Harvest strategy evaluations and co-management for the Moreton Bay Trawl Fishery

Non-Technical Summary Seafood CRC Project 2009/774. Harvest strategy evaluations and co-management for the Moreton Bay Trawl Fishery Principal Investigator: Dr Tony Courtney, Principal Fisheries Biologist Fisheries and Aquaculture, Agri-Science Queensland Department of Agriculture, Fisheries and Forestry Level B1, Ecosciences Precinct, Joe Baker St, Dutton Park, Queensland 4102 Email: tony.courtney@daff.qld.gov.au Project objectives: 1. Review the literature and data (i.e., economic, biological and logbook) relevant to the Moreton Bay trawl fishery. 2. Identify and prioritise management objectives for the Moreton Bay trawl fishery, as identified by the trawl fishers. 3. Undertake an economic analysis of Moreton Bay trawl fishery. 4. Quantify long-term changes to fishing power for the Moreton Bay trawl fishery. 5. Assess priority harvest strategies identified in 2 (above). Present results to, and discuss results with, Moreton Bay Seafood Industry Association (MBSIA), fishers and Fisheries Queensland. Note: Additional, specific objectives for 2 (above) were developed by fishers and the MBSIA after commencement of the project. These are presented in detail in section 5 (below). The project was an initiative of the MBSIA, primarily in response to falling profitability in the Moreton Bay prawn trawl fishery. The analyses were undertaken by a consortium of DAFF, CSIRO and University of Queensland researchers. This report adopted the Australian Standard Fish Names (http://www.fishnames.com.au/). Trends in catch and effort The Moreton Bay otter trawl fishery is a multispecies fishery, with the majority of the catch composed of Greasyback Prawns (Metapenaeus bennettae), Brown Tiger Prawns (Penaeus esculentus), Eastern King Prawns (Melicertus plebejus), squid (Uroteuthis spp., Sepioteuthis spp.), Banana Prawns (Fenneropenaeus merguiensis), Endeavour Prawns (Metapenaeus ensis, Metapenaeus endeavouri) and Moreton Bay bugs (Thenus parindicus). Other commercially important byproduct includes blue swimmer crabs (Portunus armatus), three-spot crabs (Portunus sanguinolentus), cuttlefish (Sepia spp.) and mantis shrimp (Oratosquilla spp.). Logbook catch and effort data show that total annual reported catch of prawns from the Moreton Bay otter trawl fishery has declined to 315 t in 2008 from a maximum of 901 t in 1990. The number of active licensed vessels participating in the fishery has also declined from 207 in 1991 to 57 in 2010. Similarly, fishing effort has fallen from a peak of 13,312 boat-days in 1999 to 3817 boat-days in 2008 – a 71% reduction. The declines in catch and effort are largely attributed to reduced profitability in the fishery due to increased operational costs and depressed prawn prices. The low prawn prices appear to be attributed to Australian aquacultured prawns and imported aquacultured vannamei prawns, displacing the markets for trawl-caught prawns, especially small species such as Greasyback Prawns which traditionally dominated landings in Moreton Bay. In recent years, the relatively high Australian dollar has resulted in reduced exports of Australian wild-caught prawns. This has increased supply on the domestic market which has also suppressed price increases. Since 2002, Brown Tiger Prawns have dominated annual reported landings in the Moreton Bay fishery. While total catch and effort in the bay have declined to historically low levels, the annual catch and catch rates of Brown Tiger Prawns have been at record highs in recent years. This appears to be at least partially attributed to the tiger prawn stock having recovered from excessive effort in previous decades. The total annual value of the Moreton Bay trawl fishery catch, including byproduct, is about $5 million, of which Brown Tiger Prawns account for about $2 million. Eastern King Prawns make up about 10% of the catch and are mainly caught in the bay from October to December as they migrate to offshore waters outside the bay where they contribute to a large mono-specific trawl fishery. Some of the Eastern King Prawns harvested in Moreton Bay may be growth overfished (i.e., caught below the size required to maximise yield or value), although the optimum size-at-capture was not determined in this study. Banana Prawns typically make up about 5% of the catch, but can exceed 20%, particularly following heavy rainfall. Economic analysis of the fishery From the economic survey, cash profits were, on average, positive for both fleet segments in both years of the survey. However, after the opportunity cost of capital and depreciation were taken into account, the residual owner-operator income was relatively low, and substantially lower than the average share of revenue paid to employed skippers. Consequently, owner-operators were earning less than their opportunity cost of their labour, suggesting that the fleets were economically unviable in the longer term. The M2 licensed fleet were, on