Milkshark (Rhizoprionodon acutus) microsatellite genotype data (six loci) from samples collected from five locations in eastern Australia and central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Raw data for project "Development of a DNA based aging technique for use in fisheries assessments" Fisheries and Development Corporation project 2007/033

The primary aim of this study was to determine the relationship between telomere length and age in a range of marine invertebrates including abalone (Haliotis spp) oysters (Saccostrea glomerata), spiny lobsters (Sagmariasus verreauxi formerly Jasus verreauxi and Jasus edwardsii) and school prawns (Metapenaeus macleayi). Additionally, this relationship was studied in a vertebrate organism using the freshwater fish Silver perch (Bidyanus bidyanus). Telomere length differences between tissues were also examined in some species such as Saccostrea glomerata, Sagmariasus verreauxi and Bidyanus bidyanus. In some cases cultured specimens of known age were used and this is quoted in the spreadsheets. For other wild-caught specimens where age was not known, size was used as a proxy for age. This may be a broad size class, or be determined by shell size or carapace length depending on the organism. Each spreadsheet contains raw data of telomere length estimates from Terminal Restriction Fragment Assays (TRF) for various individuals of each species including appropriate details such as age or size and tissue. Telomere length estimates are given in base pairs (bp). In most cases replicate experiments were conducted on groups of samples three times but on a small number of occasions only two replicate experiments were conducted. Further description of the samples can be found in final report of FRDC 2007/033. The arithmetic average for each individual (sample ID) across the two or three replicate experiments is also given. Bidyanus bidyanus (SilverPerch) Two sheets are contained within. a) Comparison of telomere length between different tissues (heart, liver and muscle) within the three year old age class - two replicate experiments were conducted. b) Comparison of telomere length between fish of different but known ages (0.25, 1, 2, and 3 years old) in each of three tissues, heart, liver and muscle – three replicate experiments were conducted per tissue. Haliotis spp (Abalone species) Three species were tested. H. asinina Telomere length was compared in two age classes-11 month and 18 month old abalone using muscle tissue from the foot. Within gel-variation was also estimated using a single sample run three times on one gel (replicate experiment). H. laevigata x H. rubra hybrids Telomere length was compared in three known age classes – two, three and four years old using muscle tissue from the foot. H. rubra Telomere length was compared in a range of different sized abalone using muscle tissue from the foot. Shell size is also given for each abalone Saccostrea glomerata Three sheets are contained within the file. a) Samples came from Moreton Bay Queensland in 2007. Telomere length was compared in two tissues (gill and mantle) of oysters in three age groups (1, 3 and 4 years) b) Samples came from Moreton Bay Queensland in 2009. Telomere length was compared in three age classes using DNA from gill tissue only c) Samples came from Wallis Lake, New South Wales. Telomere length was estimated from whole body minus the shell from 1 year old oysters, gill tissue of 3 age classes (1.5 years, 3 and 4 years), mantle tissue of two age classes (3 and 4 years). Sagmariasus verreauxi (formerly Jasus verreauxi) Telomere length was estimated from abdomen tissue of puerulus, gill and muscle tissue of 3 year old, large and very large size classes of lobsters. Jasus edwardsii Telomere length was measured in two size classes of lobsters- adults of varying sizes using muscle tissue and puerulus using tissues from the abdomen minus the exoskeleton. Metapenaeus macleayi Telomere length was measured in three size classes of school prawns adults. Muscle tissue was used, minus the exoskeleton.

Using catch rate data for simple cost-effective quota setting in the Australian spanner crab (Ranina ranina) fishery.

For many fisheries, there is a need to develop appropriate indicators, methodologies, and rules for sustainably harvesting marine resources. Complexities of scientific and financial factors often prevent addressing these, but new methodologies offer significant improvements on current and historical approaches. The Australian spanner crab fishery is used to demonstrate this. Between 1999 and 2006, an empirical management procedure using linear regression of fishery catch rates was used to set the annual total allowable catch (quota). A 6-year increasing trend in catch rates revealed shortcomings in the methodology, with a 68% increase in quota calculated for the 2007 fishing year. This large quota increase was prevented by management decision rules. A revised empirical management procedure was developed subsequently, and it achieved a better balance between responsiveness and stability. Simulations identified precautionary harvest and catch rate baselines to set quotas that ensured sustainable crab biomass and favourable performance for management and industry. The management procedure was simple to follow, cost-effective, robust to strong trends and changes in catch rates, and adaptable for use in many fisheries. Application of such “tried-and-tested” empirical systems will allow improved management of both data-limited and data-rich fisheries.

