Sequencing the ant fauna of a small island: Can metagenomic analysis enable faster identification for routine ant surveys?

All known ant species from a small Western Australian island were subjected to DNA barcoding of the CO1 gene, with a view to using the database to identify ants by Next Generation Sequencing in subsequent, routine surveys. A further aim was to evaluate whether the data could be used to see if any new species had arrived on the island since the total fauna had been inventoried. Of the 125 unique ant species then known from the island, 72 were successfully barcoded. Those that were refractory to amplification were largely the result of sample age and/or contamination. Following this base-line barcoding, ants were sampled from 14 regular sampling sites and ant sequences were obtained from the bulked ‘metagenomic soup’. Prior to doing this, a parataxonomist had identified all ant species in the samples and returned them to the ‘soup’. Successful identification for each site varied from 38% (Sites 12 and 27) to 100% of species (Site 10). Comparison of the number of species recovered with the number of sequences obtained from each sample showed a positive correlation between the two variables. When a site had >1,000 sequences, the average recovery rate was 79%, which is in contrast to the lowest four recovery rates (Site samples 12, 22, 26 and 27), which had fewer than 440 amplicon sequences. The ability to detect individuals that occur at low frequencies is also important. We analysed each site individually to determine if a species was detected and how that related to the proportion of individuals in the pooled sample. Where a species was present at <4% of the total sample, it was only detected 10% of the time, indicating that adequate sequencing depth is critical to species recovery. We conclude that this technique was only partially successful in replacing conventional taxonomy and that it could have limited ability to detect incursions unless the new arrival is abundant. Current barcoding is no longer limited to the CO1 gene and other genes are characterised for identification of intractable groups where CO1 does not provide appropriate levels of resolution

A rapid non-destructive DNA extraction method for insects and other arthropods

Preparation of arthropods for morphological identification often damages or destroys DNA within the specimen. Conversely, DNA extraction methods often destroy the external physical characteristics essential for morphological identification. We have developed a rapid, simple and non-destructive DNA extraction technique for arthropod specimens. This technique was tested on four arthropod orders, using specimens that were fresh, preserved by air drying, stored in ethanol, or collected with sticky or propylene glycol traps. The technique could be completed in twenty minutes for Coleoptera, Diptera and Hemiptera, and two minutes for the subclass Acarina, without significant distortion, discolouration, or other damage to the specimens

Study protocol of the intense physical activity and cognition study: The effect of high-intensity exercise training on cognitive function in older adults

Introduction: Inconsistent results from previous studies of exercise and cognitive function suggest that rigorously designed randomized controlled trials are urgently needed. Here, we describe the design of the Intense Physical Activity and Cognition (IPAC) study, which will assess the impact of a 6-month high-intensity exercise intervention on cognitive function and biomarkers of dementia risk, compared with a 6-month moderate-intensity exercise intervention and control group (no study-related exercise). Methods: One-hundred and five cognitively healthy men and women aged between 60 and 80 years are randomized into a high-intensity exercise, moderate-intensity exercise, or control group. Individuals randomized to an exercise intervention undertake 6 months of cycle-based exercise twice a week, at 50 minutes per session. All participants undergo comprehensive neuropsychological testing, blood sampling, brain magnetic resonance imaging, fitness testing, and a body composition scan at baseline, 6 months (immediately after intervention), and 18 months (12 months after intervention). Discussion: The IPAC study takes a multidisciplinary approach to investigating the role of exercise in maintaining a healthy brain throughout aging. Rigorous monitoring of exertion and adherence throughout the intervention, combined with repeated measures of fitness, is vital in ensuring an optimum exercise dose is reached. Results from the IPAC study will be used to inform a large-scale multicentre randomized controlled trial, with the ultimate aim of pinpointing the frequency, duration, and intensity of exercise that provides the most benefit to the brain, in terms of enhancing cognitive function and reducing dementia risk in older adults

Identification and characterisation of ten microsatellite loci in the Noisy Scrub-bird Atrichornis clamosus using next-generation sequencing technology

The Noisy Scrub-bird is an endangered species of songbird endemic to the south coast of Western Australia that has undergone a major and prolonged population bottleneck. Using shotgun 454 next-generation DNA sequencing we have identified and characterised ten polymorphic microsatellite loci in this species. Observed allelic diversity was relatively low (2–5 alleles per locus) and significant deviations from Hardy–weinberg Equilibrium observed, although the presence of null alleles was onlypostulated for two loci. The microsatellite loci characterised in this study will be useful in a future population genetics studies in this endangered species

Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil

The Old World bollworm Helicoverpa armigera is now established in Brazil but efforts to identify incursion origin(s) and pathway(s) have met with limited success due to the patchiness of available data. Using international agricultural/horticultural commodity trade data and mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene markers, we inferred the origins and incursion pathways into Brazil. We detected 20 mtDNA haplotypes from six Brazilian states, eight of which were new to our 97 global COI-Cyt b haplotype database. Direct sequence matches indicated five Brazilian haplotypes had Asian, African, and European origins. We identified 45 parsimoniously informative sites and multiple substitutions per site within the concatenated (945 bp) nucleotide dataset, implying that probabilistic phylogenetic analysis methods are needed. High diversity and signatures of uniquely shared haplotypes with diverse localities combined with the trade data suggested multiple incursions and introduction origins in Brazil. Increasing agricultural/horticultural trade activities between the Old and New Worlds represents a significant biosecurity risk factor. Identifying pest origins will enable resistance profiling that reflects countries of origin to be included when developing a resistance management strategy, while identifying incursion pathways will improve biosecurity protocols and risk analysis at biosecurity hotspots including national ports

Revision of the ant genus melophorus (Hymenoptera, formicidae)

© Brian E. Heterick et al. The fauna of the purely Australian formicine ant genus Melophorus (Hymenoptera: Formicidae) is revised. This project involved integrated morphological and molecular taxonomy using one mitochondrial gene (COI) and four nuclear genes (AA, H3, LR and Wg). Seven major clades were identified and are here designated as the M. aeneovirens, M. anderseni, M. biroi, M. fulvihirtus, M. ludius, M. majeri and M. potteri species-groups. Within these clades, smaller complexes of similar species were also identified and designated species-complexes. The M. ludius species-group was identified purely on molecular grounds, as the morphology of its members is indistinguishable from typical members of the M. biroi species-complex within the M. biroi species-group. Most species-complexes sampled were also found to be monophyletic. Sequencing generally supported monophyly in taxa sampled but some species of the M. fieldi complex and M. biroi were not monophyletic and the implications arising from this are discussed in this monograph. Based on morphology, ninety-three species are recognized, 73 described as new. A further new species (here called 'Species K' [TERC Collection]) is noted in the taxonomic list, but is not described in this work. One species is removed from Melophorus: M. scipio Forel is here placed provisionally in Prolasius. Six species and five subspecies pass into synonymy. Of the full species, M. constans Santschi, M. iridescens (Emery) and M. insularis Wheeler are synonymized under M. aeneovirens (Lowne), M. pillipes Santschi is synonymized under M. turneri Forel, M. marius Forel is synonymized under M. biroi Forel, and M. omniparens Forel is synonymized under M. wheeleri Forel. Of the subspecies, M. iridescens fraudatrix and M. iridescens froggatti Forel are synonymized under M. aeneovirens (Lowne), M. turneri aesopus Forel and M. turneri candidus Santschi are synonymized under M. turneri Forel and M. fieldi propinqua Viehmeyer is synonymized under M. biroi. Camponotus cowlei Froggatt is reinstated as a junior synonym of Melophorus bagoti Lubbock. In addition, the subspecies M. fieldi major Forel, M. ludius sulla Forel and M. turneri perthensis Forel are raised to species. A key to workers of the genus is supplied. A lectotype is designated for M. curtus Forel, M. sulla, and M. turneri

Barcoding of mygalomorph spiders (Araneae : Mygalomorphae) in the Pilbara bioregion of Western Australia reveals a highly diverse biota

Published online 12 September 2014The Pilbara bioregion of Western Australia is an area that contains vast mineral deposits and unique ecosystems. To ensure that mineral deposits are mined with minimal impact on the natural environment, impact assessment surveys are required to determine what fauna and flora species are located within proposed development areas, in particular, by determining the distributions of short-range endemic species (SREs). One infraorder of Arachnida, the Mygalomorphae (trapdoor spiders and their kin), are frequently identified as SREs. These identifications are traditionally performed using morphological techniques; however, only males can be reliably identified to species. Furthermore, the majority of species have not been formally described and males comprise only ~5% of specimens collected. To assess mygalomorph diversity and the distribution of species in the Pilbara, we employed a molecular barcoding approach. Sequence data from the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene were obtained from 1134 specimens, and analysed using Bayesian methods. Only a fraction of the total mygalomorph fauna of the Pilbara has been documented, and using a species boundary cut-off of 9.5% sequence divergence, we report an increase in species richness of 191%. Barcoding provides a rapid, objective method to help quantify mygalomorph species identifications and their distributions, and these data, in turn, provide crucial information that regulatory authorities can use to assess the environmental impacts of large-scale developments.Mark A. Castalanelli, Roy Teale, Michael G. Rix, W. Jason Kennington and Mark S. Harve

