Dissertations / Theses on the topic 'Southern rock lobster'

The southern and western rock lobsters (Jasus edwardsii and Panulirus cygnus, respectively) form the basis of two of the major seafood export industries in Australia; between them earning over $500 M export dollars yearly. Although a major portion of the catch is exported as 'whole-cooked' or 'tailed' products, an increasing share of the catch is exported live. The majority of lobsters arrive at the processing sheds as live lobsters. However, a lack of basic physiological information has impeded advances in the design and management of transport and holding systems, often resulting in a deterioration of the physiological condition of some lobsters. Such physiological deterioration may result in the final product choice for the processors being limited, leading to a reduced value of the catch. The aim of this study was to develop an understanding of the physiology of lobsters, especially in relation to factors the lobsters may be subjected to during post-capture handling practices. This information could be used to redefine postcapture handling practices and holding system design and management. Standard oxygen consumption of both species increased in response to increases in temperature and body weight. Activity had the greatest effect on oxygen consumption rates, causing an approximate 3-fold increase above standard rates. The increase in oxygen consumption due to activity decreased at temperatures approaching the upper and lower extremes of each species. After a period of activity and emersion oxygen consumption remained elevated for up to 8 hours. A marked diurnal rhythm was evident, with a 48% and 87% (J. edwardsii and P. cygnus, respectively) increase in oxygen consumption at night. This was largely related to increased activity at night. Feeding resulted in a substantial (greater than 2-fold in P. cygnus) and sustained (up to 48 hours) increase in oxygen consumption. Both species were essentially oxygen regulators, able to maintain standard rates of oxygen consumption down to around 30% water oxygen saturation. Below that oxygen level the lobsters became oxygen conformers. Activity resulted in an approximate doubling of the water oxygen level at which lobsters acted as oxygen conformers. The total ammonia nitrogen (TAN) excretion rates of both species increased with increases in temperature and body weight. Activity had minor influence on the TAN excretion rate. A diurnal rhythm was evident in J. edwardsii but not in P. cygnus. Feeding had a large affect on the TAN excretion rate, with an approximate 6-fold increase occurring in each species. The excretion rates remained high for over 24 hours post-prandial. The effect of the dissolved oxygen level on recovery of P. cygnus from a period of activity/emersion was investigated. Based on the rate of recovery of various physiological parameters (oxygen consumption, haemolymph ammonia, lactate, glucose, and pH), the maintenance of water oxygen levels close to 100% saturation is recommended. Water oxygen levels less than 60% saturation slowed the rate of recovery. All lobsters recovering in water with oxygen levels less than 20% saturation died. Carrying P. cygnus out of water imposes physiological disturbances to the lobsters. The severity of the disturbances increased when the relative humidity was lower and when wind was present. Spraying water over the lobsters prevents some of the physiological consequences of emersion, such as decreases in pH and haemolymph ammonia buildup, however it does not prevent haemolymph lactate increases. Therefore, lobsters still rely on anaerobic metabolism when emersed in sprays. There was no evidence that failure of lobsters to recover from a period of emersion was caused by gill damage. A half hour period of emersion/handling at 23°C caused large physiological disturbances of P. cygnus. Halving the emersion/handling time did not decrease the extent of the physiological disturbances. Slow-chilling the lobsters to 11°C prior to emersion/handling, was an effective means of decreasing the physiological disturbances associated with emersion. This study has developed our understanding of the physiological responses of the southern and western rock lobsters to factors affecting them during postcapture processes, and will allow the design and management of rock lobster holding facilities to be based on a sound scientific basis. It also represents a major contribution to knowledge on respiration and nitrogen metabolism of large decapod crustaceans.

Catchability is estimated indirectly as a 'nuisance' variable in the spatially explicit stock assessment model of the southern rock lobsters Jasus edwardsii in Tasmania, Australia. This study attempted to identify the key mechanisms influencing catchability to enable direct independent estimates of monthly catchability. Seasonal variation in catchability of the southern rock lobster Jasus edwardsii was estimated in a scientific reserve in southeast Tasmania by comparing estimates of lobster density based on direct visual observations underwater with concomitant estimates from trapping surveys. Underwater density estimates of undersized and legal-sized male and female lobsters greater than 80 mm carapace length did not change significantly over the 14 month study period with the exception of undersized males (smaller than 110 mm carapace length). Sex ratios remained constant at approximately 1:1. In marked contrast, catch rates of males and females and the sex ratio of trapped lobsters varied strongly with season, implying that catchability varies seasonally and with sex. Impact of capture on subsequent catchability appeared to be weak, since the ratios of tagged animals in the population observed underwater generally reflected recapture rates of tagged animals in trap catches. Size-specific catchability generally increased with size, but also varied with sex and season. During moulting and mating, size-specific catchability and relative selectivity did not increase, and sometimes decreased for larger animals. The size-frequency distributions of lobsters captured in traps therefore rarely reflected the size-frequency distribution of the population on the ground. Negative associations between small and large lobsters in traps were stronger in winter than in summer, indicating strong behavioural interactions. These interactions can account for the lower catchability of smaller lobsters. Relative selectivity estimates using tag-recapture and size-specific catchability data provided similar results. Seasonal variation in catchability of legal-sized males and females in the scientific reserve was described by modelling the effects of water temperature, moulting and mating. Seasonal changes in water temperature described 63% of the variation of catchability for males, but were a poor predictor of catchability for females outside winter. Both moulting and mating were highly synchronised, although males and females moulted at different times of the year. Gaussian probability density functions were used to represent the timing and intensity of moulting, mating and subsequent compensation periods, and were added to the description of seasonal temperature changes. Four Gaussian functions based on independent biological data considerably improved the model fits for the catchability of males (R2 = 0.83). However, adding a single Gaussian function to the temperature model, representing a combined moulting and mating period based on independent biological data, provided a less adequate description of the variation in catchability of females (R2 = 0.49). Only models unconstrained by the observed timing of these events provided a good fit (R 2 = 0.74). The seasonal catchability models developed for the reserve population were applied to catchability over several years in two commercially fished regions of Tasmania. Catchability was estimated using commercial catch and effort data and fishery-independent estimates of exploitation rates. The seasonal catchability models suggest that similar environmental and physiological processes were the main factors determining seasonal catchability in the two fishery regions, but these factors varied considerably in their relative importance between the two regions. Interannual variation in relative catchability was correlated with density-dependent processes. Full models described 72% of the overall variation in catchability over 6 years in the south and 80% of the variation over 4 years in the north. More work is required before direct estimates of catchability can be included in stock assessment models. In particular, region-specific patterns of seasonal catchability, and the relationship between density-dependent processes and the interarmual variation in catchability need to be determined, before catchability can be reliably predicted in future years and in other regions of Tasmania. Nevertheless, this work has greatly improved our understanding of the processes that apparently underpin seasonal catchability.

