The major impediment to closing the life-cycle of Jasus edwardsii Hutton (Decapoda: Palinuridae), a spiny lobster being assessed as a candidate for aquaculture, lies with larval rearing. Larval development in J. edwardsii phyllosoma is a complex and protracted phase taking in excess of 300 days in captivity. Often the initial phyllosoma competency (survival and growth) is poor and thought to be associated with parental influences. To improve survival in culture a method to assess larval competency at hatch was determined and environmental, physiological and nutritional influences on competency assessed. The development of an activity test to assess larval competence involved short-term exposure of phyllosoma larvae to temperature and salinity stresses, responses monitored (stress indices) and later correlated with survival in starvation tests and in culture. The initial activity test (1 h in 23ºC at 10 o/oo) was refined (1 h in 21ºC at 10 o/oo) during an examination of nutritional influence on larval competency allowing the most competent larvae to be selected for culture, a significant advantage for any potential aquaculture species. The effect of exposing broodstock to elevated temperatures (17 and 19ºC) during embryonic development was assessed in relation to the larval competence of newly-hatched phyllosoma. Elevated temperature provided out-of-season larvae by accelerating embryonic development by up to 2 months however; the larvae produced were smaller and less competent than those incubated under ambient conditions (9.5-13ºC). This was a significant finding as it ended the use of this technique to provide out-of-season phyllosoma larvae and stimulated research into alternate methods to provide phyllosoma at different times during the year. Larval competence was also assessed in relation to broodstock physiology. Larger females produced larger phyllosoma, which demonstrated a greater potential for survival in culture, ascertained by stress indices and LD-50. Viable fecundity (phyllosoma number at hatch) in captivity was 45% of that expected from fisheries estimates and may indicate a reduction in fecundity associated with captivity, an area identified as requiring further dedicated studies. Size at onset of maturity was correlated with morphometric changes to male leg length and female abdominal segment width, providing non-destructive correlates for determining maturity in both males and non-ovigerous females. The ability of juvenile Artemia, the predominant food source of cultured J. edwardsii phyllosoma larvae, to assimilate a range of enrichment products was assessed. The nutritional factors targeted were those credited with improving larval competency in crustaceans and included lipids and the development of a protocol for enrichment with ascorbic acid (AA). These live feed studies demonstrated that both lipid and AA (particulate form) are assimilated by juvenile Artemia (at >1% of Artemia dw for AA) concomitant with enrichment concentrations, and maintained with short-term starvation. The lipid assimilation ability of juvenile Artemia was examined in relation to the loss of gut content, a common occurrence during the external mastication process of J. edwardsii larval feeding. Gut content did not make a significant contribution to total Artemia profiles shortly after the cessation of enrichment meaning any subsequent loss that may occur during feeding would not significantly alter Artemia nutritional profiles. It is considered that juvenile Artemia, like smaller metanauplii are powerful a tool for the delivery of specialized enrichment products. Dietary influences on the maternal lipid and fatty acid digestive gland (storage), ovary (maturation) and tail muscle profiles were examined during starvation and ovarian maturation and their roles examined in relation to the production of competent larvae. The digestive gland lipid content was high (70% dw) and dominated by triacylglycerol (energy source); it showed evidence of utilization during starvation but not during ovarian maturation. The digestive gland fatty acid profile resembled that of the diet, a fact that could be used to identify preferred wild lobster diets, i.e., through the use of dietary lipid signatures. A potential method to ascertain a range of beneficial nutritional products that may assist larval competence in wild caught larvae. The ovary and tail muscle were resilient to dietary changes in lipid or fatty acid profile, with the tail muscle approximating that of newly-hatched phyllosoma. This study demonstrated that J. edwardsii are effective in obtaining their lipid requirements in spite of minimal dietary input and reduces the emphasis on lipids and fatty acids in the nutrition of J. edwardsii broodstock. A study to ascertain the benefit of supplementary AA during broodstock maturation found that ovarian AA concentration was easily saturated, and in the absence of supplementation was sequestered from the tail muscle, the first time this has been considered as a significant AA store. There was minimal AA utilization during embryonic development, no improvement to broodstock fecundity or phyllosoma competency suggesting that there are no reproductive or larval competency benefits to providing supplementary AA to broodstock. In contrast, the delivery of mega-doses of AA to newly-hatched phyllosoma via juvenile Artemia resulted in large increases to larval AA content (161,2250g, g-1) and concomitant increases in larval survival (74%). This is the first time Artemia enrichment protocols have resulted in an improvement to larval survival. This thesis has identified factors which contribute to the production of competent phyllosoma larvae; a dietary mix of live and pellet feed is sufficient to supply the lipid and AA requirements of broodstock, large females producing large eggs and phyllosoma should be targeted as broodstock, while incubation should be conducted under conditions of ambient temperature. The development of an activity test is an effective tool that provides a quick and easy determination of larval competency at hatch, capable of enhancement by feeding with juvenile Artemia supplemented with a particulate form of AA. Adoption of these procedures should ensure the most competent larvae are available to improve the success of phyllosoma larval rearing in the spiny lobster J. edwardsii.

