Recrudescent Infection Supports Hendra Virus Persistence in Australian Flying-Fox Populations

Zoonoses from wildlife threaten global public health. Hendra virus is one of several zoonotic viral diseases that have recently emerged from Pteropus species fruit-bats (flying-foxes). Most hypotheses regarding persistence of Hendra virus within flying-fox populations emphasize horizontal transmission within local populations (colonies) via urine and other secretions, and transmission among colonies via migration. As an alternative hypothesis, we explore the role of recrudescence in persistence of Hendra virus in flying-fox populations via computer simulation using a model that integrates published information on the ecology of flying-foxes, and the ecology and epidemiology of Hendra virus. Simulated infection patterns agree with infection patterns observed in the field and suggest that Hendra virus could be maintained in an isolated flying-fox population indefinitely via periodic recrudescence in a manner indistinguishable from maintenance via periodic immigration of infected individuals. Further, post-recrudescence pulses of infectious flying-foxes provide a plausible basis for the observed seasonal clustering of equine cases. Correct understanding of the infection dynamics of Hendra virus in flying-foxes is fundamental to effectively managing risk of infection in horses and humans. Given the lack of clear empirical evidence on how the virus is maintained within populations, the role of recrudescence merits increased attention.

Wheat biomass and yield increased when populations of the root-lesion nematode (Pratylenchus thornei) were reduced through sequential rotation of partially resistant winter and summer crops

The root-lesion nematode, Pratylenchus thornei, can reduce wheat yields by >50%. Although this nematode has a broad host range, crop rotation can be an effective tool for its management if the host status of crops and cultivars is known. The summer crops grown in the northern grain region of Australia are poorly characterised for their resistance to P. thornei and their role in crop sequencing to improve wheat yields. In a 4-year field experiment, we prepared plots with high or low populations of P. thornei by growing susceptible wheat or partially resistant canaryseed (Phalaris canariensis); after an 11-month, weed-free fallow, several cultivars of eight summer crops were grown. Following another 15-month, weed-free fallow, P. thornei-intolerant wheat cv. Strzelecki was grown. Populations of P. thornei were determined to 150 cm soil depth throughout the experiment. When two partially resistant crops were grown in succession, e.g. canaryseed followed by panicum (Setaria italica), P. thornei populations were <739/kg soil and subsequent wheat yields were 3245 kg/ha. In contrast, after two susceptible crops, e.g. wheat followed by soybean, P. thornei populations were 10 850/kg soil and subsequent wheat yields were just 1383 kg/ha. Regression analysis showed a linear, negative response of wheat biomass and grain yield with increasing P. thornei populations and a predicted loss of 77% for biomass and 62% for grain yield. The best predictor of wheat yield loss was P. thornei populations at 0-90 cm soil depth. Crop rotation can be used to reduce P. thornei populations and increase wheat yield, with greatest gains being made following two partially resistant crops grown sequentially.

Micro-economic drivers of profitability in an ITQ-managed fishery: An analysis of the Queensland Coral Reef Fin-Fish Fishery

An economic survey of the commercial operators currently active in the Queensland Coral Reef Fin-Fish Fishery has been carried out, as part of a research project aimed at evaluating alternative management options for this fishery. This paper presents the background analysis used as a basis to develop the sampling design for this survey. The background analysis focuses on activity patterns of the fleet based on effort and catch information, as well as patterns of quota ownership. Based on this information, a fishing business profile describing the micro-economic structure of fishing operations is developed. This profile, in conjunction with the qualitative information gained in undertaking the economic surveys, allows preliminary understanding of the key drivers of profitability in the CRFFF, and possible impacts of external factors on fishing operations.

Applications of a sugar-based surveillance system to track arboviruses in wild mosquito populations

Effective arbovirus surveillance is essential to ensure the implementation of control strategies, such as mosquito suppression, vaccination, or dissemination of public warnings. Traditional strategies employed for arbovirus surveillance, such as detection of virus or virus-specific antibodies in sentinel animals, or detection of virus in hematophagous arthropods, have limitations as an early-warning system. A system was recently developed that involves collecting mosquitoes in CO2-baited traps, where the insects expectorate virus on sugar-baited nucleic acid preservation cards. The cards are then submitted for virus detection using molecular assays. We report the application of this system for detecting flaviviruses and alphaviruses in wild mosquito populations in northern Australia. This study was the first to employ nonpowered passive box traps (PBTs) that were designed to house cards baited with honey as the sugar source. Overall, 20/144 (13.9%) of PBTs from different weeks contained at least one virus-positive card. West Nile virus Kunjin subtype (WNVKUN), Ross River virus (RRV), and Barmah Forest virus (BFV) were detected, being identified in 13/20, 5/20, and 2/20 of positive PBTs, respectively. Importantly, sentinel chickens deployed to detect flavivirus activity did not seroconvert at two Northern Territory sites where four PBTs yielded WNVKUN. Sufficient WNVKUN and RRV RNA was expectorated onto some of the honey-soaked cards to provide a template for gene sequencing, enhancing the utility of the sugar-bait surveillance system for investigating the ecology, emergence, and movement of arboviruses. © 2014, Mary Ann Liebert, Inc.