The aim of this project was to define more clearly the culture conditions for the propagation of the southern rock lobster (Jasus echvardsii) in relation to environmental bioenergetic constraints. The effects of temperature and photoperiod on the first three stages of development were first studied in small-scale culture experiments. Larvae reared at 18°C developed faster and reached a larger size at stage IV than larvae cultured at 14°C. Development through stage II was shorter under continuous light. However, the pattern of response to photoperiod shifted at stage III when growth was highest in all the light/dark phase treatments than under continuous light. The influence of temperature and light intensity in early-stage larvae was further investigated through behavioural and physiological studies. Results obtained in stages I, II and III larvae indicated an energetic imbalance at high temperature (~22°C). The behavioural response of stage I larvae to light intensity suggested that light may be used to control behaviour in culture conditions. Early-stage larvae showed higher oxygen consumption, nitrogen excretion, and feed intake under light than in the dark. This may be due to the demonstrated increased activity under light conditions. A technique based on the chemical immobilisation of larvae was developed to assess the effect of temperature on the standard metabolic rate and the energetic cost of swimming in phyllosomas. Estimates of larval locomotor activity at different temperatures obtained through measurements of oxygen consumption were in agreement with behavioural response under the same conditions. The water quality requirements off. edwardsii larvae were determined for dissolved oxygen, salinity, and ammonia. A critical oxygen tension of `4.3` `ml` `O_2` `1^-1` was found for stage I larvae at 18°C. Stage I larvae were found to be stenohaline and a 3 ppt departure from normal salinity (34 ppt) during culture had a significant effect on growth. The cost of osmoregulation was examined in newly-hatched larvae and in stage I phyllosomas acclimated or not to sub-normal salinities. Safe levels of total ammonia concentration determined for stages I, II, III, and IV were `2.65` `mg` `1^-1`, `3.83` `mg` `1^-1`, `4.37` `mg` `1^-1`, and `2.98` `mg` `1^-1`, respectively. The results documented throughout this thesis highlighted the significance of environmental manipulation to achieve greater survival and growth during the larval development of J. edwardsii. In addition, information on the environmental physiology and behaviour of early-stage larvae provided an insight into an integrated approach, which at term will allow for the definition of system and dietary requirements of all developmental stages.

Understanding the mechanisms driving larval dispersal and connectivity is of ecological relevance and is beneficial in fisheries management. Defining population structure and stock boundaries helps in management of spawning stock biomass and annual harvests. Moreover, determining if there are patterns in dispersal can help identifying source populations that need management strategies directed towards maintaining appropriate levels of egg production. The Southern rock lobster, Jasus edwardsii, extends around southeast Australia and New Zealand and supports valuable fisheries in both countries. Adults J. edwardsii do not migrate and their phyllosoma larvae, the dispersal stage, are adapted for drifting for approximately 12 to 24 months of pelagic larval duration. Consequently there has been an assumption of genetic homogeneity within the population throughout Australia. The assumption of panmixia has been supported by larval transport simulations and previous studies on genetic connectivity. The general eastward flow of currents in southeast Australia has been identified as the likely main dispersal mechanism. South Australia is a highly productive area, and is predicted by oceanographic models to be a source of larvae to the Tasmanian fishery. A second prediction from larval transport simulations is that regional self-recruitment varies markedly across the species range in Australia. Long-term monitoring of recruitment throughout the fishery shows high year-to-year variability in recruitment, as well as regional fluctuations. This has been linked to changes in environmental conditions. Fluctuations in recruitment magnitude can reduce the accuracy of population modeling of the stock, which is used to determine harvest strategies. In this thesis I assessed variability in genetic identity of Southern rock lobster at different spatio-temporal scales to evaluate drivers of population structure. I reviewed possible biological, environmental (e.g., dispersal history) or adaptive drivers (e.g., natural selection) by analyzing single nucleotide polymorphisms (SNPs) markers generated using double digest restriction site-associated DNA sequencing (ddRADseq). I measured genetic variability in J. edwardsii across three spatial scales, broad (1,000’s km), medium (100’s km) and fine-scale (10’s km), as well as two temporal scales, within a year and between years. In chapter 2, large-scale connectivity and potential for local adaptation between adult J. edwardsii from Australia and New Zealand was investigated using neutral and outlier markers. There was large-scale genetic divergence between Australia and New Zealand, two countries thousands of kilometres apart, at neutral regions of the genome (F\(_{ST}\) = 0.022), supporting previous findings of limited larval dispersal across the Tasman Sea. A much larger genetic differentiation was detected (F\(_{ST}\) = 0.134), using regions of the genome under putative selection suggesting local adaptation and post-settlement mortality of unfit genotypes. In chapter 3 I assessed the extent and patterns of genetic variability in new recruits through time on a medium spatial scale. To determine the role of genetics in the observed interannual variability and how post-settlement selection acts to modify the observed structure in recruits, pueruli and post-pueruli settling during four consecutive years were analyzed. Interannual genetic variability of recruits within and between two sites located 100’s of kilometres apart in South Australia and Tasmania provided support for chaotic genetic patchiness. Lower genetic diversity was observed during years of low puerulus catch rates at the Tasmanian site, suggesting regional genetic differences in recruitment. Additionally, the magnitude and strength of genetic divergence detected in the markers under putative positive selection also exhibited temporal and spatial variability. Both locations exhibited a single marker under putative positive selection in common across years, providing weak evidence for post-settlement selection. In chapter 4 I assessed fine-scale temporal and spatial genetic and phenotypic divergence in recruits across a latitudinal gradient. This was done using new recruits within one recruitment season in Tasmania from sites 10’s of kilometres apart. There was a lack of overall population structure identified between three sites along a latitudinal gradient, but genetic divergence at a small spatial scale suggested chaotic genetic patchiness. Individuals sampled from the southernmost site during three consecutive monthly collections were genetically divergent from each other. There were also phenotypic differences of pueruli between sites and months of settlement; individuals at the northernmost site were consistently smaller at settlement. Collective dispersal is a possible mechanism of larval J. edwardsii, based on significant phenotypic differences between sites that were persistent through time. This implied that larvae released during the same spawning event could maintain cohesiveness until settlement, leading to genetic patchiness among individuals recruiting during the same year. In chapter 5 I tested a number of the dispersal pathways projected by a larval transport simulation model for J. edwardsii. The predicted population of origin of pueruli caught in collectors in South Australia and Tasmania was then tested using genetic assignment to determine if they were the likely point of origin. All three adult lobster sampling sites were assigned as equally likely source for recruits in both South Australia and Tasmania. These results further evidenced the high level of genetic exchange in the Australian J. edwardsii population. In general, the findings of this thesis provide new evidence on the dispersal mechanisms used by larval J. edwardsii driving the observed genetic variation in recruits. The high level of genetic admixture found herein highlights the need of a coordinated fisheries management strategy between states in order to protect subpopulations that constitute important source of recruits.

