Info-gap theory and robust design of surveillance for invasive species : the case study of Barrow Island

Surveillance for invasive non-indigenous species (NIS) is an integral part of a quarantine system. Estimating the efficiency of a surveillance strategy relies on many uncertain parameters estimated by experts, such as the efficiency of its components in face of the specific NIS, the ability of the NIS to inhabit different environments, and so on. Due to the importance of detecting an invasive NIS within a critical period of time, it is crucial that these uncertainties be accounted for in the design of the surveillance system. We formulate a detection model that takes into account, in addition to structured sampling for incursive NIS, incidental detection by untrained workers. We use info-gap theory for satisficing (not minimizing) the probability of detection, while at the same time maximizing the robustness to uncertainty. We demonstrate the trade-off between robustness to uncertainty, and an increase in the required probability of detection. An empirical example based on the detection of Pheidole megacephala on Barrow Island demonstrates the use of info-gap analysis to select a surveillance strategy.

Improved design method for biosecurity surveillance and early detection of non-indigenous rats

A recent advance in biosecurity surveillance design aims to benefit island conservation through early and improved detection of incursions by non-indigenous species. The novel aspects of the design are that it achieves a specified power of detection in a cost-managed system, while acknowledging heterogeneity of risk in the study area and stratifying the area to target surveillance deployment. The design also utilises a variety of surveillance system components, such as formal scientific surveys, trapping methods, and incidental sightings by non-biologist observers. These advances in design were applied to black rats (Rattus rattus) representing the group of invasive rats including R. norvegicus, and R. exulans, which are potential threats to Barrow Island, Australia, a high value conservation nature reserve where a proposed liquefied natural gas development is a potential source of incursions. Rats are important to consider as they are prevalent invaders worldwide, difficult to detect early when present in low numbers, and able to spread and establish relatively quickly after arrival. The ‘exemplar’ design for the black rat is then applied in a manner that enables the detection of a range of non-indigenous species of rat that could potentially be introduced. Many of the design decisions were based on expert opinion as data gaps exist in empirical data. The surveillance system was able to take into account factors such as collateral effects on native species, the availability of limited resources on an offshore island, financial costs, demands on expertise and other logistical constraints. We demonstrate the flexibility and robustness of the surveillance system and discuss how it could be updated as empirical data are collected to supplement expert opinion and provide a basis for adaptive management. Overall, the surveillance system promotes an efficient use of resources while providing defined power to detect early rat incursions, translating to reduced environmental, resourcing and financial costs.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Priority threat management of non-native plants to maintain ecosystem integrity across heterogeneous landscapes

Invasive non-native plants have negatively impacted on biodiversity and ecosystem functions world-wide. Because of the large number of species, their wide distributions and varying degrees of impact, we need a more effective method for prioritizing control strategies for cost-effective investment across heterogeneous landscapes. Here, we develop a prioritization framework that synthesizes scientific data, elicits knowledge from experts and stakeholders to identify control strategies, and appraises the cost-effectiveness of strategies. Our objective was to identify the most cost-effective strategies for reducing the total area dominated by high-impact non-native plants in the Lake Eyre Basin (LEB). We use a case study of the ˜120 million ha Lake Eyre Basin that comprises some of the most distinctive Australian landscapes, including Uluru-Kata Tjuta National Park. More than 240 non-native plant species are recorded in the Lake Eyre Basin, with many predicted to spread, but there are insufficient resources to control all species. Lake Eyre Basin experts identified 12 strategies to control, contain or eradicate non-native species over the next 50 years. The total cost of the proposed Lake Eyre Basin strategies was estimated at AU$1·7 billion, an average of AU$34 million annually. Implementation of these strategies is estimated to reduce non-native plant dominance by 17 million ha – there would be a 32% reduction in the likely area dominated by non-native plants within 50 years if these strategies were implemented. The three most cost-effective strategies were controlling Parkinsonia aculeata, Ziziphus mauritiana and Prosopis spp. These three strategies combined were estimated to cost only 0·01% of total cost of all the strategies, but would provide 20% of the total benefits. Over 50 years, cost-effective spending of AU$2·3 million could eradicate all non-native plant species from the only threatened ecological community within the Lake Eyre Basin, the Great Artesian Basin discharge springs. Synthesis and applications. Our framework, based on a case study of the ˜120 million ha Lake Eyre Basin in Australia, provides a rationale for financially efficient investment in non-native plant management and reveals combinations of strategies that are optimal for different budgets. It also highlights knowledge gaps and incidental findings that could improve effective management of non-native plants, for example addressing the reliability of species distribution data and prevalence of information sharing across states and regions.

