A Bayesian hurdle model for analysis of an insect resistance monitoring database

Motivated by the analysis of the Australian Grain Insect Resistance Database (AGIRD), we develop a Bayesian hurdle modelling approach to assess trends in strong resistance of stored grain insects to phosphine over time. The binary response variable from AGIRD indicating presence or absence of strong resistance is characterized by a majority of absence observations and the hurdle model is a two step approach that is useful when analyzing such a binary response dataset. The proposed hurdle model utilizes Bayesian classification trees to firstly identify covariates and covariate levels pertaining to possible presence or absence of strong resistance. Secondly, generalized additive models (GAMs) with spike and slab priors for variable selection are fitted to the subset of the dataset identified from the Bayesian classification tree indicating possibility of presence of strong resistance. From the GAM we assess trends, biosecurity issues and site specific variables influencing the presence of strong resistance using a variable selection approach. The proposed Bayesian hurdle model is compared to its frequentist counterpart, and also to a naive Bayesian approach which fits a GAM to the entire dataset. The Bayesian hurdle model has the benefit of providing a set of good trees for use in the first step and appears to provide enough flexibility to represent the influence of variables on strong resistance compared to the frequentist model, but also captures the subtle changes in the trend that are missed by the frequentist and naive Bayesian models. © 2014 Springer Science+Business Media New York.

Effect of Broadcast Baiting on Abundance Patterns of Red Imported Fire Ants (Hymenoptera: Formicidae) and Key Local Ant Genera at Long-Term Monitoring Sites in Brisbane, Australia

In 2001, the red imported fire ant (Solenopsis invicta Buren) was identified in Brisbane, Australia. An eradication program involving broadcast bait treatment with two insect growth regulators and a metabolic inhibitor began in September of that year and is currently ongoing. To gauge the impacts of these treatments on local ant populations, we examined long-term monitoring data and quantified abundance patterns of S. invicta and common local ant genera using a linear mixed-effects model. For S. invicta, presence in pitfalls reduced over time to zero on every site. Significantly higher numbers of S. invicta workers were collected on high-density polygyne sites, which took longer to disinfest compared with monogyne and low-density polygyne sites. For local ants, nine genus groups of the 10 most common genera analyzed either increased in abundance or showed no significant trend. Five of these genus groups were significantly less abundant at the start of monitoring on high-density polygyne sites compared with monogyne and low-density polygyne sites. The genus Pheidole significantly reduced in abundance over time, suggesting that it was affected by treatment efforts. These results demonstrate that the treatment regime used at the time successfully removed S. invicta from these sites in Brisbane, and that most local ant genera were not seriously impacted by the treatment. These results have important implications for current and future prophylactic treatment efforts, and suggest that native ants remain in treated areas to provide some biological resistance to S. invicta.

Rapid monitoring of nitrogen in mango trees

Nitrogen (N) is an essential nutrient in mango, influencing both productivity and fruit quality. In Australian mango orchards, tree N is traditionally assessed once a year at the dormant pre-flowering stage using laboratory analysis of leaf N. This single assessment is insufficient to determine tree N status at all stages of the annual phenological cycle. Development of a field-based rapid N test would allow more frequent monitoring of tree N status and improved fertiliser management. These experiments examined the accuracy and useability of several devices used in other horticultural crops to rapidly assess mango leaf N in the field; the Konica Minolta 'SPAD-502 chlorophyll meter', Horiba 'Cardy Meter' and the Merck 'RQflex 10.' Regression and correlation analyses were used to determine the relationship between total leaf N and the measurements from the rapid test devices. The relationship between the chlorophyll index measured by the SPAD-502 meter and leaf N was highly significant at late fruit set (R 2=0.72, n=40) and post-harvest (R 2=0.81, n=40) stages and significant at the flowering stage (R 2=0.51, n=40) in the cultivar 'Kensington Pride', indicating the device can be used to rapidly assess mango leaf N in the field. Correlation analysis indicated the relationship between petiole sap measured with the Cardy or Merck devices and leaf N was non-significant.

Is stocking barramundi (Lates calcarifer) in north-eastern Queensland a threat to aquatic biodiversity?

The stocking of predators can have significant consequences on recipient aquatic ecosystems. We investigated some potential ecological impacts of stocking a predatory fish (Lates calcarifer) into a coastal river and a large impoundment in north-eastern Australia. L. calcarifer was mostly found in slower-moving, larger reaches of the river or in the main body of the impoundment where there was abundant suitable habitat. In the tidally influenced freshwater reaches of the coastal river, L. calcarifer predominately consumed aytid and palaemonid shrimp that were associated with local macrophyte beds or littoral grasses. In this area the diets of juvenile stocked and wild L. calcarifer were similar and stocked fish displayed a high degree of site fidelity. Further upstream in the river, away from tidal influence, and in the impoundment, fish were the main prey item. Cannibalism was uncommon and we suggest that, at the current stocking densities, there was little dietary evidence of predatory impacts from L. calcarifer on species of conservation concern. We caution against introducing novel predatory species such as L. calcarifer in or near areas that are outside their natural range and are known to support rare, threatened or endangered species.

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.