Pratylenchus thornei populations reduce water uptake in intolerant wheat cultivars

Pratylenchus thornei is a major pathogen of wheat crops in the northern grain region of Eastern Australia with an estimated annual yield loss of $38 million. Damaged crops show symptoms of water and nutrient stress that suggest uptake is significantly affected. In order to understand the mechanisms involved in reducing water uptake and consequently plant yield, detailed measurements of water extraction and leaf area were conducted on a range of wheat cultivars with differing levels of tolerance and resistance to P. thornei.

Evaluating and validating abundance monitoring methods in the absence of populations of known size: review and application to a passive tracking index

Rarely is it possible to obtain absolute numbers in free-ranging populations and although various direct and indirect methods are used to estimate abundance, few are validated against populations of known size. In this paper, we apply grounding, calibration and verification methods, used to validate mathematical models, to methods of estimating relative abundance. To illustrate how this might be done, we consider and evaluate the widely applied passive tracking index (PTI) methodology. Using published data, we examine the rationality of PTI methodology, how conceptually animal activity and abundance are related and how alternative methods are subject to similar biases or produce similar abundance estimates and trends. We then attune the method against populations representing a range of densities likely to be encountered in the field. Finally, we compare PTI trends against a prediction that adjacent populations of the same species will have similar abundance values and trends in activity. We show that while PTI abundance estimates are subject to environmental and behavioural stochasticity peculiar to each species, the PTI method and associated variance estimate showed high probability of detection, high precision of abundance values and, generally, low variability between surveys, and suggest that the PTI method applied using this procedure and for these species provides a sensitive and credible index of abundance. This same or similar validation approach can and should be applied to alternative relative abundance methods in order to demonstrate their credibility and justify their use.

Stock assessment of the Queensland east coast common coral trout (Plectropomus leopardus) fishery