Antarctic krill use a variety of strategies to cope with, and thrive in the highly variable Southern Ocean environment. Despite much detailed information on its basic biology produced so far, the linkages between krill populations and the environment are yet to be systematically investigated. There is a practical need to have standardised indicators to assess the 'condition' of krill in relation to seasonal cycles and shifts in physical regimes and this study has aimed to develop such indicators. The level of nucleic acids in abdominal tissue was determined as an estimator of growth rates of individual krill that could otherwise only be obtained by on-board experiments. The dynamics of the major digestive organ, the digestive gland, in its size, protein and lipid content and enzyme activities, were examined in relation to changing food regimes. The potential of using eye diameter as a long-term starvation indicator was also examined. The amount of RNA and RNA:DNA ratio in krill muscle exhibited a significant relationship with individual growth rates, although the predictability was only modest. This was the case with both field-caught specimens and experimental juveniles. RNA-based indices were clearly different between well-fed, high-growth krill and underfed low-growth krill, and the RNA content levelled off when the growth rates became negative. The moult cycle had no significant effect on nucleic acid content. Overall, the content of nucleic acids varied considerably between individuals. Starved krill also tended to have higher DNA per unit biomass, which implies shrinkage of cells rather than loss of cells. The experimental krill showed a rapid response to the food conditions in their growth rates, either in a positive or negative direction, well within a single moult cycle. The digestive enzyme activities in the digestive gland of field-caught adults decreased considerably during one week of starvation. The size of the gland decreased substantially both in length and weight, accompanied by a loss of lipid and protein, with the former being more readily utilised. In a laboratory experiment where juvenile krill were alternately fed and starved, the digestive enzyme activities changed in response to the food regime. These changes largely mirrored the mass gain and loss of the digestive glands. The gland size-specific activities of digestive enzymes showed no consistent trends even after a long period of starvation. When the food supply was resumed, the gland regained its mass and enzyme activities. The digestive gland appears to serve as a reserve, which can provide against a few days' starvation and be rebuilt relatively quickly. Its size showed a prompt and steady response to short-term changes in feeding regime, proving a reliable indicator of recent feeding activities. By tracking individuals over time and examining specimens sampled as groups, it was demonstrated that fed and starved krill are distinguishable by the relationship between the eye diameter and body length. The eye diameter of starved krill did not decrease even when the animals were shrinking in overall body length. The eye digmeter of well-fed krill continued to increase as overall length increased. This created a distinction between fed and starved krill while no simultaneous separation was detected in terms of the body length to weight relationship. It would take approximately 2 moult cycles of shrinkage or more at modest rates for the eye diameter to body length relationship to significantly change. Whether this feature is manifested in the wild would be best seen at the end of winter, after the most likely period of extended food limitation. Nucleic acid content has only limited predictive power as an estimator of growth rates. Growth rates measured by the 'instantaneous growth rate' technique are still the best representation of in situ growth, which is determined by the condition during the period since the last moult. The size of the digestive gland of krill, a crucial short-term storage organ, was more responsive to food condition than enzyme activities. The gland size is a result of feeding activities over the past few weeks and will not be affected by immediate past events such as cod-end feeding. The digestive gland size should, at least, be a simple measure of whether krill have recently undergone severe, sustained food shortage. Long-term, seasonal starvation and the shrinkage it caused over a few moult cycles can be seen in the body length to eye diameter relationship more obviously than the traditional body length to weight relationship. This suite of measurements will provide a matrix of methods to determine the 'condition' of krill, in time scales from a week to a few months. These techniques are now ready for repeated measurements in the field over wider temporal and spatial extent to examine their applicability and to contribute to unravelling the outstanding questions in krill biology.