average, earning similar boat cash profits as the T1/M1 fleet, although after the higher capital costs were accounted for the T1/M1 boats were earning substantially lower returns to owner-operator labour. The mean technical efficiency for the fleet as a whole was estimated to be 0.67. That is, on average, the boats were only catching 67 per cent of what was possible given their level of inputs (hours fished and hull units). Almost one-quarter of observations had efficiency scores above 0.8, suggesting a substantial proportion of the fleet are relatively efficient, but some are also relatively inefficient. Both fleets had similar efficiency distributions, with median technical efficiency score of 0.71 and 0.67 for the M2 and T1/M1 boats respectively. These scores are reasonably consistent with other studies of prawn trawl fleets in Australia, although higher average efficiency scores were found in the NSW prawn trawl fleet. From the inefficiency model, several factors were found to significantly influence vessel efficiency. These included the number of years of experience as skipper, the number of generations that the skipper’s family had been fishing and the number of years schooling. Skippers with more schooling were significantly more efficient than skippers with lower levels of schooling, consistent with other studies. Skippers who had been fishing longer were, in fact, less efficient than newer skippers. However, this was mitigated in the case of skippers whose family had been involved in fishing for several generations, consistent with other studies and suggesting that skill was passed through by families over successive generations. Both the linear and log-linear regression models of total fishing effort against the marginal profit per hour performed reasonably well, explaining between 70 and 84 per cent of the variation in fishing effort. As the models had different dependent variables (one logged and the other not logged) this is not a good basis for model choice. A better comparator is the square root of the mean square error (SMSE) expressed as a percentage of the mean total effort. On this criterion, both models performed very similarly. The linear model suggests that each additional dollar of average profits per hour in the fishery increases total effort by around 26 hours each month. From the log linear model, each percentage increase in profits per hour increases total fishing effort by 0.13 per cent. Both models indicate that economic performance is a key driver of fishing effort in the fishery. The effect of removing the boat-replacement policy is to increase individual vessel profitability, catch and effort, but the overall increase in catch is less than that removed by the boats that must exit the fishery. That is, the smaller fleet (in terms of boat numbers) is more profitable but the overall catch is not expected to be greater than before. This assumes, however, that active boats are removed, and that these were also taking an average level of catch. If inactive boats are removed, then catch of the remaining group as a whole could increase by between 14 and 17 per cent depending on the degree to which costs are reduced with the new boats. This is still substantially lower than historical levels of catch by the fleet. Fishing power analyses An analysis of logbook data from 1988 to 2010, and survey information on fishing gear, was performed to estimate the long-term variation in the fleet’s ability to catch prawns (known as fishing power) and to derive abundance estimates of the three most commercially important prawn species (i.e., Brown Tiger, Eastern King and Greasyback Prawns). Generalised linear models were used to explain the variation in catch as a function of effort (i.e., hours fished per day), vessel and gear characteristics, onboard technologies, population abundance and environmental factors. This analysis estimated that fishing power associated with Brown Tiger and Eastern King Prawns increased over the past 20 years by 10–30% and declined by approximately 10% for greasybacks. The density of tiger prawns was estimated to have almost tripled from around 0.5 kg per hectare in 1988 to 1.5 kg/ha in 2010. The density of Eastern King Prawns was estimated to have fluctuated between 1 and 2 kg per hectare over this time period, without any noticeable overall trend, while Greasyback Prawn densities were estimated to have fluctuated between 2 and 6 kg per hectare, also without any distinctive trend. A model of tiger prawn catches was developed to evaluate the impact of fishing on prawn survival rates in Moreton Bay. The model was fitted to logbook data using the maximum-likelihood method to provide estimates of the natural mortality rate (0.038 and 0.062 per week) and catchability (which can be defined as the proportion of the fished population that is removed by one unit of effort, in this case, estimated to be 2.5 ± 0.4 E-04 per boat-day). This approach provided a method for industry and scientists to develop together