Recent interest in the aquaculture of southern rock lobster Jasus edwardsii has developed with increasing demand for lobsters and declining wild fisheries. The potential economic success oflobster aquaculture will depend on the development of efficient formulated feeds specifically designed to meet the nutritional requirements of this species. Experimental lobster feeds are currently based on fish meal and fish oil formulations, and although good survival and growth up to that of lobsters fed fresh blue mussels has been achieved, the potential to increase growth through nutrient level manipulation has not been achieved to date. Investigations of appropriate experimental methods, and subsequent determination of ingredient digestibility, lipid utilisation, histological assessment of energy storage, lipid class and fatty acid composition and energy substrate for metabolism were performed through a series of experiments with juvenile J edwardsii. Apparent digestibility of protein and carbon from novel dietary ingredients was assessed to screen potential protein sources for dietary inclusion. The apparent digestibility of crude protein in mussel meal (98%), prawn meal (77%), and lupin flour (100%) were higher than the current standard fish meal (63%), and the defatting of fish meal decreased the apparent protein digestibility (53%). Squid (7%) and canola meal (38%) were poorly digested by lobster. The examination oflobster metabolism when fed varying protein levels was measured through oxygen consumption and ammonia-N excretion and their atomic ratio. Lipids were metabolized in feeds containing low protein levels, and carbohydrate and protein were metabolized in high protein feeds, and suggested that carbohydrates were not well utilised. Isonitrogenous and isolipidic diets were formulated to include a range of potential protein meals and lipid sources, to assess the effect of lipid composition and source on the growth and composition of juvenile lobsters. Fish oil was replaced with vegetable and alternate marine oils in formulated feeds with no significant reduction in weight gain (1.2 - 2.87 g), however lobsters fed the reference feed (fresh blue mussel, Mytilus edulis) gained more weight than those fed formulated feeds (5.65 g). Lipid class analysis of the digestive gland lipids indicated high levels of triglycerides (TAG) and diglycerides (DG) in the digestive gland oflobsters fed fresh mussels (FrM), mussel meal (MM) and fish oil with lecithin (FOL). High TAG and DG were associated with digestive gland lipid storage, and were correlated to high productive protein values (r=0.755, P=0.005, n=12). Lipid histology of the digestive gland confirmed lipid deposition as droplets in R-cells, and the presence of abundant reserve cells in the digestive gland of fast growing lobsters was observed. Dietary phospholipids produced the fastest growth rates in FrM and MM, while dietary triglycerides did not promote growth. Fatty acid composition of lobster digestive gland closely resembled the dietary lipid profile however the predominantly structural lipids in the whole body tissue, more strongly reflected the profiles of control lobsters. The addition of lecithin to fish oil improved the deposition of lipid droplets in the digestive gland. This study provides greater understanding of the interactions between dietary ingredients and their effects on protein and lipid metabolism, retention and growth and provides valuable information to develop formulated feeds for J. edwardsii.

The Tasmanian southern rock lobster (Jasus edwardsii) fishery has a single Tasmania-wide management system despite large spatial variations in the biology (growth) and market traits(shell colour, body shape and live transport condition). This has created uneven distribution of harvest rates around the State where red, fast-growing, shallow-water lobsters are heavily targeted by fishers due to their high market demand, while pale, slow-growing, deep-water rock lobsters have a much lower rate of exploitation. In an attempt to improve yield, marketability and value of deep-water southern rock lobsters, translocation of lobsters between regions was examined as a supplementary management strategy for the Tasmanian rock lobster fishery. Adult deep-water lobsters were moved inshore to shallow-water reefs where changes to growth, market traits and body condition were monitored through recapture surveys. Red pigmentation in shell colour decreased with depth across southern Australia. Most of the catch is sold into Asian live markets where there is a preference for red lobsters. This market preference has lead to the price discounting of lobsters, which was estimated at a total of AUS$6.67 million / year for the Tasmanian Rock Lobster Fishery. Morphological market traits of leg length and abdomen shape were also different between deep and shallow-water J. edwardsii populations and between the sexes in each population. Nutritional indicators of condition did not differ among adult deep-water, shallow-water and translocated male lobsters, however fatty acid profiles indicated dietary differences between deep and shallow-water lobsters. Haemolymph condition indices detected significant differences in the post-harvest condition between deep-water and shallowwater lobsters. Translocating small, pale adult lobsters into a shallow water habitat resulted in a number of changes important to the yield and value of the fishery. Growth rates of translocated adult lobsters increased at their first moult in their new habitat, exceeding that of resident deep-water lobsters from the original site. Growth of translocated females exceeded resident shallowwater females in the first year post-release. Translocation changed the pale colouration of deep-water lobsters into the bright red grade most sought after by the Asian market, however changes in morphology were only partial and may require several moults for a complete change in shape. Dietary fatty-acid profiles of translocated lobsters matched those of the resident lobsters, while significant levels of essential omega-3 fatty acids in the muscle tissue of translocated lobsters suggest enhanced nutritional condition after translocation. The post-harvest condition of resident shallow-water lobsters and translocated lobsters were similar when recaptured 12 months later. Translocation could be an effective management tool to add value to the less marketable deep-water southern rock lobsters. These results on the magnitude and timing of improvements in market traits will now contribute towards the economic and biological evaluation of the feasibility of translocation as a fisheries enhancement strategy for the Tasmanian Rock Lobster Fishery.

This study examined the life history of juvenile Jasus edwardsii, with a particular emphasis on ontogenetic shifts in ecology, and how these shifts and other ecological factors may influence recruitment rates to maturity and the fishery. The aspects examined included settlement, density and distribution, shelter utilisation and availability, diet, morphology, as well as growth, survival and movement. Shifts in ecology, particularly in dispersion pattems, shelter utilisation and diet were found throughout the juvenile size range. However, a distinct early benthic phase was recognised, with a rapid transition from this phase occurring at approximately 35 mm carapace length (CL). More gradual shifts in ecology occurred after this size. Early benthic phase lobsters were solitary dwellers, randomly to evenly dispersed over the reef and consumed predominantly ophiuroids, isopods and bivalves. In contrast, larger juveniles were gregarious, cohabiting in shelters with conspecifics and having clumped shelter distributions. They also consumed predominantly bivalves, crabs and urchins. These changes corresponded with allometric changes in morphology. Early benthic lobsters had specific shelter requirements compared to the broader range of shelters used by larger lobsters, and were more likely to be affected by limitations in shelter availability. Shelter availability was dependent on the substrate type and structure, but was not found to be limiting during this study. However, settlement rates during this study were low, and shelter may be limiting at higher settlement rates. Intemal microtagging techniques were developed to examine the population dynamics of newly settled lobsters (from 10 mm CL or 0.6 g). The growth of microtagged lobsters released in the wild was seasonal, ranging from a mean of 2.5 mm CL per month in summer to a mean of 1.1 mm CL per month in the winter. The loss rates of tagged lobsters from the study area, due to mortality and emigration, were high and varied between release batches, the probability of survival ranging from a maximum of 51% to less than 1%. Lobsters remaining in the study area had a high fidelity to particular shelters. The results of this study suggest that the early benthic phase is a critical phase in determining recruitment rates to maturity and the fishery, particularly due to the influences of specific shelter requirements, increased susceptibility to predation and variations in growth and survival.