Overcoming barriers to the successful implementation of a classical biological control strategy for the exotic invasive weed Mikania micrantha in the Asia-Pacific region

Mikania micrantha (Asteraceae) commonly known as mikania, is a major invasive alien plant (IAP) in the tropical humid agricultural and forest zones of the Asia-Pacific region. This fast-growing Neotropical vine is able to smother plants in agricultural ecosystems, agroforestry and natural habitats, reducing productivity and biodiversity. Fungal pathogens were first investigated for the classical biological control of this weed in 1996. This resulted in the selection and screening of the highly host-specific and damaging rust pathogen, Puccinia spegazzinii (Pucciniales). It was first released in India and China in 2005/6, although it is not believed to have established. Since then, it has been released successfully in Taiwan, Papua New Guinea (PNG), Fiji and most recently Vanuatu. The rust has established and is spreading rapidly after applying lessons learned from the first releases on the best rust pathotype and release strategy. In PNG, direct monitoring of vegetation change has demonstrated that the rust is having a significant impact on M. micrantha, with no unpredicted non-target impacts. Despite this, the authorities in many countries where mikania is a problem remain cautious about releasing the rust. In Western Samoa, introduction of the rust was not pursued because of a conflict of interest, and the perception that mikania suppresses even worse weeds. For some, ‘pathophobia’ is still a major obstacle. In Indonesia, where insects for weed CBC have been introduced, pathogens will currently not be considered. In other countries such as Bhutan and Myanmar, there are no baseline data on the presence and impact of IAPs and, with no history of CBC, no institutional framework for implementing this approach. Malaysia has a well-developed framework, but capacity needs to be built in the country. Overall, it remains critical to have champions at decision making levels. Hence, even with an effective ‘off-the-shelf’ agent available, implementation of mikania CBC still requires significant inputs tailored to the countries’ specific needs.

Biodiversity, biosecurity and integrated pest management

Breaches of biosecurity, leading to incursions by invasive species, have the potential to cause substantial economic, social and environmental losses, including drastic reduction in biodiversity. It is argued that improving biosecurity reduces risk to biodiversity, while maintaining stable ecosystems through biodiversity can be a safeguard against biosecurity breaches. The global costs of invasive alien species (IAS) have been estimated at around US$350 billion, while alien invertebrate and vertebrate pests and weeds are estimated to cost Australia at least $7 billion a year. A striking, current, example is the incursion by Myrtle Rust (Puccinia psidii) an organism which can infect all members of the Myrtaceae, the most important family in the Australian flora. Myrtle rust was first detected on a property on the central coast of New South Wales in late April 2010. Two years later the disease has been detected in numerous locations in Queensland and New South Wales ranging from commercial plant nurseries and public amenities to large areas of bushland. This particular breach of biosecurity will, inevitably, diminish biodiversity of flora and fauna over large areas of the continent. Integrated pest management (IPM), an enrichment of diversity in managing invasive and other pest species, offers the best opportunity to address problems such as these. Australia's response to increasing biosecurity risk is comprehensive and includes national networking of scientists engaged in a complex program of biosecurity research and development, including studies of IPM. This network is being enhanced by the development of international linkages.

Otolith morphology of four mackerel species (Scomberomorus spp.) in Australia: Species differentiation and prediction for fisheries monitoring and assessment

Four species of large mackerels (Scomberomorus spp.) co-occur in the waters off northern Australia and are important to fisheries in the region. State fisheries agencies monitor these species for fisheries assessment; however, data inaccuracies may exist due to difficulties with identification of these closely related species, particularly when specimens are incomplete from fish processing. This study examined the efficacy of using otolith morphometrics to differentiate and predict among the four mackerel species off northeastern Australia. Seven otolith measurements and five shape indices were recorded from 555 mackerel specimens. Multivariate modelling including linear discriminant analysis (LDA) and support vector machines, successfully differentiated among the four species based on otolith morphometrics. Cross validation determined a predictive accuracy of at least 96% for both models. An optimum predictive model for the four mackerel species was an LDA model that included fork length, feret length, feret width, perimeter, area, roundness, form factor and rectangularity as explanatory variables. This analysis may improve the accuracy of fisheries monitoring, the estimates based on this monitoring (i.e. mortality rate) and the overall management of mackerel species in Australia.

Managing reforestation to sequester carbon, increase biodiversity potential and minimize loss of agricultural land

Reforestation will have important consequences for the global challenges of mitigating climate change, arresting habitat decline and ensuring food security. We examined field-scale trade-offs between carbon sequestration of tree plantings and biodiversity potential and loss of agricultural land. Extensive surveys of reforestation across temperate and tropical Australia (N = 1491 plantings) were used to determine how planting width and species mix affect carbon sequestration during early development (< 15 year). Carbon accumulation per area increased significantly with decreasing planting width and with increasing proportion of eucalypts (the predominant over-storey genus). Highest biodiversity potential was achieved through block plantings (width > 40 m) with about 25% of planted individuals being eucalypts. Carbon and biodiversity goals were balanced in mixed-species plantings by establishing narrow belts (width < 20 m) with a high proportion (>75%) of eucalypts, and in monocultures of mallee eucalypt plantings by using the widest belts (ca. 6–20 m). Impacts on agriculture were minimized by planting narrow belts (ca. 4 m) of mallee eucalypt monocultures, which had the highest carbon sequestering efficiency. A plausible scenario where only 5% of highly-cleared areas (<30% native vegetation cover remaining) of temperate Australia are reforested showed substantial mitigation potential. Total carbon sequestration after 15 years was up to 25 Mt CO2-e year−1 when carbon and biodiversity goals were balanced and 13 Mt CO2-e year−1 if block plantings of highest biodiversity potential were established. Even when reforestation was restricted to marginal agricultural land (<$2000 ha−1 land value, 28% of the land under agriculture in Australia), total mitigation potential after 15 years was 17–26 Mt CO2-e year−1 using narrow belts of mallee plantings. This work provides guidance on land use to governments and planners. We show that the multiple benefits of young tree plantings can be balanced by manipulating planting width and species choice at establishment. In highly-cleared areas, such plantings can sequester substantial biomass carbon while improving biodiversity and causing negligible loss of agricultural land.