Choosing a fishery's governance structure using data poor methods

Multi-species fisheries are complex to manage and the ability to develop an appropriate governance structure is often seriously impeded because trading between sustainability objectives at the species level, economic objectives at the fleet level, and social objectives at the community scale, is complex. Many of these fisheries also tend to have a mix of information, with stock assessments available for some species and almost no information on other species. The fleets themselves comprise fishers from small family enterprises to large vertically integrated businesses. The Queensland trawl fishery in Australia is used as a case study for this kind of fishery. It has the added complexity that a large part of the fishery is within a World Heritage Area, the Great Barrier Reef Marine Park, which is managed by an agency of the Australian Commonwealth Government whereas the fishery itself is managed by the Queensland State Government. A stakeholder elicitation process was used to develop social, governance, economic and ecological objectives, and then weight the relative importance of these. An expert group was used to develop different governance strawmen (or management strategies) and these were assessed by a group of industry stakeholders and experts using multi-criteria decision analysis techniques against the different objectives. One strawman clearly provided the best overall set of outcomes given the multiple objectives, but was not optimal in terms of every objective, demonstrating that even the "best" strawman may be less than perfect. © 2012.

Pollination methods, stigma receptivity and pollen tube growth in Eucalyptus argophloia

Eucalyptus argophloia Blakely (Western white gum) has shown potential as a commercial forestry timber species in marginal environments of north-eastern Australia. We measured early pollination success in Eucalyptus argophloia to compare pollination methods, determine the timing of stigma receptivity and compare fresh and stored pollen. Early pollination success was measured by counting pollen tubes in the style of E. argophloia 12 days after pollination. We compared the early pollination success of 1) Artificially Induced Protogyny (AIP), one-stop and three-stop methods of pollination; 2) flowers pollinated at 2 day intervals between 2 days before and 6 days after anthesis and 3) fresh pollen and pollen that had been stored for 9 months. Our results show significantly more pollen tubes from unpollinated AIP and AIP treatments than either the one-stop pollination or three-stop pollination treatments. This indicates that self-pollination occurs in the unpollinated AIP treatment. There was very little pollen tube growth in the one-stop method indicating that the three-stop method is the most suitable for this species. Stigma receptivity in E. argophloia commenced six days after anthesis and no pollen tube growth was observed prior to this. Fresh pollen resulted in pollen tube growth in the style whereas the stored pollen resulted in a total absence of pollen tube growth. We recommend that breeding programs incorporating E. argophloia as a female parent use the three-stop pollination method, and controlled pollination be carried out at least six days after anthesis using fresh pollen.

Monitoring wild pig populations: a review of methods

Wild pigs (Sus scrofa) are widespread across many landscapes throughout the world and are considered to be an invasive pest to agriculture and the environment, or conversely a native or desired game species and resource for hunting. Wild pig population monitoring is often required for a variety of management or research objectives, and many methods and analyses for monitoring abundance are available. Here, we describe monitoring methods that have proven or potential applications to wild pig management. We describe the advantages and disadvantages of methods so that potential users can efficiently consider and identify the option(s) best suited to their combination of objectives, circumstances, and resources. This paper offers guidance to wildlife managers, researchers, and stakeholders considering population monitoring of wild pigs and will help ensure that they can fulfill their monitoring objectives while optimizing their use of resources.

Scale- and Context-Dependent Selection of Recreational Harvest Estimation Methods: The Australasian Experience

Fisheries managers are becoming increasingly aware of the need to quantify all forms of harvest, including that by recreational fishers. This need has been driven by both a growing recognition of the potential impact that noncommercial fishers can have on exploited resources and the requirement to allocate catch limits between different sectors of the wider fishing community in many jurisdictions. Marine recreational fishers are rarely required to report any of their activity, and some form of survey technique is usually required to estimate levels of recreational catch and effort. In this review, we describe and discuss studies that have attempted to estimate the nature and extent of recreational harvests of marine fishes in New Zealand and Australia over the past 20 years. We compare studies by method to show how circumstances dictate their application and to highlight recent developments that other researchers may find of use. Although there has been some convergence of approach, we suggest that context is an important consideration, and many of the techniques discussed here have been adapted to suit local conditions and to address recognized sources of bias. Much of this experience, along with novel improvements to existing approaches, have been reported only in "gray" literature because of an emphasis on providing estimates for immediate management purposes. This paper brings much of that work together for the first time, and we discuss how others might benefit from our experience.