Striped trumpeter, Latris lineata (Forster), are being experimentally cultured by the Tasmanian Aquaculture and Fisheries Institute (TAFI) at Taroona, Hobart, Tasmania, Australia. Fish that survive beyond 30 days develop nervous aberrations associated with a severe granulomatous meningoencephalomyelitis. The myxozoan parasite Pentacapsula neurophila was described as the parasite causing the disease in the striped trumpeter juveniles. Molecular Bayesian phylogenetic analysis using small subunit ribosomal DNA (ssu rDNA) gene sequence and the covariotide evolutionary model, has shown P. neurophila to reside firmly within the clade comprised of Kudoa species, histozoic parasites of fish from the order Multivalvulida with 4 or more shell valves containing polar capsules. This has provided molecular evidence resulting in the proposed new combination of the Kudoidae to include this Pentacapsula species. A polymerase chain reaction (PCR) diagnostic assay was developed from the ssu rDNA gene sequence to detect Kudoa neurophila (formerly known as Pentacapsula neurophila). The assay is sufficiently species specific and sensitive enough to detect a small fragment of the parasite ssu rDNA gene (0.1 spore or 60 fg DNA or 4 spores g-1 /25 microlitres PCR reaction). Specifically, the test is capable of detecting early stages of the life cycle within the fish host and consequently diagnosing an infection not normally detected using histology. The PCR test can also be used to screen water supplies and prey cultures throughout the hatchery system to determine bio-security efficacy, assist in epizootiology studies, identify infected alternative or other primary hosts indicating the location of the disease reservoir, and enable a targeted approach to disease prevention in an aquaculture situation. Histology and in situ hybridisation techniques were incorporated into the study of the histopathology of the disease caused by this parasite to elucidate its entry point on the fish host and migratory pathway to terminal stage sporulation. Kudoa neurophila enters the fish via epithelial cells as early as 25 days post hatch (dph). Parasite cells then appear within plasmodia in skeletal muscle tissue between 50-80 dph. This appears to be the first key proliferation stage which is followed by another plasmodial stage in the peripheral nerve pathways near the spinal cord (70-115 dph). It is during this stage that clinical signs of the disease, such as whirling, become apparent. The presporogonic cells then enter the spinal cord where terminal stage sporulation occurs throughout the brain and spinal cord (105-130 dph) causing acute pathology, eventually resulting in the death of the animal. The information gained from the research conducted in this thesis, along with incorporated epizootiology studies, form the foundation of understanding that has assisted the hatchery management team to make informed health management decisions with an outlook to produce healthy juvenile striped trumpeter for on-going research into the development of this species for marine sea cage aquaculture.