Common coral trout Plectropomus leopardus is an iconic fish of the Great Barrier Reef (GBR) and is the most important fish for the commercial fishery there. Most of the catch is exported live to Asia. This stock assessment was undertaken in response to falls in catch sizes and catch rates in recent years, in order to gauge the status of the stock. It is the first stock assessment ever conducted of coral trout on the GBR, and brings together a multitude of different data sources for the first time. The GBR is very large and was divided into a regional structure based on the Bioregions defined by expert committees appointed by the Great Barrier Reef Marine Park Authority (GBRMPA) as part of the 2004 rezoning of the GBR. The regional structure consists of six Regions, from the Far Northern Region in the north to the Swains and Capricorn–Bunker Regions in the south. Regions also closely follow the boundaries between Bioregions. Two of the northern Regions are split into Subregions on the basis of potential changes in fishing intensity between the Subregions; there are nine Subregions altogether, which include four Regions that are not split. Bioregions are split into Subbioregions along the Subregion boundaries. Finally, each Subbioregion is split into a “blue” population which is open to fishing and a “green” population which is closed to fishing. The fishery is unusual in that catch rates as an indicator of abundance of coral trout are heavily influenced by tropical cyclones. After a major cyclone, catch rates fall for two to three years, and rebound after that. This effect is well correlated with the times of occurrence of cyclones, and usually occurs in the same month that the cyclone strikes. However, statistical analyses correlating catch rates with cyclone wind energy did not provide significantly different catch rate trends. Alternative indicators of cyclone strength may explain more of the catch rate decline, and future work should investigate this. Another feature of catch rates is the phenomenon of social learning in coral trout populations, whereby when a population of coral trout is fished, individuals quickly learn not to take bait. Then the catch rate falls sharply even when the population size is still high. The social learning may take place by fish directly observing their fellows being hooked, or perhaps heeding a chemo-sensory cue emitted by fish that are hooked. As part of the assessment, analysis of data from replenishment closures of Boult Reef in the Capricorn–Bunker Region (closed 1983–86) and Bramble Reef in the Townsville Subregion (closed 1992–95) estimated a strong social learning effect. A major data source for the stock assessment was the large collection of underwater visual survey (UVS) data collected by divers who counted the coral trout that they sighted. This allowed estimation of the density of coral trout in the different Bioregions (expressed as a number of fish per hectare). Combined with mapping data of all the 3000 or so reefs making up the GBR, the UVS results provided direct estimates of the population size in each Subbioregion. A regional population dynamic model was developed to account for the intricacies of coral trout population dynamics and catch rates. Because the statistical analysis of catch rates did not attribute much of the decline to tropical cyclones, (and thereby implied “real” declines in biomass), and because in contrast the UVS data indicate relatively stable population sizes, model outputs were unduly influenced by the unlikely hypothesis that falling catch rates are real. The alternative hypothesis that UVS data are closer to the mark and declining catch rates are an artefact of spurious (e.g., cyclone impact) effects is much more probable. Judging by the population size estimates provided by the UVS data, there is no biological problem with the status of coral trout stocks. The estimate of the total number of Plectropomus leopardus on blue zones on the GBR in the mid-1980s (the time of the major UVS series) was 5.34 million legal-sized fish, or about 8400 t exploitable biomass, with an 2 additional 3350 t in green zones (using the current zoning which was introduced on 1 July 2004). For the offshore regions favoured by commercial fishers, the figure was about 4.90 million legal-sized fish in blue zones, or about 7700 t exploitable biomass. There is, however, an economic problem, as indicated by relatively low catch rates and anecdotal information provided by commercial fishers. The costs of fishing the GBR by hook and line (the only method compatible with the GBR’s high conservation status) are high, and commercial fishers are unable to operate profitably when catch rates are depressed (e.g., from a tropical cyclone). The economic problem is compounded by the effect of social learning in coral trout, whereby catch rates fall rapidly if fishers keep returning to the same fishing locations. In response, commercial fishers tend to spread out over the GBR, including the Far Northern and Swains Regions which are far from port and incur higher travel costs. The economic problem provides some logic to a reduction in the TACC. Such a reduction during good times, such as when the fishery is rebounding after a major tropical cyclone, could provide a net benefit to the fishery, as it would provide a margin of stock safety and make the fishery more economically robust by providing higher catch rates during subsequent periods of depressed catches. During hard times when catch rates are low (e.g., shortly after a major tropical cyclone), a change to the TACC would have little effect as even a reduced TACC would not come close to being filled. Quota adjustments based on catch rates should take account of long-term trends in order to mitigate variability and cyclone effects in data.

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.

Measuring Physiological Stress in Australian Flying-Fox Populations

Flying-foxes (pteropid bats) are the natural host of Hendra virus, a recently emerged zoonotic virus responsible for mortality or morbidity in horses and humans in Australia since 1994. Previous studies have suggested physiological and ecological risk factors for infection in flying-foxes, including physiological stress. However, little work has been done measuring and interpreting stress hormones in flying-foxes. Over a 12-month period, we collected pooled urine samples from underneath roosting flying-foxes, and urine and blood samples from captured individuals. Urine and plasma samples were assayed for cortisol using a commercially available enzyme immunoassay. We demonstrated a typical post-capture stress response in flying-foxes, established urine specific gravity as an attractive alternative to creatinine to correct urine concentration, and established population-level urinary cortisol ranges (and geometric means) for the four Australian species: Pteropus alecto 0.5–305.1 ng/mL (20.1 ng/mL); Pteropus conspicillatus 0.3–370.9 ng/mL (18.9 ng/mL); Pteropus poliocephalus 0.3–311.3 ng/mL (10.1 ng/mL); Pteropus scapulatus 5.2–205.4 ng/mL (40.7 ng/mL). Geometric means differed significantly except for P. alecto and P. conspicillatus. Our approach is methodologically robust, and has application both as a research or clinical tool for flying-foxes, and for other free-living colonial wildlife species

Screening Eucalyptus cloeziana and E. argophloia populations for resistance to Puccinia psidii

Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations. Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations.

Diagnostic Molecular Markers for Phosphine Resistance in U.S. Populations of Tribolium castaneum and Rhyzopertha dominica

Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T.castaneum and R.dominica with strong resistance was identified as P45S in T.castaneum and P49S in R.dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T.castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.

Atypical correlation of otolith strontium : calcium and barium : calcium across a marine–freshwater life history transition of a diadromous fish

Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr : Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr : Ca and Ba : Ca, however, showed the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35–45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4 mg L–1) of the freshwater resulted in the Sr : Ca being substantially higher than the marine water. Importantly, the otolith Sr : Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr : Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr : Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element : Ca ratios and that inferences of marine–freshwater habitat use from otolith Sr : Ca alone can be problematic without an understanding of water chemistry.