Abundance indices for long-lived tropical snappers: estimating standardized catch rates from spatially and temporally coarse logbook data

The Northern Demersal Scalefish Fishery has historically comprised a small fleet (≤10 vessels year−1) operating over a relatively large area off the northwest coast of Australia. This multispecies fishery primarily harvests two species of snapper: goldband snapper, Pristipomoides multidens and red emperor, Lutjanus sebae. A key input to age-structured assessments of these stocks has been the annual time-series of the catch rate. We used an approach that combined Generalized Linear Models, spatio-temporal imputation, and computer-intensive methods to standardize the fishery catch rates and report uncertainty in the indices. These analyses, which represent one of the first attempts to standardize fish trap catch rates, were also augmented to gain additional insights into the effects of targeting, historical effort creep, and spatio-temporal resolution of catch and effort data on trap fishery dynamics. Results from monthly reported catches (i.e. 1993 on) were compared with those reported daily from more recently (i.e. 2008 on) enhanced catch and effort logbooks. Model effects of catches of one species on the catch rates of another became more conspicuous when the daily data were analysed and produced estimates with greater precision. The rate of putative effort creep estimated for standardized catch rates was much lower than estimated for nominal catch rates. These results therefore demonstrate how important additional insights into fishery and fish population dynamics can be elucidated from such “pre-assessment” analyses.

Rhipicephalus (Boophilus) microplus tick in vitro feeding methods for functional (dsRNA) and vaccine candidate (antibody) screening

Rhipicephalus (Boophilus) microplus (Acari: Ixodidae) ticks cause economic losses for cattle industries throughout tropical and subtropical regions of the world estimated at $US2.5 billion annually. Lack of access to efficacious long-lasting vaccination regimes and increases in tick acaricide resistance have led to the investigation of targets for the development of novel tick vaccines and treatments. In vitro tick feeding has been used for many tick species to study the effect of new acaricides on the transmission of tick-borne pathogens. Few studies have reported the use of in vitro feeding for functional genomic studies using RNA interference and/or the effect of specific anti-tick antibodies. In particular, in vitro feeding reports for the cattle tick are limited due to its relatively short hypostome. Previously published methods were further modified to broaden optimal tick sizes/weights, feeding sources including bovine and ovine serum, optimisation of commercially available blood anti-coagulant tubes, and IgG concentrations for effective antibody delivery. Ticks are fed overnight and monitored for ∼5–6 weeks to determine egg output and success of larval emergence using a humidified incubator. Lithium-heparin blood tubes provided the most reliable anti-coagulant for bovine blood feeding compared with commercial citrated (CPDA) and EDTA tubes. Although >30 mg semi-engorged ticks fed more reliably, ticks as small as 15 mg also fed to repletion to lay viable eggs. Ticks which gained less than ∼10 mg during in vitro feeding typically did not lay eggs. One mg/ml IgG from Bm86-vaccinated cattle produced a potent anti-tick effect in vitro (83% efficacy) similar to that observed in vivo. Alternatively, feeding of dsRNA targeting Bm86 did not demonstrate anti-tick effects (11% efficacy) compared with the potent effects of ubiquitin dsRNA. This study optimises R. microplus tick in vitro feeding methods which support the development of cattle tick vaccines and treatments.