Development of type I genetic markers from expressed sequence tags in highly polymorphic species

Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplification; - 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions, and; - 3) at least occasionally, a PCR primer straddles an exon–intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters.

Sewage disposal and wildlife health in Antarctica

Sewage and its microbiology, treatment and disposal are important to the topic of Antarctic wildlife health because disposal of untreated sewage effluent into the Antarctic marine environment is both allowed and commonplace. Human sewage contains enteric bacteria as normal flora, and has the potential to contain parasites, bacteria and viruses which may prove pathogenic to Antarctic wildlife. Treatment can reduce levels of micro-organisms in sewage effluent, but is not a requirement of the Environmental Protocol to the Antarctic Treaty (the Madrid Protocol). In contrast, the deliberate release of non-native organisms for any other reason is prohibited. Hence, disposal of sewage effluent to the marine environment is the only activity routinely undertaken in Antarctica knowing that it will likely result in the release of large numbers of potentially non-native species. When the Madrid Protocol was negotiated, the decision to allow release of untreated sewage effluent was considered the only pragmatic option, as a prohibition would have been costly, and may not have been achievable by many Antarctic operators. In addition, at that time the potential for transmission of pathogens to wildlife from sewage was not emphasised as a significant potential risk. Since then, the transmission of disease-causing agents between species is more widely recognised and it is now timely to consider the risks of continued discharge of sewage effluent in Antarctica and whether there are practical alternatives.

An ESR study of irradiated poly(tetrafluoroethylene-co-perfluoropropyl vinyl ether) (PFA)

Poly(tetrafluoroethylene-co-perfluoropropyl vinyl ether) (PFA) with 2 mol% perfluoropropyl vinyl ether (PPVE) was exposed to γ-irradiation in vacuum at both 77 K and room temperature and the ESR spectra recorded. Both the main chain, CF2–C.F–CF2, and end chain, CF2C.F2 radicals were identified at both temperatures and their thermal stabilities measured. No radicals unique to the radiolytic cleavage at the PPVE units were observed at room temperature, either due to the low concentration of the comonomer or β-scission to form a chain end radical and a non-radical species. G-values for radical formation at room temperature and 77 K were found to be 0.93 and 0.16, respectively.