This thesis examines the development of sustainability indicator systems (SIS) as a tool to implement the concept of sustainability into fisheries management. This research focuses upon the identification and evolution of these systems, their application as a management tool, and their response to problems in fisheries sustainability. The thesis presents a series of ten case studies that outline differing approaches to developing SIS in marine capture fisheries. These national, regional and non government case studies provide an opportunity to strategically assess and evaluate the use of SIS in fisheries management. The United Nations Conference on Environment and Development in 1992 addressed sustainable development as a means to satisfy the needs of human societies within the constraints presented by natural systems. Over the last ten years, sustainable development has been adopted by local, regional, national, and international institutions and instruments. Implementing and operationalising the concept of sustainable development has, however, provided significant challenges. Marine capture fisheries witnessed rapid development in the second half of the 20th Century. As pressure increases on capture fisheries, it is important that measures are introduced to ensure sustainable use of such fisheries. These measures include methodologies and frameworks for the assessment and management of fisheries incorporating biological, environmental, economic and socio-political relationships - the core of sustainable development. This thesis examines the viability of sustainability indicators as a tool for assessing progress towards sustainability. Indicator systems have been implemented across a range of fisheries jurisdictions with varying degrees of success. In assessing SIS in practice, several key components were distilled from the case studies and the assessment framework. The research demonstrates that SIS are used in national environmental reporting and fisheries specific systems across a range of legal and policy contexts, can link directly to the fisheries management process, and focus at the scale of fishery operations. Target species indicators are well advanced in SIS practice, ecosystem indicators are being rapidly developed and tested, and socio-economic and governance indicators require further progress. In terms of addressing sustainability outcomes, SIS are shown to facilitate scientific and policy coordination, increase transparency, accountability and co-management, increase the participation of environmental and non-government organisations, and provide the structure to implement ecosystem based management and precautionary approaches. While some SIS have been successful in developing measurement frameworks, criteria, objectives and indicators and adapting to specific policy contexts, further progress is required in developing reporting protocols, visualisation tools and aggregation methods.

Several major reviews have recently highlighted the interest amongst life scientists in understanding the ecological and evolutionary significance of animal personality traits (e.g., Wilson 1998; Gosling 2001; Sih et al. 2004a). The term personality trait as it is used here simply refers to consistent individual differences in an animal's behavioural style (as opposed to its discrete acts), and therefore, represent a potential suite of behavioural traits that can describe behavioural individuality in animals. Using personality descriptors such as shyness-boldness, activity, etc., has the advantage in that we can describe holistic, aggregate behaviour of animals that may be important for selection between individuals. Understanding how animal personalities interact with life history strategies may help explain how individuals make-up populations, an important issue in evolutionary and population ecology. While intuitively appealing, our knowledge of how intra-population individual differences in behaviour influence life histories is in its infancy (Wilson 1998). Cephalopods are well-known for their inter-individual variation in several key life history traits (e.g. growth and age-at-maturity), represent important commercial species in a number of worldwide fisheries, and also display complex individual behaviours (Sinn et al. 2001). Through a series of four experiments this project investigated personality traits in squid and their biological and ecological consequences. Four traits (shy-bold, activity, reactivity, and bury persistence) were identified across two ecologically important contexts in wild-caught adult squid. Trait expression was sex-independent, context-specific (i.e. bold squid in threat tests were not necessarily bold in feeding ones), and was related to body size and reproductive maturity. There was high individual variability in developmental processes associated with all traits, but some of this variation was partially explained by context, age, and developmental groups of squid. A quantitative genetic study was undertaken to describe the genetic structure of traits, in order to understand the potential for traits to respond to selection as well as provide a genotypic basis to understand potential fitness-related processes. In general, there were significant patterns of additive genetic variance for threat traits but not their feed counterparts, while age-related patterns of heritability indicated age-specific genetic expression for traits in both contexts. Reproductive experiments indicated no direct relationship between a female squid's personality and her short-term fitness, but an individual's levels of feeding boldness did have consequences for its subsequent success in mate pairings. Finally, a three year field study examined the frequencies of personality phenotypes across two populations in relation to density, body size, and sex ratios of squid within each population. Observations indicated differences between years and populations in mean change and patterns of frequencies of behavioural phenotypes, but these changes appeared to be independent of patterns in population body size and sex-ratio. This study is a first attempt to relate individualized behaviour to life history variables in a cephalopod mollusc, and the results should contribute to our knowledge of how individuals make up populations, a process that is of importance to a number of life sciences, including behavioural, population, fisheries and evolutionary ecology.