The southern rock lobster (SRL), Jasus edwardsii (Hutton, 1875) (Crustacea: Decapoda: Palinuridae), is one of Australia and New Zealand’s most valuable fishery resources. A large scale and prolonged reduction in the recruitment of SRL during years 2000 – 2010 translated into significant stock declines across the Australian fisheries. The geographical range of SRL spans more than 5000 km from Western Australia to New South Wales along the southern coast of Australia including Tasmania and around the entire New Zealand. Connectivity between distant populations is achieved solely through larval dispersal with adult movement being limited (Booth, 1997; Linnane et al., 2015). The SRL has a pelagic larval duration (PLD) of up to 24 months, one of the longest known in the marine environment and the longest among all rock lobsters (Booth, 1994; Bradbury and Snelgrove, 2001). SRL larvae can be carried hundreds of kilometres offshore and away from their origin, potentially connecting spawning grounds and recruitment sites hundreds of kilometres apart. This potential for widespread dispersal combined with unpredictable inter-annual and spatial variability of egg production and recruitment, make biophysical modelling an ideal approach to examine population connectivity for this species. This thesis assesses the population connectivity of SRL throughout its geographical distribution by the means of a larval dispersal model built utilising the best available hydrodynamic models and evidence based species-specific biological parameters. Prior to setting up the larval dispersal model, I performed a validation of two hydrodynamic models available in the study area, by comparing the model predicted time series of seawater temperature and ocean currents to in situ mooring measurements (Chapter 2). I found that the accuracy of the hydrodynamic models varied with the parameter investigated, the depth of the measurement and the geographical region. The model predictions of water temperature were more accurate than the predictions of ocean current velocities. This study identified important inaccuracies in the hydrodynamic models’ estimations of ocean parameters and on time scales relevant to larval dispersal studies. The largest errors in global ocean models are seen in coastal regions, where models have poor coverage due to their lower spatial resolution. Many global ocean models also do not explicitly resolve key hydrodynamic features in the coastal regions. I investigated the effect of nesting a highly-resolved coastal hydrodynamic model – ETAS – within the global BRAN model, on the passive dispersal of larvae released on the east coast of Tasmania (Chapter 3). I found significant differences in larval trajectories and dispersal metrics between the simulations using the nested ocean models and the simulations using only the global ocean model. Finally, an individual-based biophysical model was built for SRL larval dispersal (Chapter 4), the larval survival during dispersal and the probability of pueruli successfully settling in suitable habitat were estimated (Chapter 5). Larvae were released throughout the species geographic range during the egg hatching period over release dates spanning twenty years. In addition to dispersal metrics, I report the connectivity matrix between 16 fishery management zones across the dispersal domain. Dominated by the large west-flowing currents in the study region, the main larval transport was from west to east. The highest rates of survival to settlement were seen in larvae that metamorphosed early during the competency window or within few hundred of km from their release locations. South Australian and Victorian fisheries were important larval sources for most other fisheries east from them, while Victorian and Tasmanian fisheries received the largest proportion of successful pueruli from all other fisheries. The highest self-recruitment rates were observed in New Zealand, Northern South Australia and Tasmania 2 fisheries. This study offers valuable insight into the applications and limitations of hydrodynamic models in larval dispersal modelling and calls for the development of highly-resolved coastal ocean models. The SRL larval dispersal model developed in this work provides new information on this species’ potential for dispersal and the predicted population connectivity can be used to inform new fishery policies and help improve management of the SRL stock.

This research examines traceability in the SRL export supply chain to investigate the use of low-cost image-based biometrics in lobster grading and identification. The SRL industry is a strategic export fishery contributing $250 million annually to the Australian economy with over 90% of its turnover coming from the Chinese market (prior to the COVID19 crisis). While the industry continues to grow, challenges have been identified that pose risks to the fishery's economic and environmental sustainability including: (1) Outbreaks of marine biotoxin and fish mortality/damage during transportation have raised food safety and quality concerns, (2) Product substitution via fraudulent business in export markets impacts the SRL premium brand, (3) The China Free Trade Agreement (ChAFTA) is changing requirements for food compliance regulations and, (4) consumer expectations for food quality, authenticity and provenance information on products is increasing. The SRL industry has identified product traceability as an important part of its response to these challenges. Traceability is broadly defined as the ability to track and trace food products at either item or batch level along part or all of the supply chain. Currently, some parts of the SRL supply chain do utilise product tracking such as barcodes and radio-frequency identification (RFID) tags in batch level traceability. However, item level traceability remains limited, with the granularity, form and availability of information on individual products, varying considerably along the chain. This is partly due to the high proportion of small SRL businesses continuing to rely on manual handling practices and paper-based traceability techniques. But it is also because of the continued relatively high cost of tools and techniques available to automate and digitise traceability data at the item level. Image-based biometrics deploying computer vision techniques have previously been trialled in individual animal tracking studies. These studies highlight the importance of understanding identifiable animal characteristics and the processes for image capture and analyses. In this research the key attributes of SRL captured and analysed relate to the lobster's size, weight, colour and spiny shell carapace patterns. Using these data, the feasibility of combining image processing and machine learning technologies to support automatic grading and individual identification of lobsters for processors, distributors and consumers in the SRL export supply chain were investigated. The research methodology involved a two-phase research strategy. Phase one identified key lobster characteristics and developed and tested image capture and analysis methods for both automatic grading and individual lobster identification. A key consideration for these methods is how to utilise low-cost equipment that would be readily accessible to SRL small businesses and consumers. Using the output of the automatic lobster grading, a physical prototype system was developed and tested to simulate an automatic grading operation in a fish processor. Based on the grading attributes and individual biometric characteristics selected and tested, a multimodal biometric identification model was developed. Building on these results, phase two focused on approaches to implementing traceability along the SRL supply chain through the design, testing and laboratory simulation of product tracking using a mobile application and verification server. The research design involved data collection at a Tasmanian fish processor where 8Mps Raspberry Pi cameras using a fixed distance and angle compiled a dataset of 4000 images of 200 lobsters. The lobster carapace was the "region of interest" (ROI) during the development of automatic grading and individual biometric identification. This ROI was extracted from lobster images using: (1) traditional image processing techniques and (2) convolution neural networks (CNNs). The preliminary results highlighted a pre-trained Mask-RCNN outperformed the traditional image processing techniques and the Mask-RCNN was utilised for individually analysing the grading attributes of size, weight (converted from size) and colour. These results were used to build and test a prototype grading system to simulate an automatic grading operation for use in a fish processor, integrating software, a conveyor belt, relay and cameras. In the analyses of individual techniques for lobster identification, colour histograms, texture and Siamese networks were tested and evaluated. Based on the outputs of the automatic grading and individual identification, a multimodal biometric identification model that combined lobster size, colour histogram, texture and deep learning results was developed and tested. However, the false-positive rate of this model remained high (64.5%) and this meant that the results achieved were insufficiently reliable for individual lobster identification when used as a standalone solution. For this reason, two hybrid biometric verification models for product tracking along the SRL supply chain were designed and tested. In both cases, lobster image identification was used as part of a layered hybrid authentication approach along with product tags attached on individual lobsters and/or boxes of lobsters. These approaches aimed to create '1-to-1' and/or '1-to-some' matching mechanisms. In both scenarios, a species-specific identification module was also developed and deployed to handle unmatched cases. This module was designed to enhance consumer confidence because it ensured that only genuine SRL products could be verified even if there were problems with individual verification based on tag identity number (ID) or lobster image. Using the main image library collected in Phase one, a biometric verification server and mobile application were used to demonstrate the operation of these two tracking models. The analyses on lobster grading yielded positive results in which size accuracy is 90% with a range of +/- 5% error compared with the actual sizes, and weight accuracy is 85% with a range of +/- 10% error compared with the actual weights. Colour classification also achieved a good result based on Euclidean distances between the average HSV colours of the ROIs and a base colour (black in this research) that helped identify a possible threshold to separate between the pale red and dark red groups. The testing with an automatic grading system also produced an important proof of concept where each lobster could be profiled with ID, images, size, weight, colour and other historical information. For lobster identification, the testing results with individual techniques including colour histogram, texture and Siamese network showed an ability to filter from one hundred objects down to a group of between 10-15 best candidates during the matching processes. The multimodal biometric model highlighted a further improvement of the matching process with the average of 5 candidates returned from the testing cases. However, the challenge of the false-positive rate in lobster identification remained high with 64.5% within this model. In the simulations for the two hybrid models, the false-positive rate showed a decrease to 0.35% for the '1-to-1' matching and 45% for '1-to-some' matching. For the species identification, the use of Support Vector Machine (SVM) for classifying between SRL and non-SRL products based on colour histogram of the carapace regions also achieved a positive result with 92% accuracy. The simulation of the product traceability also demonstrated a range of important functions for end-users supported by the central verification server and mobile application including image capture, lobster grading, barcode scanning and individual product verification. The results obtained across two phases demonstrated how low-cost computer vision technology can be utilised to analyse grading attributes of lobsters (RQ1) and highlighted the current capability of this technology in identifying individual lobsters (RQ2). The research also demonstrated approaches to using low-cost biometric grading and identification outcomes to improve the traceability performance along the SRL supply chain (RQ3). Based on the image-based biometric models developed and tested in this research several contributions can be identified: • From the technical viewpoint, the research strengthens the case for utilising lowcost computer vision in food traceability. Although the false-positive rate for the individual identification led to the deployment of hybrid traceability models, the multimodal biometric model developed does provide a platform for ongoing improvements to the accuracy of low-cost image-based biometric identification. • From the traceability viewpoint, the research offers an enhancement to conventional product tracking relying on physical tags. Importantly, the low-cost image-based biometric verification solutions developed support small SRL businesses to improve item tracking level based on the existing box-tagging practices. Additionally, the ability to integrate both the grading and identification functions into a mobile application offers direct traceability communication between overseas consumers and the Australian SRL exporters. • From the SRL industry viewpoint, the research provides industry stakeholders with a response to the concerns of food safety, quality and security. With the ability of verifying the authenticity and provenance of individual lobsters, the confidence of end consumers in the safety and authenticity of SRL products can be consolidated and the Australian sellers can be better protected from fraudulent activities in export markets. The approach also illustrates how Australian SRL businesses may be better prepared for any compliance requirements imposed by ChAFTA. Future work will be able to further improve identification techniques and testing in live environments and it is anticipated that low-cost tag-less image-based traceability will be available in the SRL and other seafood industry export supply chains in the near future.