a realistic model of the dynamics of the fishery. Several aspects need to be developed further to make this model acceptable to industry. Firstly, there is considerable evidence to suggest that temperature influences prawn catchability. This ecological effect should be incorporated before developing meaningful harvest strategies. Secondly, total effort has to be allocated between each species. Such allocation of effort could be included in the model by estimating several catchability coefficients. Nevertheless, the work presented in this report is a stepping stone towards estimating essential fishery parameters and developing representative mathematical models required to evaluate harvest strategies. Developing a method that allowed an effective discussion between industry, management and scientists took longer than anticipated. As a result, harvest strategy evaluations were preliminary and only included the most valuable species in the fishery, Brown Tiger Prawns. Additional analyses and data collection, including information on catch composition from field sampling, migration rates and recruitment, would improve the modelling. Harvest strategy evaluations As the harvest strategy evaluations are preliminary, the following results should not be adopted for management purposes until more thorough evaluations are performed. The effects, of closing the fishery for one calendar month, on the annual catch and value of Brown Tiger Prawns were investigated. Each of the 12 months (i.e., January to December) was evaluated. The results were compared against historical records to determine the magnitude of gain or loss associated with the closure. Uncertainty regarding the trawl selectivity was addressed using two selectivity curves, one with a weight at 50% selection (S50%) of 7 g, based on research data, and a second with S50% of 14 g, put forward by industry. In both cases, it was concluded that any monthly closure after February would not be beneficial to the industry. The magnitude of the benefit of closing the fishery in either January or February was sensitive to which mesh selectivity curve that was assumed, with greater benefit achieved when the smaller selectivity curve (i.e., S50% = 7 g) was assumed. Using the smaller selectivity (S50% = 7 g), the expected increase in catch value was 10–20% which equates to $200,000 to $400,000 annually, while the larger selectivity curve (S50% = 14 g) suggested catch value would be improved by 5–10%, or $100,000 to $200,000. The harvest strategy evaluations showed that greater benefits, in the order of 30–60% increases in the tiger annual catch value, could have been obtained by closing the fishery early in the year when annual effort levels were high (i.e., > 10,000 boat-days). In recent years, as effort levels have declined (i.e., ~4000 boat-days annually), expected benefits from such closures are more modest. In essence, temporal closures offer greater benefit when fishing mortality rates are high. A spatial analysis of Brown Tiger Prawn catch and effort was also undertaken to obtain a better understanding of the prawn population dynamics. This indicated that, to improve profitability of the fishery, fishers could consider closing the fishery in the period from June to October, which is already a period of low profitability. This would protect the Brown Tiger Prawn spawning stock, increase catch rates of all species in the lucrative pre-Christmas period (November–December), and provide fishers with time to do vessel maintenance, arrange markets for the next season’s harvest, and, if they wish, work at other jobs. The analysis found that the instantaneous rate of total mortality (Z) for the March–June period did not vary significantly over the last two decades. As the Brown Tiger Prawn population in Moreton Bay has clearly increased over this time period, an interesting conclusion is that the instantaneous rate of natural mortality (M) must have increased, suggesting that tiger prawn natural mortality may be density-dependent at this time of year. Mortality rates of tiger prawns for June–October were found to have decreased over the last two decades, which has probably had a positive effect on spawning stocks in the October–November spawning period. Abiotic effects on the prawns The influence of air temperature, rainfall, freshwater flow, the southern oscillation index (SOI) and lunar phase on the catch rates of the four main prawn species were investigated. The analyses were based on over 200,000 daily logbook catch records over 23 years (i.e., 1988–2010). Freshwater flow was more influential than rainfall and SOI, and of the various sources of flow, the Brisbane River has the greatest volume and influence on Moreton Bay prawn catches. A number of time-lags were also considered. Flow in the preceding month prior to catch (i.e., 30 days prior, Logflow1_30) and two months prior (31–60 days prior, Logflow31_60) had strong positive effects on Banana Prawn catch rates. Average air temperature in