Methods to determine resistance to anthelmintics when continuing larval development occurs

The in vivo faecal egg count reduction test (FECRT) is the most commonly used test to detect anthelmintic resistance (AR) in gastrointestinal nematodes (GIN) of ruminants in pasture based systems. However, there are several variations on the method, some more appropriate than others in specific circumstances. While in some cases labour and time can be saved by just collecting post-drench faecal worm egg counts (FEC) of treatment groups with controls, or pre- and post-drench FEC of a treatment group with no controls, there are circumstances when pre- and post-drench FEC of an untreated control group as well as from the treatment groups are necessary. Computer simulation techniques were used to determine the most appropriate of several methods for calculating AR when there is continuing larval development during the testing period, as often occurs when anthelmintic treatments against genera of GIN with high biotic potential or high re-infection rates, such as Haemonchus contortus of sheep and Cooperia punctata of cattle, are less than 100% efficacious. Three field FECRT experimental designs were investigated: (I) post-drench FEC of treatment and controls groups, (II) pre- and post-drench FEC of a treatment group only and (III) pre- and post-drench FEC of treatment and control groups. To investigate the performance of methods of indicating AR for each of these designs, simulated animal FEC were generated from negative binominal distributions with subsequent sampling from the binomial distributions to account for drench effect, with varying parameters for worm burden, larval development and drench resistance. Calculations of percent reductions and confidence limits were based on those of the Standing Committee for Agriculture (SCA) guidelines. For the two field methods with pre-drench FEC, confidence limits were also determined from cumulative inverse Beta distributions of FEC, for eggs per gram (epg) and the number of eggs counted at detection levels of 50 and 25. Two rules for determining AR: (1) %reduction (%R) < 95% and lower confidence limit <90%; and (2) upper confidence limit <95%, were also assessed. For each combination of worm burden, larval development and drench resistance parameters, 1000 simulations were run to determine the number of times the theoretical percent reduction fell within the estimated confidence limits and the number of times resistance would have been declared. When continuing larval development occurs during the testing period of the FECRT, the simulations showed AR should be calculated from pre- and post-drench worm egg counts of an untreated control group as well as from the treatment group. If the widely used resistance rule 1 is used to assess resistance, rule 2 should also be applied, especially when %R is in the range 90 to 95% and resistance is suspected.

Quantitative methods to measure pigmentation variation in farmed Giant Tiger Prawns, Penaeus monodon, and the effects of different harvest methods on cooked colour

Cooked prawn colour is known to be a driver of market price and a visual indicator of product quality for the consumer. Although there is a general understanding that colour variation exists in farmed prawns, there has been no attempt to quantify this variation or identify where this variation is most prevalent. The objectives of this study were threefold: firstly to compare three different quantitative methods to measure prawn colour or pigmentation, two different colorimeters and colour quantification from digital images. Secondly, to quantify the amount of pigmentation variation that exists in farmed prawns within ponds, across ponds and across farms. Lastly, to assess the effects of ice storage or freeze-thawing of raw product prior to cooking. Each method was able to detect quantitative differences in prawn colour, although conversion of image based quantification of prawn colour from RGB to Lab was unreliable. Considerable colour variation was observed between prawns from different ponds and different farms, and this variation potentially affects product value. Different post-harvest methods prior to cooking were also shown to have a profound detrimental effect on prawn colour. Both long periods of ice storage and freeze thawing of raw product were detrimental to prawn colour. However, ice storage immediately after cooking was shown to be beneficial to prawn colour. Results demonstrated that darker prawn colour was preserved by holding harvested prawns alive in chilled seawater, limiting the time between harvesting and cooking, and avoiding long periods of ice storage or freeze thawing of uncooked product.