Tail fan necrosis (TFN) is a disease that affects southern rock lobsters during live-holding. The damage to affected tail fan uropods is seen as a major constraint in the development of a live-holding industry. A previous study has demonstrated that various Vibrio species are associated with diseased tissue (May, 2002. B.Sc. Honours Thesis, University of Adelaide). However, that study was restricted to an examination of TFN lesions that formed 8 weeks post infection for lobsters held under optimal growth conditions. Although damage to tail fan tissue by instruments contaminated by organisms isolated from TFN affected tissue was shown to result in formation of TFN-like lesions, the microbial community of lesions associated with TFN over time in terms of both the cultivable and non-cultivable communities was not identified. The extent of damage to tail fan tissue by bacteria and the response of lobster immune cells to infection was also not determined. Furthermore, the presence of potentially pathogenic Vibrio spp. within the diseased tissue was identified as a potential public health risk, particularly in food preparation facilities where live lobsters are handled. The work described in this thesis specifically examined the development and effect of TFN on the overall health of affected lobsters, as well a confirmation that the Vibrio spp. involved in establishment of TFN may represent a public health risk. To answer these questions, a larger infection trial was set up. Uropod tissue of groups of lobsters were intentionally damaged with sterile instruments or instruments contaminated with a Vibrio spp. isolated from a TFN lesion. The lobsters were maintained in controlled environment aquaria and uropod tissue samples taken and subjected to microbiological, microscopic and molecular analysis. Microscopic analysis of developing lesions demonstrated that several morphologically different bacterial cell types colonise the surface of TFN lesions. Bacteria involved in infection are essentially restricted to the surface of the lesions, but where significant damage to the uropod tissue occurs, these bacteria may invade the damaged tissue and penetrate deeper underlying tissue. Infection of tail fan tissue results in inflammation and concomitant loss of internal structure of the carapace and deposition of fibrous material within the soft tissue underlying the chitinous exoskeleton. In cases of severe inflammation, a central core develops within the fibrous tissue consisting of a number of cell types, including hyaline cells, granulocytes and fibrocytes. However, there was no evidence of deep bacterial invasion into the underlying inflamed tissue. Viable counts and identification of the bacteria associated with the diseased tissue demonstrated that the bacterial population of TFN lesions is dominated by Vibrio species. Whilst there was no significant increase (P < 0.05) in the total viable bacterial counts associated with the diseased tissue compared with healthy tail fan tissue, Vibrio species were isolated more frequently from tissue samples from uropods subjected to simultaneous damage and infection. 8% of bacterial isolates recovered from lesions were identified as V. vulnificus and 27% of isolates were identified as V. parahemolyticus. Isolates of V. vulnificus displayed colony morphology consistent with pathogenic strains. Similarly, all isolates of V. parahaemolyticus were tdh negative, but 41% were trh positive. The majority of these species were able to express cytolysins capable of lysing CHO cells. This data indicated that vibrios responsible for establishment of TFN may have potential to cause human infections and therefore lobsters with TFN lesions should be regarded as a potential health risk to consumers. The majority of isolates of Vibrio spp. recovered from infected tissue expressed extracellular lipase and/or chitinase, and this indicated that these enzymes may enable Vibrio spp. to induce TFN in damaged tail fan tissue. The predominance of Vibrio spp. associated with lesions was confirmed by analysis of amplicons representative of genes encoding 16S rRNA prepared from lesion tissue DNA extracts. This was achieved by sequencing randomly selected clones of amplicons and by use of Denaturing Gradient Gel Electrophoresis to separate amplicons according to nucleotide sequence diversity. Unlike other crustacean shell diseases, TFN does not induce changes in serum protein levels, lead to significant bacteraemia or changes in the circulating haemocyte population. Furthermore, TFN has apparently little effect on the overall health of affected lobsters. This observation may explain the lack of mortality associated with this disease. Only a non-specific activation of lobster phenoloxidase in response to TFN was observed and only limited activation of phagocytosis of Vibrio spp. in vitro could be demonstrated. This data suggested that the lobster immune system is unable to respond to infection and may explain why the bacteria are able to induce persistent infection resulting in formation of TFN lesions. Nevertheless, localised melanisation surrounding the wound site induced by carapace degradation products is able to restrict bacterial invasion into the haemolymph. The impact of TFN on appearance and consumer acceptance is dependent on the extent of damage caused by TFN. Minor lesions are resolved during moulting, whereas more severe lesions are maintained across more than one moult cycle.
Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2008.