the preceding 4-6 months (Temp121_180) also had a large positive effect on Banana Prawn catch rates. Flow in the month immediately preceding catch (Logflow1_30) had a strong positive influence on Greasyback Prawn catch rates. Air temperature in the preceding two months prior to catch (Temp1_60) had a large positive effect on Brown Tiger Prawn catch rates. No obvious or marked effects were detected for Eastern King Prawns, although interestingly, catch rates declined with increasing air temperature 4–6 months prior to catch. As most Eastern King Prawn catches in Moreton Bay occur in October to December, the results suggest catch rates decline with increasing winter temperatures. In most cases, the prawn catch rates declined with the waxing lunar phase (high luminance/full moon), and increased with the waning moon (low luminance/new moon). The SOI explains little additional variation in prawn catch rates (~ <2%), although its influence was higher for Banana Prawns. Extrapolating findings of the analyses to long-term climate change effects should be interpreted with caution. That said, the results are consistent with likely increases in abundance in the region for the two tropical species, Banana Prawns and Brown Tiger Prawns, as coastal temperatures rise. Conversely, declines in abundance could be expected for the two temperate species, Greasyback and Eastern King Prawns. Corporate management structures An examination of alternative governance systems was requested by the industry at one of the early meetings, particularly systems that may give them greater autonomy in decision making as well as help improve the marketing of their product. Consequently, a review of alternative management systems was undertaken, with a particular focus on the potential for self-management of small fisheries (small in terms of number of participants) and corporate management. The review looks at systems that have been implemented or proposed for other small fisheries internationally, with a particular focus on self-management as well as the potential benefits and challenges for corporate management. This review also highlighted particular opportunities for the Moreton Bay prawn fishery. Corporate management differs from other co-management and even self-management arrangements in that ‘ownership’ of the fishery is devolved to a company in which fishers and government are shareholders. The company manages the fishery as well as coordinates marketing to ensure that the best prices are received and that the catch taken meets the demands of the market. Coordinated harvesting will also result in increased profits, which are returned to fishers in the form of dividends. Corporate management offers many of the potential benefits of an individual quota system without formally implementing such a system. A corporate management model offers an advantage over a self-management model in that it can coordinate both marketing and management to take advantage of this unique geographical advantage. For such a system to be successful, the fishery needs to be relatively small and self- contained. Small in this sense is in terms of number of operators. The Moreton Bay prawn fishery satisfies these key conditions for a successful self-management and potentially corporate management system. The fishery is small both in terms of number of participants and geography. Unlike other fisheries that have progressed down the self-management route, the key market for the product from the Moreton Bay fishery is right at its doorstep. Corporate management also presents a number of challenges. First, it will require changes in the way fishers operate. In particular, the decision on when to fish and what to catch will be taken away from the individual and decided by the collective. Problems will develop if individuals do not join the corporation but continue to fish and market their own product separately. While this may seem an attractive option to fishers who believe they can do better independently, this is likely to be just a short- term advantage with an overall long-run cost to themselves as well as the rest of the industry. There are also a number of other areas that need further consideration, particularly in relation to the allocation of shares, including who should be allocated shares (e.g. just boat owners or also some employed skippers). Similarly, how harvesting activity is to be allocated by the corporation to the fishers. These are largely issues that cannot be answered without substantial consultation with those likely to be affected, and these groups cannot give these issues serious consideration until the point at which they are likely to become a reality. Given the current structure and complexity of the fishery, it is unlikely that such a management structure will be feasible in the short term. However, the fishery is a prime candidate for such a model, and development of such a management structure in the future should be considered as an option for the longer term.

