A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Effective Use in Livestock Feeds of Mouldy and Weather-damaged Grain Containing Mycotoxins-Case Histories and Economic Assessments Pertaining to Pig and Poultry Industries of Queensland

Mould growth in field crops or stored grain reduces starch and lipid content, with consequent increases in fibre, and an overall reduction in digestible energy; palatability is often adversely affected. If these factors are allowed for, and mycotoxin concentrations are low, there are sound economic reasons for using this cheaper grain. Mycotoxins are common in stock feed but their effects on animal productivity are usually slight because either the concentration is too low or the animal is tolerant to the toxin. In Australia, aflatoxins occur in peanut by-products and in maize and sorghum if the grain is moist when stored. Zearalenone is found in maize and in sorghum and wheat in wetter regions. Nivalenol and deoxynivalenol are found in maize and wheat but at concentrations that rarely affect pigs, with chickens and cattle being even more tolerant. Other mycotoxins including cyclopiazonic acid, T-2 toxin, cytochalasins and tenuazonic acid are produced by Australian fungi in culture but are not found to be significant grain contaminants. Extremely mouldy sorghum containing Alternaria and Fusarium mycotoxins decreased feed conversion in pigs and chickens by up to 14%. However, E moniliforme- and Diplodia maydis-infected maize produced only slight reductions in feed intake by pigs and Ustilago- infected barley produced no ill effects. Use of these grains would substantially increase profits if the grain can be purchased cheaply.

Designing better on-farm research in Australia using a participatory workshop process

There are renewed calls for end-user participation and the integration of local knowledge in agricultural research. In Australia, the response has included an increased emphasis on participatory on-farm research with farmers and commercial agronomists that tests accepted principals to answer practical local farming questions. However, this pursuit of greater relevance has often led to compromises in research designs, unclear results and frustration amongst farmers, commercial agronomists and Research Development and Extension (RDE) agency researchers. This paper reports on a series of pre-season planning workshops from `Doing successful on-farm research', a workshop-based initiative that provides guidelines and a series of interactive activities to plan better participatory on-farm research. The workshop approach helps people design on-farm research that is appropriate to their own needs and local conditions. It assists them to clearly identify their issues, develop specific research questions and decide the best approach to answer those questions with the appropriate rigour for their own situations. These `Doing successful on-farm research' workshops address four potential deficiencies in on-farm research and farming systems RDE more generally in Australia: (1) variable participation of scientists and farmers in on-farm research; (2) the lack of clear guidelines for effective participatory practice and on-farm research; (3) limited support for on-farm research beyond the intensive investigations conducted by RDE agencies and (4) limited support for industry and farmers to contextualise information and research outcomes for specific individual circumstances and faster adaptation of technology. This may be a valuable contribution to balancing the demands for both relevance and rigour in on-farm research in Australia. In "Ground–breaking Stuff’- Proceedings of the 13th Australian Society of Agronomy Conference, 10-14 September 2006, Perth, Western Australia.

A review of Australian classical biological control of weeds programs and research activities over the past 12 years

Considerable progress has been made towards the successful classical biological control of many of Australia’s exotic weeds over the past decade. Some 43 new arthropod or pathogen agents were released in 19 projects. Effective biological control was achieved in several projects with the outstanding successes being the control of rubber vine, Cryptostegia grandiflora, and bridal creeper, Asparagus asparagoides. Significant developments also occurred in target prioritization, procedures for target and agent approval, funding, infrastructure and cooperation between agencies. Scientific developments included greater emphasis on climate matching, plant and agent phylogeny, molecular diagnostics, agent prioritization and agent evaluation.

Cost effective formulation of vegetable-protein based diets

The project will provide information on the use of phytase in sorghum based diets so that producers and nutrionists will have confidence in vegetable protein based diets.

Remote sensing to implement an effective pest management strategy for canegrubs

Develop a remote-sensing system that can identify canegrub infestations and provide early- warning to growers via the internet.