During 2012 an extensive bloom of the toxic dinoflagellate Alexandrium catenella occurred on the east coast of Tasmania causing paralytic shellfish toxins (PST) to accumulate in bivalve shellfish at 12 times the regulatory maximum level (ML; 0.8 mg STX.2HCl equiv. kg\(^{−1}\)). Southern Rock Lobster, Jasus edwarsdii, accumulated PST in the hepatopancreas to 3.9 mg STX.2HCl equiv. kg\(^{−1}\), resulting in the first closure of an Australian lobster fishery due to marine biotoxins. Recurrent blooms since 2012 have had an on-going impact on both the commercial fishery in Tasmania, valued at AUD 93 M, and the significant recreational fishing sector. The present body of work aimed to address the following knowledge gaps exposed by this novel risk: (1) the toxicokinetics associated with PST uptake and depuration in J. edwardsii from A. catenella blooms; (2) the impact of PST on lobster health; (3) the supply chain risk of PST accumulation in J. edwarsdii; and (4) to determine and validate where appropriate cost-effective methods to appropriately monitor and manage PST accumulation in lobster the field. In elucidating these questions, information was sought that could inform management of public health and market access risks and determine whether PST accumulation could adversely affect lobster performance, health and catchability. To examine toxicokinetics of PST in J. edwardsii (Aim 1), an experimental study was undertaken in a biosecure aquaculture facility in South Australia. Adult male lobsters were fed highly toxic mussels (6 mg STX.2HCl equiv. kg\(^{−1}\)) sourced from the impacted area in Tasmania for four weeks, then allowed to depurate for a further 5 weeks. Control (fed non-toxic mussels) and exposed lobster were harvested at regular intervals, tissues dissected and analysed for PST. The lobsters rapidly accumulated PST in the hepatopancreas (exponential rate of 6% per day), exceeding the bivalve ML within one week, and reaching a maximum of 9.0 mg STX.2HCl equiv. kg\(^{−1}\). Once toxic feed was removed, the lobster depurated at a rate of 7% per day. Toxins were found in lobster antennal glands at concentrations two orders of magnitude lower than found in the hepatopancreas. This is the first report of PST in lobster antennal glands which, along with the gills, represent possible excretion routes for PST. However, PST were not detected at significant levels in the lobster haemolymph, which means there is no option for non-destructive sampling of lobster for PST. During the experiment, lobster health was assessed to determine the impact of PST accumulation in the hepatopancreas (Aim 2). A comprehensive range of behavioural (vitality score, righting ability and reflex impairment score), health (haemocyte count, bacteriology, gill necrosis and parasite load), nutritional (hepatopancreas index and haemolymph refractive index) and haemolymph biochemical (21 parameters including electrolytes, metabolites, and enzymes) parameters were examined. Accumulation of PST increased the apparent feed intake but did not result in mortality nor significant changes in the behavioural, health, or nutritional measures suggesting limited gross impact on lobster performance. Furthermore, most haemolymph biochemical parameters measured exhibited no significant difference between control and exposed animals. However, in the lobsters fed toxic mussels, the concentration of potassium in the haemolymph increased with PST, whilst the concentration of lactate and the sodium:potassium ratio decreased with PST. In addition, lobsters with elevated levels of PST in the hepatopancreas showed a hyperglycaemic response, indicative of stress. These findings suggest that PST accumulation results in some measurable indicators of stress for lobsters, but these changes appear to be within the adaptive range for J. edwardsii and do not result in a significant impairment of gross performance. To determine whether J. edwardsii could accumulate PST in the supply chain (Aim 3), a controlled experiment was conducted where adult male lobsters were exposed to highly toxic cultures of A. catenella at field relevant concentrations (2 × 10\(^5\) cells L\(^{−1}\)) over a period of 21 days. In contrast to the feeding experiment, no PST accumulated in lobster from exposure to toxic algal cells. The same lobster health parameters were assessed, with no change seen in any of the behavioural, health, nutritional or haemolymph biochemical parameters examined. To assess appropriate management strategies (Aim 4), regulatory monitoring results since September 2012 were combined with field studies to examine uptake and depuration of toxins in J. edwardsii on the east coast of Tasmania during A. catenella blooms. Results from 496 lobster hepatopancreas PST samples were analysed. A high degree of variability was seen across years, months, sites and between individuals. The highest risk sites are on the central east coast, with exceedances of the bivalve ML occurring between July and January. Mussel sentinel lines were installed in each lobster management zone on the east coast of Tasmania and monitored fortnightly during high-risk periods. These lines proved effective in indicating a risk of elevated PST in lobster hepatopancreas. Field uptake and depuration rates of PST in lobster were similar to those seen during the experimental studies (maximum of 2% and 3% per day respectively), but always less than rates measured simultaneously in mussels. Analysis of hepatopancreas PST levels during bloom development and decline occurred to determine the level of confidence in the regulatory sampling regime (5 individual lobster hepatopancreas samples are analysed from each site during an event). When PST in the hepatopancreas of all lobsters sampled is < 0.5 mg STX.2HCl equiv. kg\(^{−1}\) there is 97.5% confidence that any lobster from that site would be below the bivalve ML. In conducting this research, it became apparent that international regulations for maximum levels of PST in seafood and research into PST accumulation vary in the units used for PST concentration. Some standards/research reports use mg STX.2HCl equiv. kg\(^{−1}\), some mg STX equiv. kg\(^{−1}\) (effectively producing total PST results that are 24% lower), and some only state mg kg\(^{−1}\). Similarly, the toxic equivalency factors (TEF) used to convert analogue concentrations to total PST in toxicity equivalents are varied, and often not stated. A call for uniform reporting units was published in Toxicon correspondence to highlight this issue, recommending countries and researchers adopt the Codex Alimentarius Commission protocols of reporting in mg STX.2HCl equiv. kg\(^{−1}\), using FAO/WHO TEF. The combined field and experimental work detailed in this thesis has informed improvements to the biotoxin risk management program for J. edwardsii in Tasmania. Implications for biotoxin risk monitoring are: (1) lobsters continue to feed during bloom periods and high concentrations of PST can occur; (2) animal toxin monitoring should be frequent at the start of a bloom in case of a rapid accumulation of PST; (3) mussel sentinel lines are a cost-effective early warning system for toxin accumulation; (4) it is adequate to sample 5 individuals per site as long as a reduced trigger level of closure of harvest is employed; (5) depuration is relatively quick at up to 7% per day so that sampling to confirm re-opening should occur soon after bloom collapse (as indicated by mussel PST levels); (6) non-lethal sampling is not possible as haemolymph PST levels do not reflect levels in the hepatopancreas. Importantly, (7) lobsters exposed to toxic algae during wet storage in long supply chains (on vessel, in sea-cages or at processing facilities) do not take up PST. Furthermore, (8) survival, quality, and safety of this high-value product are not impacted by accumulation of PST or by exposure to toxic cells in the water.