Spatially based data delivery and recording sys-Aust Sugar Cane industry

Establish an internet platform where spatially referenced data can be viewed, entered and stored.

Internet based spatial data delivery and reporting system for cotton industry

Development of an internet based spatial data delivery and reporting system for the Australian Cotton Industry.

A hidden Markov model approach for determining vessel activity from vessel monitoring system data.

Many fisheries worldwide have adopted vessel monitoring systems (VMS) for compliance purposes. An added benefit of these systems is that they collect a large amount of data on vessel locations at very fine spatial and temporal scales. This data can provide a wealth of information for stock assessment, research, and management. However, since most VMS implementations record vessel location at set time intervals with no regard to vessel activity, some methodology is required to determine which data records correspond to fishing activity. This paper describes a probabilistic approach, based on hidden Markov models (HMMs), to determine vessel activity. A HMM provides a natural framework for the problem and, by definition, models the intrinsic temporal correlation of the data. The paper describes the general approach that was developed and presents an example of this approach applied to the Queensland trawl fishery off the coast of eastern Australia. Finally, a simulation experiment is presented that compares the misallocation rates of the HMM approach with other approaches.

Fishing power and standardised catch rates: Implications of missing vessel-characteristic data from the Australian eastern king prawn fishery

Standardised time series of fishery catch rates require collations of fishing power data on vessel characteristics. Linear mixed models were used to quantify fishing power trends and study the effect of missing data encountered when relying on commercial logbooks. For this, Australian eastern king prawn (Melicertus plebejus) harvests were analysed with historical (from vessel surveys) and current (from commercial logbooks) vessel data. Between 1989 and 2010, fishing power increased up to 76%. To date, both forward-filling and, alternatively, omitting records with missing vessel information from commercial logbooks produce broadly similar fishing power increases and standardised catch rates, due to the strong influence of years with complete vessel data (16 out of 23 years of data). However, if gaps in vessel information had not originated randomly and skippers from the most efficient vessels were the most diligent at filling in logbooks, considerable errors would be introduced. Also, the buffering effect of complete years would be short lived as years with missing data accumulate. Given ongoing changes in fleet profile with high-catching vessels fishing proportionately more of the fleet’s effort, compliance with logbook completion, or alternatively ongoing vessel gear surveys, is required for generating accurate estimates of fishing power and standardised catch rates.

Short- and long-term movement patterns in the freshwater whipray (Himantura dalyensis) determined by the signal processing of passive acoustic telemetry data.

Patterns of movement in aquatic animals reflect ecologically important behaviours. Cyclical changes in the abiotic environment influence these movements, but when multiple processes occur simultaneously, identifying which is responsible for the observed movement can be complex. Here we used acoustic telemetry and signal processing to define the abiotic processes responsible for movement patterns in freshwater whiprays (Himantura dalyensis). Acoustic transmitters were implanted into the whiprays and their movements detected over 12 months by an array of passive acoustic receivers, deployed throughout 64 km of the Wenlock River, Qld, Australia. The time of an individual's arrival and departure from each receiver detection field was used to estimate whipray location continuously throughout the study. This created a linear-movement-waveform for each whipray and signal processing revealed periodic components within the waveform. Correlation of movement periodograms with those from abiotic processes categorically illustrated that the diel cycle dominated the pattern of whipray movement during the wet season, whereas tidal and lunar cycles dominated during the dry season. The study methodology represents a valuable tool for objectively defining the relationship between abiotic processes and the movement patterns of free-ranging aquatic animals and is particularly expedient when periods of no detection exist within the animal location data.

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.