Hierarchical Bayesian models for estimating the extent of plant pest invasions

Plant biosecurity requires statistical tools to interpret field surveillance data in order to manage pest incursions that threaten crop production and trade. Ultimately, management decisions need to be based on the probability that an area is infested or free of a pest. Current informal approaches to delimiting pest extent rely upon expert ecological interpretation of presence / absence data over space and time. Hierarchical Bayesian models provide a cohesive statistical framework that can formally integrate the available information on both pest ecology and data. The overarching method involves constructing an observation model for the surveillance data, conditional on the hidden extent of the pest and uncertain detection sensitivity. The extent of the pest is then modelled as a dynamic invasion process that includes uncertainty in ecological parameters. Modelling approaches to assimilate this information are explored through case studies on spiralling whitefly, Aleurodicus dispersus and red banded mango caterpillar, Deanolis sublimbalis. Markov chain Monte Carlo simulation is used to estimate the probable extent of pests, given the observation and process model conditioned by surveillance data. Statistical methods, based on time-to-event models, are developed to apply hierarchical Bayesian models to early detection programs and to demonstrate area freedom from pests. The value of early detection surveillance programs is demonstrated through an application to interpret surveillance data for exotic plant pests with uncertain spread rates. The model suggests that typical early detection programs provide a moderate reduction in the probability of an area being infested but a dramatic reduction in the expected area of incursions at a given time. Estimates of spiralling whitefly extent are examined at local, district and state-wide scales. The local model estimates the rate of natural spread and the influence of host architecture, host suitability and inspector efficiency. These parameter estimates can support the development of robust surveillance programs. Hierarchical Bayesian models for the human-mediated spread of spiralling whitefly are developed for the colonisation of discrete cells connected by a modified gravity model. By estimating dispersal parameters, the model can be used to predict the extent of the pest over time. An extended model predicts the climate restricted distribution of the pest in Queensland. These novel human-mediated movement models are well suited to demonstrating area freedom at coarse spatio-temporal scales. At finer scales, and in the presence of ecological complexity, exploratory models are developed to investigate the capacity for surveillance information to estimate the extent of red banded mango caterpillar. It is apparent that excessive uncertainty about observation and ecological parameters can impose limits on inference at the scales required for effective management of response programs. The thesis contributes novel statistical approaches to estimating the extent of pests and develops applications to assist decision-making across a range of plant biosecurity surveillance activities. Hierarchical Bayesian modelling is demonstrated as both a useful analytical tool for estimating pest extent and a natural investigative paradigm for developing and focussing biosecurity programs.

Hierarchical Bayesian modelling of early detection surveillance for plant pest invasions

Early detection surveillance programs aim to find invasions of exotic plant pests and diseases before they are too widespread to eradicate. However, the value of these programs can be difficult to justify when no positive detections are made. To demonstrate the value of pest absence information provided by these programs, we use a hierarchical Bayesian framework to model estimates of incursion extent with and without surveillance. A model for the latent invasion process provides the baseline against which surveillance data are assessed. Ecological knowledge and pest management criteria are introduced into the model using informative priors for invasion parameters. Observation models assimilate information from spatio-temporal presence/absence data to accommodate imperfect detection and generate posterior estimates of pest extent. When applied to an early detection program operating in Queensland, Australia, the framework demonstrates that this typical surveillance regime provides a modest reduction in the estimate that a surveyed district is infested. More importantly, the model suggests that early detection surveillance programs can provide a dramatic reduction in the putative area of incursion and therefore offer a substantial benefit to incursion management. By mapping spatial estimates of the point probability of infestation, the model identifies where future surveillance resources can be most effectively deployed.

Impacts of invasive plants on Australian rangelands

In Australia, the spread and dominance of non-native plant species has been identified as a serious threat to rangeland biodiversity and ecosystem functioning. Rangelands extend over 70% of Australia’s land mass or more than 6 million km2. These rangelands consist of a diverse set of ecosystems including grasslands, shrub-lands, and woodlands spanning numerous climatic zones, ranging from arid to mesic. Because of the high economic, social, and environmental values, sustainable management of these vast landscapes is critical for Australia’s future. More than 2 million people live in these areas and major industries are ranching, mining, and tourism. In terms of biodiversity values, 53 of 85 of Australia’s biogeographical regions and 5 of 15 identified biodiversity hotspots are found in rangelands.