Sweetpotato consumer research: insights to increasing consumption

This report provides an evaluation of the behaviours and purchasing drivers of key sweetpotato consumers defined by Nielsen consumer research as Established Couples (two or more adults with no children 17 and under, and head of house 35-59), Senior Couples (two or more adults with no children 17 or under, and head of house 60 or over), and Independent Singles (one person household 35 or over, no children 17 or under). Research was qualitative in nature. Methods used included focus groups, depth interviews and shop-a-longs. The report found that preferences for sweetpotato amongst these groups were varied. In general a smaller torpedo shaped vegetable was valued for ease of preparation and the convenience of being of sufficient size for a meal for two. Satisfaction with sweetpotato was high with negative comments on quality exceedingly rare within discussions. However, shop-a-longs revealed that some quality issues were apparent at retail such as withered product, pitting and occasionally damage. A display with stock resting in any amount of water was a barrier to purchase for consumers and this was apparent on two out 15 occasions. A high quality sweetpotato was of a deep orange/red colour, had a smooth skin and was extremely dense and hard. An inferior sweetpotato was wrinkly, spongy, pitted and damaged. Awareness of sweetpotato was a relatively recent phenomenon amongst the respondents of this study with most recalling eating the vegetable in the last five to 10 years. Life-time eating patterns emerged as a consequence of childhood food experiences such as growing up with a ‘meat and three’ veg philosophy and traditional Australian meals. However, this was dependent on cultural background and those with ties to diverse cultures were more likely to have always known of the vegetable. Sweetpotato trial and consumption coincided with a breaking away from these traditional patterns, or was integrated into conventional meals such as a baked vegetable to accompany roasts. Increased health consciousness also led to awareness of the vegetable. A primary catalyst for consumption within the Established and Senior Couples groups was the health benefits associated with sweetpotato. Consumers had very little knowledge of the specific health properties of the vegetable and were surprised at the number of benefits consumption provided. Sweetpotato was important for diabetics for its low Glycemic Index status. Top-of-the-mind awareness of the vegetable resulted from the onset of the disease. Increasing fibre was a key motive for this demographic and this provided a significant link between consumption and preventing bowel cancer. For those on a weight loss regime, sweetpotato was perceived as a tasty, satisfying food that was low in carbohydrates. Swapping behaviours where white potato was replaced by sweetpotato was often a response to these health concerns. Other health properties mentioned by participants through the course of the research included the precursor β-carotene and Vitamins A & C. The sweetpotato was appreciated for its hedonic and timesaving qualities. For consumers with a high involvement in food, the vegetable was valued for its versatility in meals. These consumers took pride in cooking and the flavour and texture of sweetpotato lent itself to a variety of meals such as soups, salads, roasts, curries, tagines and so on. Participants who had little time or desire to prepare and cook meals valued sweetpotato because it was an easy way to add colour and variety to the plate and because including an orange vegetable to meals is a shortcut to ensuring vitamin intake. Several recommendations are made to the sweetpotato industry. • Vigorously promote the distinct nutritional and health properties of sweetpotatoes, particularly if they can be favourably compared to other vegetables or foods • Promote the salient properties to specific targets such as diabetics, those that are at risk to bowel cancer, and those embarking on a weight-loss regime. Utilise specialist channels of communication such as diabetic magazines and websites • Promote styles of cooking of sweetpotato that would appeal to traditionalists such as roasts and BBQs • Promote the vegetable as a low maintenance vegetable, easy to store, easy to cook and particularly focusing on it as a simple way to boost the appearance and nutritional value of meals. • Promote the vegetable to high food involvement consumers through exotic recipes and linking it to feelings of accomplishment with cooking • Promote the versatility of the vegetable • Devise promotions that link images and tone of communications with enjoying life to the fullest, having time to enjoy family and grandchildren, and of partaking in social activities • Educate retailers on consumer perceptions of quality and ensuring moisture and mould is not present at displays Qualitative information while providing a wealth of detail cannot be extrapolated to the overall target population and this may be considered a limitation to the research. However, within research theory, effective quantitative design is believed to stem from the insights developed from qualitative studies. • Develop and implement a quantitative study on sweetpotato attitudes and behaviours based on the results of this study.

Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes

Despite international protection of white sharks Carcharodon carcharias, important conservation parameters such as abundance, population structure and genetic diversity are largely unknown. The tissue of 97 predominately juvenile white sharks sampled from spatially distant eastern and southwestern Australian coastlines was sequenced for the mitochondrial DNA (mtDNA) control region and genotyped with 6 nuclear-encoded microsatellite loci. MtDNA population structure was found between the eastern and southwestern coasts (F-ST = 0.142, p < 0.0001), implying female reproductive philopatry. This concurs with recent satellite and acoustic tracking findings which suggest the sustained presence of discrete east coast nursery areas. Furthermore, population subdivision was found between the same regions with biparentally inherited micro satellite markers (F-ST = 0.009, p < 0.05), suggesting that males may also exhibit some degree of reproductive philopatry; 5 sharks captured along the east coast had mtDNA haplotypes that resembled western Indian Ocean sharks more closely than Australian/New Zealand sharks, suggesting that transoceanic dispersal, or migration resulting in breeding, may occur sporadically. Our most robust estimate of contemporary genetic effective population size was low and close to thresholds at which adaptive potential may be lost. For a variety of reasons, these contemporary estimates were at least 1, possibly 2, orders of magnitude below our historical effective size estimates. Population decline could expose these genetically isolated populations to detrimental genetic effects. Regional Australian white shark conservation management units should be implemented until genetic population structure, size and diversity can be investigated in more detail.