Responses of Super Rice (Oryza sativa L.) to Different Planting Methods for Grain Yield and Nitrogen-Use Efficiency in the Single Cropping Season

To break the yield ceiling of rice production, a super rice project was developed in 1996 to breed rice varieties with super high yield. A two-year experiment was conducted to evaluate yield and nitrogen (N)-use response of super rice to different planting methods in the single cropping season. A total of 17 rice varieties, including 13 super rice and four non-super checks (CK), were grown under three N levels [0 (N0), 150 (N150), and 225 (N225) kg ha−1] and two planting methods [transplanting (TP) and direct-seeding in wet conditions (WDS)]. Grain yield under WDS (7.69 t ha−1) was generally lower than TP (8.58 t ha−1). However, grain yield under different planting methods was affected by N rates as well as variety groups. In both years, there was no difference in grain yield between super and CK varieties at N150, irrespective of planting methods. However, grain yield difference was dramatic in japonica groups at N225, that is, there was an 11.3% and 14.1% average increase in super rice than in CK varieties in WDS and TP, respectively. This suggests that high N input contributes to narrowing the yield gap in super rice varieties, which also indicates that super rice was bred for high fertility conditions. In the japonica group, more N was accumulated in super rice than in CK at N225, but no difference was found between super and CK varieties at N0 and N150. Similar results were also found for N agronomic efficiency. The results suggest that super rice varieties have an advantage for N-use efficiency when high N is applied. The response of super rice was greater under TP than under WDS. The results suggest that the need to further improve agronomic and other management practices to achieve high yield and N-use efficiency for super rice varieties in WDS.

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.

Comparison of three pollination methods for Eucalyptus argophloia, a small-flowered eucalypt

Context Most studies assess pollination success at capsule maturity, and studies of pre-zygotic processes are often lacking. Aims This study investigates the suitability of controlled pollination for a potential forestry plantation species, Eucalyptus argophloia, by examining pre- and post-zygotic pollination success. Methods Pollen tube development, capsule set and seed set are compared following three-stop pollination, artificially induced protogyny (AIP), AIP unpollinated and open pollination. The fecundity of stored pollen was compared with that of fresh pollen. Results Three-stop pollination, AIP and open pollination had similar numbers of pollen tubes, but AIP unpollinated had none. Open pollination produced significantly more capsules and total number of seeds than the other treatments. There were significantly more seeds per retained capsule for the open pollination and three-stop pollination treatments than for the AIP and AIP unpollinated pollination treatments. There were no significant differences relative to the age of pollen. Conclusions Pre-zygotic success in terms of pollen tubes was similar for open-pollinated, three stop and AIP, but was not reflected in post-zygotic success when the open pollination and three-stop method produced significantly more seeds per retained capsule than the AIP treatments and open pollination yielded more seeds. Capsule set and total seed set for open pollination, and fewer capsules in controlled pollinations, may reflect physical damage to buds because of the small E. argophloia flowers. Suitable alternative breeding strategies other than controlled pollinations are discussed for this species.

Learning from the past to predict the future: an historical analysis of grass invasions in northern Australia

An important focus of biosecurity is anticipating future risks, but time lags between introduction, naturalisation, and (ultimately) impact mean that future risks can be strongly influenced by history. We conduct a comprehensive historical analysis of tropical grasses (n = 155) that have naturalised in Australia since European settlement (1788) to determine what factors shaped historical patterns of naturalisation and future risks, including for the 21 species that cause serious negative impacts. Most naturalised species were from the Old World (78 %), were introduced for use in pasture (64.5 %), were first recorded prior to 1940 (84.5 %) and naturalised before 1980 (90.3 %). Patterns for high-impact species were similar, with all being first recorded in Australia by 1940, and only seven naturalised since then-five intentionally introduced as pasture species. Counter to expectations, we found no evidence for increased naturalisation with increasing trade, including for species introduced unintentionally for which the link was expected to be strongest. New pathways have not emerged since the 1930s despite substantial shifts in trading patterns. Furthermore, introduction and naturalisation rates are now at or approaching historically low levels. Three reasons were identified: (1) the often long lag phase between introduction and reported naturalisation means naturalisation rates reflect historical trends in introduction rates; (2) important introduction pathways are not directly related to trade volume and globalisation; and (3) that species pools may become depleted. The last of these appears to be the case for the most important pathway for tropical grasses, i.e. the intentional introduction of useful pasture species. Assuming that new pathways don't arise that might result in increased naturalisation rates, and that current at-border biosecurity practices remain in place, we conclude that most future high-impact tropical grass species are already present in Australia. Our results highlight the need to continually test underlying assumptions regarding future naturalisation rates of high-impact invasive species, as conclusions have important implications for how best to manage future biosecurity risks.