BDNF Val66Met moderates the relationship between cardiorespiratory fitness and memory in cognitively normal older adults

Higher cardiorespiratory fitness has been associated with enhanced cognitive function in older adults; yet, this relationship demonstrates a degree of variability. Thus, it is hypothesised that variation in genetic factors may influence the relationship between fitness and cognitive health. In this study we evaluate whether the BDNF Val66Met polymorphism moderates the relationship between cardiorespiratory fitness and verbal and visuospatial memory. Data from ninety-nine cognitively normal men and women aged 60 – 80 years were used. Fitness was assessed by peak oxygen consumption, and verbal and visuospatial memory were evaluated using well-validated measures. Participants were categorised into: lower-fit Met carriers, higher-fit Met carriers, lower-fit Val/Val, or higher-fit Val/Val. A significant interaction was observed between BDNF Val66Met and fitness on visuospatial memory performance; whereby lower-fit Met carriers performed 1SD lower than higher-fit Met carriers (p=0.04). We observed higher levels of fitness mitigated the deleterious effect of BDNF Met allele carriage on visuospatial memory. Future intervention studies should evaluate the effect of structured exercise on cognitive health between BDNF Val66Met carriers and Val/Val homozygotes

Multiple incursions and putative species revealed using a mitochondrial and nuclear phylogenetic approach to the Trogoderma variabile (Coleoptera: Dermestidae) trapping program in Australia

The Warehouse beetle, Trogoderma variabile (Coleoptera: Dermestidae), is an internationally significant invasive pest of packed goods and stored grain. When it was first documented in Australia at Griffith, New South Wales, in 1977, an eradication campaign was initiated. After several years and considerable effort, the eradication campaign was abandoned. To monitor the presence and spread of T. variabile, surveys were carried out by government agencies in 1992 and 2002. When survey data was compared, it was concluded that the distribution of morphologically identified T. variabile had doubled in most Australian states. Here, we used samples from the 2002 survey to conduct a phylogenetic study using partial sequences of mitochondrial genes Cytochrome oxidase I and Cytochrome B, and the nuclear gene 18S, to examine the distribution and dispersal of T. variabile and detect the presence of misidentified species. Based on our molecular results, we show that only 47% of the samples analysed were T. variabile, and the remaining were a mixture of six putative species. In addition, T. variabile was found in only 78% of the trapping sites. We discuss the importance of correct diagnosis in relation to the eradication campaign

Influence of BDNF Val66Met on the relationship between cardiorespiratory fitness and memory in cognitively normal older adults

Higher cardiorespiratory fitness has been associated with better cognitive function in older adults; yet, this relationship demonstrates a degree of variability across the older adult population. Thus, it is hypothesised that variation in genetic factors may influence the relationship between fitness and cognitive health. One such genetic factor is the brain-derived neurotrophic factor (BDNF) Val66Met polymorphism, which has previously been shown to moderate the relationship between self-reported physical activity and memory performance. In this study we aim to investigate the interaction between BDNF Val66Met polymorphism and objectively-measured cardiorespiratory fitness on performance on tasks assessing verbal and visuospatial memory. Data from ninety-nine cognitively normal men and women aged 60–80 years were used. Fitness was assessed by peak oxygen consumption, and verbal and visuospatial memory were evaluated using well-validated measures. Participants were categorised into: lower-fit Met carriers, higher-fit Met carriers, lower-fit Val/Val, or higher-fit Val/Val. Higher-fit individuals performed better on a task assessing visuospatial memory, compared with lower-fit individuals. Furthermore, an interaction between BDNF Val66Met and fitness was observed in terms of visuospatial memory performance on a continuous paired associate learning task; whereby lower-fit Met carriers performed 1 standard deviation worse than higher-fit Met carriers. No differences were observed between the higher-fit and lower-fit Val/Val homozygotes. Future intervention studies should evaluate the effect of structured exercise on cognitive health between BDNF Val66Met carriers and Val/Val homozygotes