass, herafter Lovegrass) for pasture improvement across Australia has not been successful. Instead Lovegrass, a C4 perennial grass originating from Southern African, has proven unpalatable to stock and to have low nutritional value if stocks do eat it. It has spread prolifically along roadsides, stream banks, conservation areas and pastures. Because control efforts have not been effective, our aim was to determine the putative mechanisms responsible for the dominance of Lovegrass, specifically disturbance (selective grazing) and competition.

Mass transfer properties (permeability and mass diffusivity) of four australian hardwood species

Characterization of mass transfer properties was achieved in the longitudinal, radial, and tangential directions for four Australian hardwood species: spotted gum, blackbutt, jarrah, and messmate. Measurement of mass transfer properties for these species was necessary to complement current vacuum drying modeling research. Water-vapour diffusivity was determined in steady state using a specific vapometer. Permeability was determined using a specialized device developed to measure over a wide range of permeability values. Permeability values of some species and material directions were extremely low and undetectable by the mass flow meter device. Hence, a custom system based on volume evolution was conceived to determine very low, previously unpublished, wood permeability values. Mass diffusivity and permeability were lowest for spotted gum and highest for messmate. Except for messmate in the radial direction, the four species measured were less permeable in all directions than the lowest published figures, demonstrating the high impermeability of Australian hardwoods and partly accounting for their relatively slow drying rates. Permeability, water-vapour diffusivity, and associated anisotropic ratio data obtained for messmate were extreme or did not follow typical trends and is consequently the most difficult of the four woods to dry in terms of collapse and checking degradation. © The State of Queensland, Department of Agriculture, Fisheries and Forestry, 2012.

Innovative planning approaches for generator interconnection group study

Today, a large number of wind generator interconnection requests have been queued and are being processed. The generator interconnection group study is a way to reduce the generator interconnection cycle time and increase interconnection certainty. However, it is very challenging to identify the “best” transmission upgrades for a large group of generator interconnections. It is also very important to differentiate the constraints caused by each generator interconnection request and identify their responsibilities for transmission upgrades. This paper outlines some innovative study approaches that can be used in a group study with large numbers of generator interconnection requests in a constrained area. Improved study methods are introduced, and a summary and conclusions are derived from the study.

Sampling environmental acoustic recordings to determine species richness : I

Acoustic sensors provide an effective means of monitoring biodiversity at large spatial and temporal scales. They can continuously and passively record large volumes of data over extended periods, however these data must be analysed to detect the presence of vocal species. Automated analysis of acoustic data for large numbers of species is complex and can be subject to high levels of false positive and false negative results. Manual analysis by experienced users can produce accurate results, however the time and effort required to process even small volumes of data can make manual analysis prohibitive. Our research examined the use of sampling methods to reduce the cost of analysing large volumes of acoustic sensor data, while retaining high levels of species detection accuracy. Utilising five days of manually analysed acoustic sensor data from four sites, we examined a range of sampling rates and methods including random, stratified and biologically informed. Our findings indicate that randomly selecting 120, one-minute samples from the three hours immediately following dawn provided the most effective sampling method. This method detected, on average 62% of total species after 120 one-minute samples were analysed, compared to 34% of total species from traditional point counts. Our results demonstrate that targeted sampling methods can provide an effective means for analysing large volumes of acoustic sensor data efficiently and accurately.

Clines in cuticular hydrocarbons in two Drosophila species with independent population histories

We took a comparative approach utilizing clines to investigate the extent to which natural selection may have shaped population divergence in cuticular hydrocarbons (CHCs) that are also under sexual selection in Drosophila. We detected the presence of CHC clines along a latitudinal gradient on the east coast of Australia in two fly species with independent phylogenetic and population histories, suggesting adaptation to shared abiotic factors. For both species, significant associations were detected between clinal variation in CHCs and temperature variation along the gradient, suggesting temperature maxima as a candidate abiotic factor shaping CHC variation among populations. However, rainfall and humidity correlated with CHC variation to differing extents in the two species, suggesting that response to these abiotic factors may vary in a species-specific manner. Our results suggest that natural selection, in addition to sexual selection, plays a significant role in structuring among-population variation in sexually selected traits in Drosophila.

Beyond barcoding : a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117–200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.