Raw data for "Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson)."

Abstract of Macbeth, G. M., Broderick, D., Buckworth, R. & Ovenden, J. R. (In press, Feb 2013). Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson). G3: Genes, Genomes and Genetics. Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. But, pitfalls are predicted when the effective size is large, as estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes around 5000. This was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest standard deviation of Ne estimates occurred when low frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or non-breeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were above 24,000.

Bacterial Community Structure in the Hindgut of Wild and Captive Dugongs (Dugong dugon)

Dugongs (Dugong dugon) are marine mammals that obtain nutrients through hindgut fermentation of seagrass, however, the microbes responsible have not been identified. This study used denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing to profile hindgut bacterial communities in wild dugongs. Faecal samples obtained from 32 wild dugongs representing four size/maturity classes, and two captive dugongs fed on cos lettuce were screened using DGGE. Partial 16S rRNA gene profiles of hindgut bacteria from wild dugong calves and juveniles were grouped together and were different to those in subadults and adults. Marked differences between hindgut bacterial communities of wild and captive dugongs were also observed, except for a single captive whose profile resembled wild adults following an unsuccessful reintroduction to the wild. Pyrosequencing of hindgut communities in two wild dugongs confirmed the stability of bacterial populations, and Firmicutes (average 75.6% of Operational Taxonomic Units [OTUs]) and Bacteroidetes (19.9% of OTUs) dominated. Dominant genera were Roseburia, Clostridium, and Bacteroides. Hindgut microbial composition and diversity in wild dugongs is affected by ontogeny and probably diet. In captive dugongs, the absence of the dominant bacterial DNA bands identified in wild dugongs is probably dependent upon prevailing diet and other captive conditions such as the use of antibiotics. This study represents a first step in the characterisation of a novel microbial ecosystem-the marine hindgut of Sirenia.

Quantifying the effects of climate change and water abstraction on a population of barramundi (Lates calcarifer), a diadromous estuarine finfish

Many aquatic species are linked to environmental drivers such as temperature and salinity through processes such as spawning, recruitment and growth. Information is needed on how fished species may respond to altered environmental drivers under climate change so that adaptive management strategies can be developed. Barramundi (Lates calcarifer) is a highly prized species of the Indo-West Pacific, whose recruitment and growth is driven by river discharge. We developed a monthly age- and length-structured population model for barramundi. Monte Carlo Markov Chain simulations were used to explore the population's response to altered river discharges under modelled total licenced water abstraction and projected climate change, derived and downscaled from Global Climate Model A1FI. Mean values of exploitable biomass, annual catch, maximum sustainable yield and spawning stock size were significantly reduced under scenarios where river discharge was reduced; despite including uncertainty. These results suggest that the upstream use of water resources and climate change have potential to significantly reduce downstream barramundi stock sizes and harvests and may undermine the inherent resilience of estuarine-dependent fisheries. © 2012 CSIRO.