A study was initiated to determine the effect of selected factors on the reproductive development and early life history of blacklip (Haliotis rubra) and greenlip (H. laevigata) abalone relevant to their wild fisheries or aquaculture. In both species, the rate of gonadal and larval development was proportional to water temperature, but the relationship was not simply multiplicative, rather there was a critical minimum water temperature below which development was arrested, known as the Biological Zero Point (BZP). The BZP for gonadal development was 7.8 degrees C for H. rubra and 6.9 degrees C for H. laevigata. Corresponding BZP values for larval development were 7.8 degrees C and 7.2 degrees C, respectively. Observations of larval development relative to temperature enabled a description of the Effective Accumulative Temperature (EAT; the cumulative difference between the culture temperature and the BZP, calculated hourly) for prominent developmental stages. The difference between the EAT for metamorphic competence and that for hatchout (i.e. the interval during which the larvae remain in the water column) was 1120 and 1160 EAT degrees C-h for blacklip and greenlip abalone, respectively. These values, in combination with water temperature data, enable the prediction of the dispersal window for each species in situ. Spawning performance of blacklip and greenlip abalone was also affected by temperature, with both sexes of each species producing significantly more gametes when conditioned at 16 degrees C than 18 degrees C. Sperm production of H. rubra was an order of magnitude greater than that of equivalent sized H. laevigata. There was no apparent difference in the lipid or fatty acid composition of the ovary or testis between pre- and post-spawning animals of either species, presumably because of partial spawning and/or incomplete resorption of the gonad. Likewise, a 4 degrees C difference in conditioning temperature (i.e. 14 degrees C vs 18 degrees C) was insufficient to elicit changes in tissue biochemistry. There was a significant interaction between sperm density and contact time on the fertilisation success of eggs from both blacklip and greenlip abalone. Prolonged exposure (> 1200 s for H. rubra and > 480 s for H. laevigata) to concentrated sperm (i.e. 107 ml-1) resulted in egg destruction. Analysis of CoVariance of F50 values (i.e. the sperm concentration required for 50% fertilisation, derived from the linear regression of logit (proportion of eggs fertilised) versus sperm density) between species across a range of contact times demonstrated that contact time had a significant effect (p < 0.001) whereas species did not (p = 0.22). The lack of a species effect suggests that the fertilisation potential of blacklip and greenlip abalone eggs are similar, at least across the range of sperm densities and contact times used.

This thesis documents research on two aspects of the biology of the giant crab Pseudocarcinus gigas: the development, behaviour, and rearing of the larvae; and the reproductive biology of both sexes. Larvae were reared from hatch to juvenile crabs. The larval development of 5 zoeal and one megalopal stages were described which permitted identification of P. gigas larvae from plankton samples. Samples from different depths were sorted to obtain information on vertical migration patterns, although few P. gigas larvae were collected. Vertical migration was further investigated in experiments which analysed the swimming response to gravity, light intensity, change in light intensity, light wavelength, change in pressure, current, temperature, and thermoclines. Response to temperature involved a feed-back mechanism that positioned larvae at temperatures optimal for growth, survival, and metamorphosis to megalopa (14-16C). Light intensity and photoperiod had little effect on survival although larvae reached megalopa most rapidly with long photoperiod and high intensity and were smaller in continuous darkness treatments. Cannibalism of stage 1 and 2 zoeas was highest with long photoperiod and low intensity. Mycosis and epibiotic fouling of larvae necessitated trials with prophylactic treatments. Survival was highest with a broad spectrum antibiotic (oxytetracyline) while promising results were obtained with carbendazim and copper oxychloride. Suitable concentrations for indefinite baths were established by monitoring toxic effects as increased mortality, deformity, prolonged intermoult, or death during moulting. The male reproductive tract is typical of brachyurans with ovoid, enveloped, spermatophores stored in the mid vas deferens (MVD). Males pass through three morphological stages (of chela development) and individuals from all three stages had spermatophores in the MVD. Mating pairs were never observed but patterns of limb loss indicate that mating involves female-centred competition. Females appear to mate while soft-shelled with stored sperm remaining viable for at least four years. Broods are produced annually although females occasionally skip a reproductive season, which may be associated with moulting. Several broods may be produced between moults although fecundity declines with successive broods. The hepatopancreas underwent little change in composition during gonadogenesis. Fecundity increased with female size, although not in a simple cubic (volumetric) relationship as larger females produced larger eggs. This increase in egg size was associated with a significant, albeit small, decrease in protein and carotenoid, and an increase in moisture, while lipid appeared unaffected. Protein was used preferentially to lipid during embryogenesis. Techniques for immobilising, humanely killing, and internal imaging of crabs were employed for research on reproduction and are described.