Historical demography of Lantana camara L. reveals clues about the influence of land use and weather in the management of this widespread invasive species

Weather is a general stochastic influence on the life history of weeds. In contrast, anthropogenic disturbance (e.g. land use) is an important deterministic influence on weed demography. Our aim with this study was to investigate the relative contributions of land use and weather on the demography of Lantana camara (lantana), a weed of agricultural and natural habitats, based on the intensive monitoring of lantana populations under three land uses (viz. farm[pasture], and burnt and grazed forests) in subtropical Australia. Lantana populations were growing vigorously across all land uses (asymptotic population growth rate, lambda > 3). Examination of historical demography using retrospective perturbation analyses showed that weather was a strong influence on lantana demography with the transition from an El Nino (2008-09) to a La Nina (2009-10) year having a strong positive effect on population growth rate. This effect was most marked at the grazed site, and to a lesser extent at the burnt site, with seedling-to-juvenile and juvenile-to-adult transitions contributing most to these effects. This is likely the result of burning and grazing having eliminated/reduced interspecific competition at these sites. Prospective perturbation analyses revealed that lambda was most sensitive to proportionate changes in growth transitions, followed by fecundity and survival transitions. Examination of context-specific patterns in elasticity revealed that growth and fecundity transitions are likely to be the more critical vital rates to reduce lambda in wet years at the burnt and grazed forest sites, compared to the farm/pasture site. Management of lantana may need to limit the transition of juveniles into the adult stages, especially in sites where lantana is free from competition (e.g. in the presence of fire or grazing), and this particularly needs to be achieved in wet years. Collectively, these results shed light on aspects of spatial and temporal variation in the demography of lantana, and offer insights on its context-specific management.

Effect of crop establishment methods and weed control treatments on weed management, and rice yield

Lower water availability coupled with labor shortage has resulted in the increasing inability of growers to cultivate puddled transplanted rice (PTR). A field study was conducted in the wet season of 2012 and dry season of 2013 to evaluate the performance of five rice establishment methods and four weed control treatments on weed management, and rice yield. Grass weeds were higher in dry-seeded rice (DSR) as compared to PTR and nonpuddled transplanted rice (NPTR). The highest total weed density (225-256plantsm-2) and total weed biomass (315-501gm-2) were recorded in DSR while the lowest (102-129plantsm-2 and 75-387gm-2) in PTR. Compared with the weedy plots, the treatment pretilachlor followed by fenoxaprop plus ethoxysulfuron plus 2,4-D provided excellent weed control. This treatment, however, had a poor performance in NPTR. In both seasons, herbicide efficacy was better in DSR and wet-seeded rice. PTR and DSR produced the maximum rice grain yields. The weed-free plots and herbicide treatments produced 84-614% and 58-504% higher rice grain yield, respectively, than the weedy plots in 2012, and a similar trend was observed in 2013.

Revolutionising Fish Ageing: Using Near Infrared Spectroscopy to Age Fish

The project aimed to evaluate the innovative application of NIRS as a reliable, repeatable, and cost-effective method of ageing fish, using otoliths of Barramundi and Snapper as study species. Specific research questions included assessing how geographic and seasonal variation in otoliths affects NIRS predictive models of fish age, as well as how the NIR spectra of otoliths change in the short-term (i.e., <12 months) and long-term (i.e., historical otolith collections) and what effect this has on the predictive ability of NIRS models. The cost-effectiveness of using NIRS to supplement standard fish ageing methods was also evaluated using a hypothetical case study of Barramundi.