Depredation within fisheries occurs when a predator preys upon target species caught within fishing gear. In many cases predators can be habituated to commercial catches from fisheries, especially when prey are too large or too fast for the predator to forage successfully in the natural system. Depredation in fisheries has received much attention over the last few decades in light of conservation and economic implications. Current knowledge is still focused, however, on the direct impacts of depredation on fisheries (e.g. financial losses), or predator populations, without consideration of the implications for prey populations. Recent advances in predator–prey theory have demonstrated that predation not only generates direct impacts on prey populations via consumption, but also has indirect impacts via causing changes in prey activity, behaviour, physiology and development, i.e. ‘non-consumptive’ effects of predation or predation risk. For example, prey under predation risk are forced to make behavioural choices between vital activities, such as feeding and predator avoidance, by reducing activity or seeking out shelters. Hence, individual-level decision making (e.g. sheltering vs feeding) can have profound implications on prey life history traits such as survival, growth and reproduction, which can in turn impact populations and ecosystems. In regards to the prey, consumptive and non-consumptive effects have not yet been thoroughly examined in a fishing context, particularly on fishing grounds where predator habituation to fishing gear occurs and the implications may be extended to the prey population. In this thesis, the interaction between the Maori octopus (Pinnoctopus cordiformis) and the southern rock lobster (Jasus Edwardsii) is used as a predator–prey case study, with particular emphasis on octopus depredation within the southern rock lobster fishery (SRLF) in Australia. A multi-level approach examines predation risk at the population level from fishery-dependent information on fishing grounds, and at the individual level from laboratory experiments designed to elucidate the physiological responses of lobsters under predation risk. In-pot lobster mortality is used as a proxy of predation risk for the fishery (i.e., ‘in-pot predation risk’), and its examination across spatial and temporal scales and with a range of life history traits forms the basic understanding of this case study. At a finer-scale individual level, information from experiments provides new insights on prey decision-making processes under predation risk, elucidating the non-consumptive effects of octopus predation on lobster. Specifically, this study comprises four linked, but stand-alone, chapters addressing the following: understanding spatio-temporal patterns of octopus predation in the SRLF (Chapter 2) and the identification of lobster life history traits associated with octopus depredation in the SRLF (Chapter 3); and the examination of physiological responses of adult J. Edwardsii under predation risk (Chapter 4); and how such responses can be altered under the combination of temperature and predation risk in key lobster life stages such as sub-adults (Chapter 5). Different spatial and temporal patterns in octopus depredation were found in the SRLF, demonstrating the dynamic nature of this predator–fishery interaction. Using fisheries information from Tasmania, it was evident that while octopus depredation reached maximum levels during winter on the east coast, predation risk increased during summer time on the west coast. Such spatial- temporal variability in predation risk was examined further with time series modelling using fishing and environmental variables as explanatory variables of in-pot lobster mortality within stock assessment areas. Most eastern areas showed a stronger effect of fishing variables, such as lobster CPUE and fishing effort, than sea surface temperature, with the opposite pattern along the west coast. A classification of SRLF stock assessment areas based on predation risk levels was developed and implications for fisheries management highlighted. In-pot predation risk increased with lobster size and was elevated for male lobsters (i.e., size- and sex-dependent mortality). The effect of individual traits of J. Edwardsii such as body length and sex on in-pot predation risk was examined in the fishing zones of South Australia, using mixed- modelling techniques. Predation risk was also associated with the catch rate of lobsters (used as a proxy of lobster abundance), revealing a density-dependent rate of mortality that varied among fishing zones. Findings from these two components of the thesis provide new insights on spatial and seasonal components of predation risk in the SRLF, how predation risk was related to lobster life history traits, and the ecological and economic implications associated with octopus depredation on the lobster fishing grounds. Individual-level information from physiological experiments revealed that lobster metabolism was strongly affected under predation risk scenarios. Adult individuals exposed to predator cues (kairomones) during the nocturnal-active phase of lobster activity reduced their metabolism as a predator avoidance mechanism. Low metabolism is suggested to reflect lobster inactivity or sheltering. Although such an anti-predator response may serve as a strategic mechanism to survive, deleterious effects on other vital functions such as feeding are expected to influence rates of growth and reproduction and affect population-level dynamics. In defining lobster decision making under predation risk (e.g. feeding vs. sheltering), environmental changes associated with temperature (e.g. warming waters) may force individuals to be more active during high-risk scenarios in order to satisfy metabolic demands. This was examined in sub-adults J. Edwardsii using an experimental approach combining predation risk and thermal acclimation scenarios; the latter was used as a proxy of projected temperatures for the south-east Australian region under climate change. Individuals acclimated at warming temperatures (e.g 23°C) did not exhibit anti-predator responses such as a reduction of metabolic rates observed in sub-adults at ambient temperatures (20°C). Instead, lobsters at warmer temperature increased their activity once energetic requirements were elevated. This suggests that anti-predator responses such as sheltering may be cancelled under projected temperatures for the region. Such findings can be used as a proxy to understand how climatic variability associated with climate change can generate direct impacts on the survival of individuals, and indicate the longer-term implications for local ecosystems and fisheries. This study provides insights on depredation in fisheries by articulating information at different organizational levels. Hence, it provides an ecological framework to examine fishing grounds as high-risk environments for lobsters, serving as a baseline for future studies on predation risk and its implications for lobster populations. At the same time, findings from this thesis will provide a better understanding of predator–fishery interactions, which can enhance fishing management especially in the context of implementing ecosystem-based fishery management.

Understanding how fishers behave and make decisions is critical in determining how best to manage fisheries. If the response of fishers to management measures can be predicted, unexpected and undesirable outcomes can be avoided. Individual transferable quota (ITQ) management has been introduced in many international fisheries, with the purpose of accounting for human behaviour, as it theoretically generates behavioural incentives that are aligned with management objectives (e.g. reducing fishing costs). The ability of ITQ systems to meet continuing economic, ecological and social objectives therefore is centred on ensuring fisher behavioural incentives remain aligned with those objectives. This thesis used the Tasmanian southern rock lobster (TSRL) fishery in Australia as a case study to assess changing fishing practices and behaviour of fishers under ITQ management and how this had evolved through time. The aim was to improve general understanding of how ITQ implementation and design may affect fisher decision-making and improve certainty in fishery management outcomes. It is critical that an ITQ system is able to manage interactions with all ecosystem components (e.g. non-target species) as required under ecosystem based fisheries management (EBFM) principles. The TSRL fishery to some extent, was more successful than other fisheries in accounting for these interactions, due to the selective and benign nature of potting. In many sustainably certified fisheries, input controls continue to be used in place of ITQ systems to manage ecosystem components, particularly in non-selective fisheries (e.g. trawl). The continued use of input controls however, can reduce the security of a fisher’s ITQ right through loss of access and potentially separate their incentives and behaviour from management objectives. Successful ITQ management also requires the managing authority to set a binding total allowable catch (TAC). Between 2008 and 2010, the TSRL had a non-binding TAC, which reduced the price of quota on the market and caused a reactivation of latent effort, increase in fleet capacity, reduction in economic efficiency and dissipation of economic rent, as fishers engaged in a competitive race to fish during times of high revenue. Changing fishing practices such as “double night fishing” during these years also had the potential to lead to localised stock depletion through concentration of effort, however the format of the commercial logbook prevented a precise assessment of the fleet-wide extent and impact of double night fishing. Consequently, this research highlighted the importance of being able to collect fine-scale spatial and temporal data on fishing effort in order to enhance decision-making. It is also important in an ITQ system that those actively fishing own the majority of their quota units. An implicit assumption behind the theory of ITQs is that those fishing are quota owners, however in many developed ITQ fisheries, with free transferability of quota units, the majority of the fishing is undertaken by lease quota fishers. Following analysis of the physical risk tolerance of both quota owners and lease quota fishers in the TSRL fishery, it was evident that their behavioural drivers were divergent. Lease quota fishers were more responsive to changes in expected revenue than quota owners, leading in some areas to significantly higher risk tolerance levels. In other words lease quota fishers were more prepared to take greater risks at sea than quota owners when expected revenue was high. This result was not entirely unexpected as lease quota fishers face high costs of leasing quota and an increasing “cost price squeeze” between what that must pay to lease quota and what they are paid for their catch. Consequently, their behavioural incentives and underlying business structures are likely to be different. This was also evident in a series of economic experiments that were conducted to examine the propensity of groups with varying numbers of quota owners and lease quota fishers, to coordinate to prevent assignment problems that cause economic rent dissipation. Heterogeneous groups of lease quota fishers and quota owners were less successful in coordinating with communication than homogenous groups of quota owners. This was because lease quota fishers were less likely to adopt a socially-optimal strategy for preventing rent dissipation compared with quota owners due to having: (i) inequality in wealth; (ii) insecurity of tenure and; (iii) asymmetric information exchange. It was only through the institution of income-sharing cooperatives that lease quota fishers chose to coordinate because income-sharing offset the incentive to over-appropriate the resource, if participants doubt that others would do the same. While requiring external validation in the field, the results highlight the importance of recognising and understanding the differing behavioural incentives of lease quota fishers and quota owners. They also highlight the need for managers to consider the trade-offs associated with allowing free transferability of quota units and whether this meets overarching management objectives. While contributing to further discussion and debate on the costs and benefits of ITQ management, this research highlighted the importance of understanding behavioural incentives of different types of fishers in order to inform management decision making. This type of research now and in the future has the potential to inform and ultimately improve the design and implementation of ITQ management systems.