Arthropod parasites and micropredators, such as ticks and mosquitoes, influence terrestrial ecosystems and harm their hosts directly and indirectly by vectoring micro-organisms. Whether micropredators similarly affect marine ecosystems and hosts is not well understood. In coral reef fish communities, the most abundant micropredators are isopods, in particular, gnathiids. Our understanding of how isopods affect fishes has been restricted by a lack of information regarding basic isopod biology including; patterns of abundance, parasite identity, host specificity and host pathology. Also it is unknown if small juvenile fish are parasitised by isopods, and if this affects their survival. Sequentially, the aims of my PhD thesis were to understand the ecology of several lesser known parasites in sufficient detail to perform manipulative experiments that could test the effects of micropredation on small juvenile reef fish. All field studies took place at Lizard Island, Great Barrier Reef My first study aimed to describe temporal and spatial patterns of isopod abundance by measuring emergence rates. Gnathiid isopod juveniles emerge from the benthos into the water column to find hosts or change locations. Although diel patterns have been demonstrated, the relationship between substrate and emergence on coral reefs is not clear. I measured emergence rates of parasitic isopods (Gnathiidea and Flabellifera) in 6 “habitats” at 2 very different sites at Lizard Island. Isopods were collected from the periphery and centres of 3 sizes of reef, and from the substrate between these reefs (sand or rubble). At both sites, the most abundant gnathiid species (Gnathia falcipenis and Gnathia sp C), was exclusive to that site. Although strong diel patterns in emergence were observed, gnathiid abundance could not be predicted by habitat. However, gnathiids were larger and more often fed over reef borders than in the centres of reefs. To explain these patterns, I suggested that first stage larvae had the largest influence on total abundance and were patchily distributed in accordance with adults from which they had recently hatched. As later stage larvae also depend on fish, more successful (fed and older larvae) are found on the edges of reefs where appropriate hosts may be more abundant. Gnathiids were over-dispersed in all habitats investigated, including apparently homogeneous beds of coral rubble and sand. This indicated that gnathiid distribution may be better predicted by very fine scale differences in substrate, or that larvae are simply gregarious, and that abundance may be difficult to predict on the basis of substrate. Without reliable differences in parasite abundance among habitats at Lizard Island, subsequent studies would rely on manipulating parasite abundance via excluding wild parasites in the field (which proved very difficult) or by controlling abundance in laboratory simulations. I then investigated host specificity in the 2 most abundant gnathiid species from the previous study. Discrete species distributions between the two sites suggested that the 2 parasites may have had different diets. Host-specificity data for gnathiid isopods are scarce because the parasitic juvenile stages are difficult to identify and host-parasite contact is often brief. Engorged third stage gnathiids were photographed and permitted to moult into adults to allow identification. I compared mtDNA sequences from their blood meals to host sequences available on GenBank. The host frequency distributions used by each species were significantly different; only four host families were