Ecological risk assessment of the East Coast Otter Trawl Fishery in the Great Barrier Reef Marine Park: Data report

An ecological risk assessment of the East Coast Otter Trawl Fishery in the Great Barrier Reef Region was undertaken in 2010 and 2011. It assessed the risks posed by this fishery to achieving fishery-related and broader ecological objectives of both the Queensland and Australian governments, including risks to the values and integrity of the Great Barrier Reef World Heritage Area. The risks assessed included direct and indirect effects on the species caught in the fishery as well as on the structure and functioning of the ecosystem. This ecosystem-based approach included an assessment of the impacts on harvested species, by-catch, species of conservation concern, marine habitats, species assemblages and ecosystem processes. The assessment took into account current management arrangements and fishing practices at the time of the assessment. The main findings of the assessment were: Current risk levels from trawling activities are generally low. Some risks from trawling remain. Risks from trawling have reduced in the Great Barrier Reef Region. Trawl fishing effort is a key driver of ecological risk. Zoning has been important in reducing risks. Reducing identified unacceptable risks requires a range of management responses. The commercial fishing industry is supportive and being proactive. Further reductions in trawl by-catch, high compliance with rules and accurate information from ongoing risk monitoring are important. Trawl fishing is just one of the sources of risk to the Great Barrier Reef.

Correlation between NIRS generated and chemically measured feed quality data in barley (Hordeum vulgare), and potential use in QTL analysis identification

A study was performed to investigate the value of near infrared reflectance spectroscopy (NIRS) as an alternate method to analytical techniques for identifying QTL associated with feed quality traits. Milled samples from an F6-derived recombinant inbred Tallon/Scarlett population were incubated in the rumen of fistulated cattle, recovered, washed and dried to determine the in-situ dry matter digestibility (DMD). Both pre- and post-digestion samples were analysed using NIRS to quantify key quality components relating to acid detergent fibre, starch and protein. This phenotypic data was used to identify trait associated QTL and compare them to previously identified QTL. Though a number of genetic correlations were identified between the phenotypic data sets, the only correlation of most interest was between DMD and starch digested (r = -0.382). The significance of this genetic correlation was that the NIRS data set identified a putative QTL on chromosomes 7H (LOD = 3.3) associated with starch digested. A QTL for DMD occurred in the same region of chromosome 7H, with flanking markers fAG/CAT63 and bPb-0758. The significant correlation and identification of this putative QTL, highlights the potential of technologies like NIRS in QTL analysis.

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.

Dingoes at the doorstep: Preliminary data on the ecology of dingoes in urban areas

Wild carnivores are becoming increasing common in urban areas. In Australia, dingoes exist, in most large cities and towns within their extended range. However, little empirical data is available to inform dingo management or address potential dingo–human conflicts during urban planning. From GPS tracking data, the nine dingoes, predominately juvenile and female, we tracked lived within 700 m of residential homes at all times and frequently crossed roads, visited backyards and traversed built-up areas. Home range sizes ranged between 0.37 km2 and 100.32 km2. Dingoes were mostly nocturnal, averaging 591 m/h between dusk and dawn. Juvenile and adult dingoes spent up to 19% and 72% of their time in urban habitats. Fresh scats from most areas surveyed tested positive to a variety of common zoonoses. These data suggest dingoes are capable of exploiting peri-urban areas and might contribute to human health and safety risks, the significance of which remains unknown.

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.

Improving the prediction of odour impacts from meat chicken farms with detailed ventilation and odour data

Odour from meat chicken (broiler) farms is an environmental issue affecting the sustainable development of the chicken meat industry but is a normal part of broiler production. Odour plumes exhausted from broiler sheds interact with the environment, where dispersion and dilution of the odours varies constantly, especially diurnally. The potential for odour impacts is greatest when odour emission rates are high and/or when atmospheric dispersion and dilution of odour plumes is limited (i.e. during stable conditions). We continuously monitored ventilation rate, on-site weather conditions, atmospheric stability, and estimated odour concentration with an artificial olfaction system. Detailed inspection of odour emission rates at critical times, i.e. dawn, dusk and night time, revealed that maximum daily and batch odour emission rates are not necessarily the cause of odour impacts. Periods of lower odour emission rates on each day are more likely to correspond with odour impacts. Odour emission rates need to be measured at the times when odour impacts are most likely to occur, which is likely to be at night. Additionally, high resolution ventilation rate data should be sought after to improve odour emission models, especially at critical times of the day. Consultants, regulators and researchers need to give more thought to odour emission rates from meat chicken farms to improved prediction and management of odour impacts.