Settlement processes and subsequent post-settlement survival influence the demographic structure of marine populations and also their resilience to human exploitation, or other perturbations. Therefore, better understanding of these two periods of the lifecycle could assist in the management and conservation of economically important species. The rock lobster, Jasus edwardsii, supports valuable fisheries throughout southern Australia and New Zealand. Settlement levels of pueruli (late larval-stage) have been monitored on artificial crevice collectors throughout the geographical range with a long-term program that commenced in the early 1990’s. Examination of the settlement patterns indicated that most areas of the Australian fishery suffered declines in settlement at some time between 2000 and 2010. Patterns in settlement at some sites appear to be partially driven by environmental processes that move pueruli inshore by onshore advection. However, a lack of correlation with environmental variables at other sites, and the strong swimming ability of the pueruli, suggested that the process of settlement inshore is complex and is influenced by the ability of pueruli to orientate onshore, although no behavioural experiments demonstrating this have been reported for J. edwardsii. Settlement behaviour is also of interest in the Tasmanian jurisdiction because climate-change has led to the loss of giant kelp (Macrocystis pyrifera) forests, which previously provided dense cover across large areas of the east coast. This change in habitat in areas important to the fishery has also raised the question of whether there were effects on puerulus settlement and post-settlement survival. This thesis used a combination of data analyses, and laboratory and field experiments to assess the influence of environmental variables and puerulus behaviour on settlement and post-settlement survival. To assess the contribution of environmental variables on settlement magnitude, time series analyses were conducted over different spatial scales (Chapter 2). In addition, laboratory and field experiments were conducted to examine whether the pueruli used chemical cues from coastal waters and from the giant kelp (Chapter 3), and underwater reef noise (Chapter 4) for orientation to find settlement habitat. The effect of kelp forest depletion on settlement and survival of pueruli and early juveniles was examined with field experiments (Chapter 5). Settlement was found to be affected by regional scale oceanic processes (100-500’s km) measured by the Southern Oscillation Index (SOI), Dipole Mode Index (DMI) and Southern Hemisphere Annular Mode (SAM) although outcomes varied between regions. At a local scale, waves, wind strength and current appeared to have some influence on pueruli transport, with sea surface temperatures being less important, but much of the settlement variability was not explained and the effect of environmental factors was not consistent between sites. In a field experiment it was found that underwater reef noise was detected by puerulus and appeared to be an attractant for settlement during calm sea conditions. Laboratory experiments showed that pueruli were attracted to chemical cues from coastal waters, but they were not attracted to chemical cues from the giant kelp. The effect of kelp was also examined in field experiments where kelp habitats increased settlement into crevice collectors and the subsequent survival of the early juveniles, indicating that decline in kelp habitat could reduce recruitment at a local scale. Overall, these results highlight the complexity of settlement and recruitment where larval behaviour and oceanographic process interact at different scales. The research helps to explain settlement processes and also has value for including puerulus behaviour into future dispersal models for exploring spatial patterns and testing dispersal hypotheses in this species which supports a valuable fishery. The apparently complex processes affecting settlement strength showed that environmental conditions that reduce settlement strength in one region of the fishery often increase settlement strength in other regions. This suggests resilience to climate change at the scale of the entire fishery. However, local habitat changes would also be expected to affect future recruitment of this valuable species.

Capture-mark-recapture (CMR) modelling is commonly used for direct estimation of demographic parameters in the wild. Whilst it is well known that the precision of estimated parameters in CMR studies increases with sample size, duration of study and the number of recapture events there are few studies that explore the design of CMR projects to achieve optimal outcomes. Research funding and time allocation are two constraints that place restrictions on the research design. This study addresses this challenge and seeks to demonstrate issues that need to be addressed and ways to design CMR that minimise costs while still providing the precision and accuracy required for assessment of marine resources. A twelve year tagging data set for Jasus edwardsii at a non-fishing site (Crayfish Point Scientific Reserve, Tasmania, Australia) was used in the study. Cormack-Jolly-Seber (CJS) modelling was used to compare estimates of survival probability with increasing numbers of surveys from 3 to 12 for both equal (annual) and unequal survey intervals. The study found that more surveys were required to obtain precise estimates of survival probability in females than in males, and the number of surveys required increased when intervals between surveys were unequal. For annual surveys, stable estimates of survival probability generally required at least five years, which is often beyond the three-year duration commonly used in scientific studies. Five annual surveys were used to determine the effect of sample size and fishing effort (the number of traps set per day and days fished) on the precision of estimated survival probability. Larger sample sizes (>=500) and more sampling effort were required to determine sex specific survival probability estimates. Tag induced mortality (TIM) and tag loss reduce the number of tagged lobsters in the population and result in an under-estimation of survival probability. TIM is often investigated in aquaria studies with small sample sizes and over short time periods. In this study, a model based on three annual-surveys was used to provide in-situ estimates of TIM proportion. Estimates of TIM proportion were high and varied being on average between 25% and 40%. Capturing sufficient lobsters during the third survey that were tagged in the first survey and also seen in the second survey was a major limitation in using this method. Tag loss is usually estimated by double tagging in the wild. This study investigated the fate of new tags and existing ( old) tags applied to lobsters. Estimated tag loss rate was different between males and females and the annual rate of tag loss was similar between years during the two year study indicating that tag loss is chronic and needs to be accounted for throughout the entire period of mark-recapture programs. In general, older tags were lost at a slightly higher rate than new tags. The design of mark-recapture programs will be dependent on the species under study and although these results are specific for J edwardsii, the issues considered and methods used in this thesis should assist researchers in the design of tagging surveys. Importantly, both tag loss and tag induced mortality can be of a magnitude that impacts estimates from mark recapture studies and the thesis demonstrates issues to be considered in designing a tagging program that meets the objectives of the study and also enables estimation of issues such as tag loss rate and TIM proportion which can bias survival probability and population estimates.