shared. I concluded that G. falcipenis and Gnathia sp C operate as preferential feeders. Importantly, this work showed that G. falcipenis was indeed a natural parasite of several species of damselfish (Pomacentridae) that could be collected as young recruits and used in manipulative experiments. I then used G. falcipenis as a model parasite to investigate the effects of isopods on recently recruited Dischistodus perspicillatus and small juvenile Acanthochromis polyacanthus damselfishes. Working with honours student Ms Rose Penfold, we determined that A. polyacanthus was infected by gnathiids in the wild at sizes as small as 4.2 mm SL. Laboratory infections revealed that larger A. polyacanthus were much better at eating gnathiids, a behaviour which prevented infection, and that smaller fish were more likely to die post-infection. Infection prevalence was > 3 % during the day, but we could not sample fish for nocturnal infection prevalence. A caging experiment suggested that most micropredation on damselfish took place at night. For D. perspicillatus, I found that exposure to 2 parasites each evening for 7 nights after settlement halved the growth of these fish. Lastly, numerous free-swimming cymothoid isopods were found associated with larval fish in light traps. Cymothoids have a multi-morphic life cycle composed of micropredatory stages that eventually become females, which are permanently attached to fishes. Because cymothoid taxonomy is based around female morphology, natatory-stage cymothoids can not be identified. I sequenced mtDNA from natatory and adult female life history stages and matched 4 of 11 natatory cymothoid morphotypes. Molecular data were also used to produce a phylogeny exploring the evolution of different forms of host attachment within the Cymothoidae. This phylogeny suggests that external attachment, formerly thought to be plesiomorphic, is a derived condition and has evolved several times independently. I suggest that attachment to the buccal cavity or gills is a primitive form of attachment. This research has provided information on emergence patterns and hostspecificity which is necessary for the future study of isopod vector biology. It also provides a platform for future taxonomic and phylogenetic studies on cymothoids. I demonstrate that gnathiids infect juvenile coral reef fish and suggest that they may influence survival both directly and indirectly by reducing growth and predisposing infected fish to size-selective mortality. Thus, interactions between isopod micropredators and recruiting fishes may determine the survivorship of individual fish and influence the subsequent community structure.

The NPF is one of the Australian Commonwealth’s most valuable fisheries. The species groups targeted include tiger, banana and endeavour prawns. The fishery is managed using input controls and, from 2001 until 2004 (the period which spans this study), the agreed target was for the level of fishing effort expended to lead to a 70% chance (or greater) that the spawning stock size of tiger prawns was at or above that corresponding to Maximum Sustainable Yield, SMSY. A key issue in the management of this fishery is that the efficiency of fishing effort is continually increasing so that past effort reductions have been fully offset by improved efficiencies. In fact, some past effort reductions did not actually lead to a real reduction in effective effort. As a consequence of this, there was no recovery in the size of the tiger prawn resource but rather, in some years, a decline, until a major effort reduction program was implemented in 2001.