Cost-effective suppression and eradication of invasive predators

Introduced predators can have pronounced effects on naïve prey species; thus, predator control is often essential for conservation of threatened native species. Complete eradication of the predator, although desirable, may be elusive in budget-limited situations, whereas predator suppression is more feasible and may still achieve conservation goals. We used a stochastic predator-prey model based on a Lotka-Volterra system to investigate the cost-effectiveness of predator control to achieve prey conservation. We compared five control strategies: immediate eradication, removal of a constant number of predators (fixed-number control), removal of a constant proportion of predators (fixed-rate control), removal of predators that exceed a predetermined threshold (upper-trigger harvest), and removal of predators whenever their population falls below a lower predetermined threshold (lower-trigger harvest). We looked at the performance of these strategies when managers could always remove the full number of predators targeted by each strategy, subject to budget availability. Under this assumption immediate eradication reduced the threat to the prey population the most. We then examined the effect of reduced management success in meeting removal targets, assuming removal is more difficult at low predator densities. In this case there was a pronounced reduction in performance of the immediate eradication, fixed-number, and lower-trigger strategies. Although immediate eradication still yielded the highest expected minimum prey population size, upper-trigger harvest yielded the lowest probability of prey extinction and the greatest return on investment (as measured by improvement in expected minimum population size per amount spent). Upper-trigger harvest was relatively successful because it operated when predator density was highest, which is when predator removal targets can be more easily met and the effect of predators on the prey is most damaging. This suggests that controlling predators only when they are most abundant is the "best" strategy when financial resources are limited and eradication is unlikely. © 2008 Society for Conservation Biology.

Climate change, sustainability and science education

The world and its peoples are facing multiple, complex challenges and we cannot continue as we are (Moss, 2010). Earth‘s “natural capital” - nature‘s ability to provide essential ecosystem services to stabilize world climate systems, maintain water quality, support secure food production, supply energy needs, moderate environmental impacts, and ensure social harmony and equity – is seriously compromised (Gough, 2005; Hawkins, Lovins & Lovins, 1999). To further summarize, current rates of resource consumption by the global human population are unsustainable (Kitzes, Peller, Goldfinger & Wackernagel, 2007) for human and non-human species, and for future generations. Further, continuing growth in world population and global political commitment to growth economics compounds these demands. Despite growing recognition of the serious consequences for people and planet, little consideration is given, within most nations, to the social and environmental issues that economic growth brings. For example, Australia is recognised as one of the developed countries most vulnerable to the impacts of climate change. Yet, to date, responses (such as carbon pricing) have been small-scale, fragmented, and their worth disputed, even ridiculed. This is at a time referred to as ‘the critical decade’ (Hughes & McMichael, 2011) when the world’s peoples must make strong choices if we are to avert the worst impacts of climate change.

Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478 bp and N50 length of 506 bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.

Assessment of an environmentally friendly, semi-pelagic fish trawl

Minimising catches of non-target animals in a trawl fishery reduces the impact on a marine community and may help to sustain the fishery resource in the long term. Hence the desirability for trawls that minimise impacts on non-target species while maintaining catches of target species. This study resulted from a need to further develop easily handled, semi-pelagic style trawls for Australia's Northern Fish Trawl Fishery. In November 1993 we compared catches from three differently rigged versions of a demersal wing trawl: one fished in a standard demersal configuration with its footrope on the sea bed, and two fished semi-pelagically, with their footropes raised to either 0.4-0.5 or 0.8-0.9 m above the sea bed. At two sites in the northeast Gulf of Carpentaria, each trawl type was used on the same combination of sites, grids within sites and times of day. Catches of the main target species (Lutjanus malabaricus and Lutjanus erythropterus) by the three trawl types were not significantly different. However, the mean catches of both these species and of other commercially important snappers, were highest in the semi-pelagic trawl raised 0.4-0.5 m above the sea bed. This increase could be due to a larger trawl spread or to the whole rig fishing higher in the water column. Of the 107 species of fishes analysed, 61 were caught in greater abundance in the demersal trawl. Seven species were caught more effectively in the semi-pelagic trawl with the footrope 0.4-0.5 m above the substrate; none was caught most effectively with the footrope set at 0.8-0.9 m. Epibenthic byproduct species (squid and Thenus orientalis), fish bycatch, sponges and other epibenthic invertebrates were also caught in lower numbers in the semi-pelagic trawls. The semi-pelagic trawls convincingly caught less (in both numbers and biomass) of the unwanted species which are normally discarded. Semi-pelagic fish trawls of the types tested would be suitable for Australia's Northern Fish Trawl Fishery and probably other demersal trawl fisheries that would benefit from the conservation of non-target epibenthic communities.