Patterns of seed bank and size asymmetry of plant growth across varying sites in the invasive Lantana camara L. (Verbenaceae)

Lantana camara L. (Verbenaceae) is a weed of great significance in Australia and worldwide, but little is known about connections among components of its life history. We document over a 3-year period, the links between L. camara seed-bank dynamics and its above-ground growth, including size asymmetry in four land-use types (a farm, a hoop pine plantation and two open eucalypt forests) invaded by the weed near Brisbane, Queensland Australia. Seed-bank populations varied appreciably across sites and in response to rainfall and control measures, and they were higher (~1,000 seeds/m2) when annual rainfall was 15-30 % below the long-term yearly average. Fire reduced seed-bank populations but not the proportion germinating (6-8 %). Nearly a quarter of fresh seeds remain germinable after 3 years of soil burial. For small seedlings (<10 cm high), the expected trade-offs in two life-history traits-survival and growth-did not apply; rather the observed positive association between these two traits, coupled with a persistent seed-bank population could contribute to the invasiveness of the plant. Relationships between absolute growth rate and initial plant size (crown volume) were positively linear, suggesting that most populations are still at varying stages of the exponential phase of the sigmoid growth; this trend also suggests that at most sites and despite increasing stand density and limiting environmental resources of light and soil moisture, lantana growth is inversely size asymmetric. From the observed changes in measures of plant size inequality, asymmetric competition appeared limited in all the infestations surveyed. © 2013 Crown Copyright as represented by: Department of Agriculture, Fisheries and Forestry, Australia.

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.

Effect of Time of Planting and Plant Size on the Productivity of ‘Festival’ and ‘Florida Fortuna’ Strawberry Plants in a Subtropical Environment

The effect of time of planting and plant size on the performance of ‘Festival’ and ‘Florida Fortuna’ strawberry (Fragaria ×ananassa) plants was studied at Nambour in southeastern Queensland, Australia, over 2 years. The main objective of the work was to determine whether small plants yielded proportionally less than large plants as planting was delayed. First, bare-rooted transplants of ‘Festival’ were divided into small (crown diameters ranging from 6 to 10 mm) or large plants (10 to 17 mm) and planted in late March, mid-April, or late April. Second, transplants of ‘Florida Fortuna’ were divided into small (5 to 8 mm) or large plants (8 to 17 mm) and planted in early April, mid-April, or early May. The early planting for each cultivar corresponded with the time that the transplants are first available from commercial strawberry nurseries. Yields were generally greater in plants planted in late March/early April compared with plants planted later. Differences in yield between the small and large plants were consistent across the different times of planting, with the small plants always having lower yields. Small transplants are an issue for the productivity of strawberry fields in this environment whether they are planted early or late. Producers should consider paying a premium for large transplants delivered early in the season.

Adsorption and release of biocides with mesoporous silica nanoparticles

In this proof-of-concept study, an agricultural biocide (imidacloprid) was effectively loaded into the mesoporous silica nanoparticles (MSNs) with different pore sizes, morphologies and mesoporous structures for termite control. This resulted in nanoparticles with a large surface area, tunable pore diameter and small particle size, which are ideal carriers for adsorption and controlled release of imidacloprid. The effect of pore size, surface area and mesoporous structure on uptake and release of imidacloprid was systematically studied. It was found that the adsorption amount and release profile of imidacloprid were dependent on the type of mesoporous structure and surface area of particles. Specifically, MCM-48 type mesoporous silica nanoparticles with a three dimensional (3D) open network structure and high surface area displayed the highest adsorption capacity compared to other types of silica nanoparticles. Release of imidacloprid from these nanoparticles was found to be controlled over 48 hours. Finally, in vivo laboratory testing on termite control proved the efficacy of these nanoparticles as delivery carriers for biopesticides. We believe that the present study will contribute to the design of more effective controlled and targeted delivery for other biomolecules.

NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

Principles and guidelines for managing cattle grazing in the grazing lands of northern Australia: stocking rates, pasture resting, prescribed fire, paddock size and water points - a review

Beef cattle grazing is the dominant land use in the extensive tropical and sub-tropical rangelands of northern Australia. Despite the considerable knowledge on land and herd management gained from both research and practical experience, the adoption of improved management is limited by an inability to predict how changes in practices and combinations of practices will affect cattle production, economic returns and resource condition. To address these issues, past Australian and international research relating to four management factors that affect productivity and resource condition was reviewed in order to identify key management principles. The four management factors considered were stocking rates, pasture resting, prescribed fire, and fencing and water point development for managing grazing distribution. Four management principles for sound grazing management in northern Australia were formulated as follows: (1) manage stocking rates to meet goals for livestock production and land condition; (2) rest pastures to maintain them in good condition or to restore them from poor condition to increase pasture productivity; (3) devise and apply fire regimes that enhance the condition of grazing land and livestock productivity while minimising undesirable impacts; and (4) use fencing and water points to manipulate grazing distribution. Each principle is supported by several more specific guidelines. These principles and guidelines, and the supporting research on which they are based, are presented.

The non-pathogenic Australian rabbit calicivirus RCV-A1 provides temporal and partial cross protection to lethal Rabbit Haemorrhagic Disease Virus infection which is not dependent on antibody titres

The endemic non-pathogenic Australian rabbit calicivirus RCV-A1 is known to provide some cross protection to lethal infection with the closely related Rabbit Haemorrhagic Disease Virus (RHDV). Despite its obvious negative impacts on viral biocontrol of introduced European rabbits in Australia, little is known about the extent and mechanisms of this cross protection. In this study 46 rabbits from a colony naturally infected with RCV-A1 were exposed to RHDV. Survival rates and survival times did not correlate with titres of serum antibodies specific to RCV-A1 or cross reacting to RHDV, but were instead influenced by the time between infection with the two viruses, demonstrating for the first time that the cross protection to lethal RHDV infection is transient. These findings are an important step towards a better understanding of the complex interactions of co-occurring pathogenic and non-pathogenic lagoviruses.

Improved estimation of size-transition matrices using tag-recapture data

We derive a new method for determining size-transition matrices (STMs) that eliminates probabilities of negative growth and accounts for individual variability. STMs are an important part of size-structured models, which are used in the stock assessment of aquatic species. The elements of STMs represent the probability of growth from one size class to another, given a time step. The growth increment over this time step can be modelled with a variety of methods, but when a population construct is assumed for the underlying growth model, the resulting STM may contain entries that predict negative growth. To solve this problem, we use a maximum likelihood method that incorporates individual variability in the asymptotic length, relative age at tagging, and measurement error to obtain von Bertalanffy growth model parameter estimates. The statistical moments for the future length given an individual’s previous length measurement and time at liberty are then derived. We moment match the true conditional distributions with skewed-normal distributions and use these to accurately estimate the elements of the STMs. The method is investigated with simulated tag–recapture data and tag–recapture data gathered from the Australian eastern king prawn (Melicertus plebejus).

Plot size matters: interference from intergenotypic competition in plant phenotyping studies

Genetic and physiological studies often comprise genotypes diverse in vigour, size and flowering time. This can make the phenotyping of complex traits challenging, particularly those associated with canopy development, biomass and yield, as the environment of one genotype can be influenced by a neighbouring genotype. Limited seed and space may encourage field assessment in single, spaced rows or in small, unbordered plots, whereas the convenience of a controlled environment or greenhouse makes pot studies tempting. However, the relevance of such growing conditions to commercial field-grown crops is unclear and often doubtful. Competition for water, light and nutrients necessary for canopy growth will be variable where immediate neighbours are genetically different, particularly under stress conditions, where competition for resources and influence on productivity is greatest. Small hills and rod-rows maximise the potential for intergenotypic competition that is not relevant to a crop’s performance in monocultures. Response to resource availability will typically vary among diverse genotypes to alter genotype ranking and reduce heritability for all growth-related traits, with the possible exception of harvest index. Validation of pot experiments to performance in canopies in the field is essential, whereas the planting of multirow plots and the simple exclusion of plot borders at harvest will increase experimental precision and confidence in genotype performance in target environments.

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.