Arthropod parasites and micropredators, such as ticks and mosquitoes, influence terrestrial ecosystems and harm their hosts directly and indirectly by vectoring micro-organisms. Whether micropredators similarly affect marine ecosystems and hosts is not well understood. In coral reef fish communities, the most abundant micropredators are isopods, in particular, gnathiids. Our understanding of how isopods affect fishes has been restricted by a lack of information regarding basic isopod biology including; patterns of abundance, parasite identity, host specificity and host pathology. Also it is unknown if small juvenile fish are parasitised by isopods, and if this affects their survival. Sequentially, the aims of my PhD thesis were to understand the ecology of several lesser known parasites in sufficient detail to perform manipulative experiments that could test the effects of micropredation on small juvenile reef fish. All field studies took place at Lizard Island, Great Barrier Reef My first study aimed to describe temporal and spatial patterns of isopod abundance by measuring emergence rates. Gnathiid isopod juveniles emerge from the benthos into the water column to find hosts or change locations. Although diel patterns have been demonstrated, the relationship between substrate and emergence on coral reefs is not clear. I measured emergence rates of parasitic isopods (Gnathiidea and Flabellifera) in 6 “habitats” at 2 very different sites at Lizard Island. Isopods were collected from the periphery and centres of 3 sizes of reef, and from the substrate between these reefs (sand or rubble). At both sites, the most abundant gnathiid species (Gnathia falcipenis and Gnathia sp C), was exclusive to that site. Although strong diel patterns in emergence were observed, gnathiid abundance could not be predicted by habitat. However, gnathiids were larger and more often fed over reef borders than in the centres of reefs. To explain these patterns, I suggested that first stage larvae had the largest influence on total abundance and were patchily distributed in accordance with adults from which they had recently hatched. As later stage larvae also depend on fish, more successful (fed and older larvae) are found on the edges of reefs where appropriate hosts may be more abundant. Gnathiids were over-dispersed in all habitats investigated, including apparently homogeneous beds of coral rubble and sand. This indicated that gnathiid distribution may be better predicted by very fine scale differences in substrate, or that larvae are simply gregarious, and that abundance may be difficult to predict on the basis of substrate. Without reliable differences in parasite abundance among habitats at Lizard Island, subsequent studies would rely on manipulating parasite abundance via excluding wild parasites in the field (which proved very difficult) or by controlling abundance in laboratory simulations. I then investigated host specificity in the 2 most abundant gnathiid species from the previous study. Discrete species distributions between the two sites suggested that the 2 parasites may have had different diets. Host-specificity data for gnathiid isopods are scarce because the parasitic juvenile stages are difficult to identify and host-parasite contact is often brief. Engorged third stage gnathiids were photographed and permitted to moult into adults to allow identification. I compared mtDNA sequences from their blood meals to host sequences available on GenBank. The host frequency distributions used by each species were significantly different; only four host families were shared. I concluded that G. falcipenis and Gnathia sp C operate as preferential feeders. Importantly, this work showed that G. falcipenis was indeed a natural parasite of several species of damselfish (Pomacentridae) that could be collected as young recruits and used in manipulative experiments. I then used G. falcipenis as a model parasite to investigate the effects of isopods on recently recruited Dischistodus perspicillatus and small juvenile Acanthochromis polyacanthus damselfishes. Working with honours student Ms Rose Penfold, we determined that A. polyacanthus was infected by gnathiids in the wild at sizes as small as 4.2 mm SL. Laboratory infections revealed that larger A. polyacanthus were much better at eating gnathiids, a behaviour which prevented infection, and that smaller fish were more likely to die post-infection. Infection prevalence was > 3 % during the day, but we could not sample fish for nocturnal infection prevalence. A caging experiment suggested that most micropredation on damselfish took place at night. For D. perspicillatus, I found that exposure to 2 parasites each evening for 7 nights after settlement halved the growth of these fish. Lastly, numerous free-swimming cymothoid isopods were found associated with larval fish in light traps. Cymothoids have a multi-morphic life cycle composed of micropredatory stages that eventually become females, which are permanently attached to fishes. Because cymothoid taxonomy is based around female morphology, natatory-stage cymothoids can not be identified. I sequenced mtDNA from natatory and adult female life history stages and matched 4 of 11 natatory cymothoid morphotypes. Molecular data were also used to produce a phylogeny exploring the evolution of different forms of host attachment within the Cymothoidae. This phylogeny suggests that external attachment, formerly thought to be plesiomorphic, is a derived condition and has evolved several times independently. I suggest that attachment to the buccal cavity or gills is a primitive form of attachment. This research has provided information on emergence patterns and hostspecificity which is necessary for the future study of isopod vector biology. It also provides a platform for future taxonomic and phylogenetic studies on cymothoids. I demonstrate that gnathiids infect juvenile coral reef fish and suggest that they may influence survival both directly and indirectly by reducing growth and predisposing infected fish to size-selective mortality. Thus, interactions between isopod micropredators and recruiting fishes may determine the survivorship of individual fish and influence the subsequent community structure.