Geographical and morphological variation within and between colour phases in Coris julis (L. 1758), a protogynous marine fish

The possible differences between sexes in patterns of morphological variation in geographical space have been explored only in gonochorist freshwater species. We explored patterns of body shape variation in geographical space in a marine sequential hermaphrodite species, Coris julis (L. 1758), analyzing variation both within and between colour phases, through the use of geometric morphometrics and spatially-explicit statistical analyses. We also tested for the association of body shape with two environmental variables: temperature and chlorophyll a concentration, as obtained from time-series of satellite-derived data. Both colour phases showed a significant morphological variation in geographical space and patterns of variation divergent between phases. Although the morphological variation was qualitatively similar, individuals in the initial colour phase showed a more marked variation than individuals in the terminal phase. Body shape showed a weak but significant correlation with environmental variables, which was more pronounced in primary specimens.

Body shape variation and colour change during growth in a protogynous fish

Protogynous sequential hermaphroditism is very common in marine fish. Despite a large number of studies on various aspects of sequential hermaphroditism in fish, the relationship between body shape and colour during growth in dichromatic species has not been assessed. Using geometric morphometrics, the present study explores the relationship between growth, body shape and colouration in Coris julis (L. 1758), a small protogynous labrid species with distinct colour phases. Results show that body shape change during growth is independent of change in colour phase, a result which can be explained by the biology of the species and by the social control of sex change. Also, during growth the body grows deeper and the head has a steeper profile. It is hypothesized that a deeper body and a steeper profile might have a function in agonistic interactions between terminal phase males and that the marked chromatic difference between colour phases allows the lack of strict interdependence of body shape and colour during growth.

The gut microbial community of midas cichlid fish in repeatedly evolved limnetic-benthic species pairs

Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.

Quantifying the state of populations and effects of disturbances at large spatio-temporal scales: The case of coral populations in the great barrier reef

This project was a step forward in applying statistical methods and models to provide new insights for more informed decision-making at large spatial scales. The model has been designed to address complicated effects of ecological processes that govern the state of populations and uncertainties inherent in large spatio-temporal datasets. Specifically, the thesis contributes to better understanding and management of the Great Barrier Reef.

Chlamydial infections of fish: Diverse pathogens and emerging causes of disease in aquaculture species

Chlamydial infections of fish are emerging as an important cause of disease in new and established aquaculture industries. To date, epitheliocystis, a skin and gill disease associated with infection by these obligate intracellular pathogens, has been described in over 90 fish species, including hosts from marine and fresh water environments. Aided by advances in molecular detection and typing, recent years have seen an explosion in the description of these epitheliocystis-related chlamydial pathogens of fish, significantly broadening our knowledge of the genetic diversity of the order Chlamydiales. Remarkably, in most cases, it seems that each new piscine host studied has revealed the presence of a phylogenetically unique and novel chlamydial pathogen, providing researchers with a fascinating opportunity to understand the origin, evolution and adaptation of their traditional terrestrial chlamydial relatives. Despite the advances in this area, much still needs to be learnt about the epidemiology of chlamydial infections in fish if these pathogens are to be controlled in farmed environments. The lack of in vitro methods for culturing of chlamydial pathogens of fish is a major hindrance to this field. This review provides an update on our current knowledge of the taxonomy and diversity of chlamydial pathogens of fish, discusses the impact of these infections on the health, and highlights further areas of research required to understand the biology and epidemiology of this important emerging group of fish pathogens of aquaculture species.

Milling innovations at Rocky Point

This paper reviews the innovations that have been introduced in the milling train at Rocky Point mill since 2001 and provides some operational, performance and maintenance comparisons of the technologies in use. The decision to install BHEM mills in the #2 and #3 mill positions to complement the six-roll mills in the #1 and #4 mill positions has proven a good one. Satisfactory performance is being obtained by these mills while maintenance costs are significantly less. Very good #1 mill extraction and final bagasse moisture content are being achieved. The innovation of using Hägglunds hydraulic drives at higher speed…

Prediction of the fate of oxytetracycline and oxolinic acid in a fish pond using simulation model: A preliminary study

The fate of two popular antibiotics, oxytetracycline and oxolinic acid, in a fish pond were simulated using a computational model. The VDC model, which is designed based on a model for predicting pesticide fate and transport in paddy fields, was modified to take into account the differences between the pond and the paddies as well as those between the fish and the rice plant behaviors. The pond conditions were set following the typical practice in South East Asia aquaculture. The two antibiotics were administered to the animal in the pond through medicated feed during a period of 5 days as in actual practice. Concentrations of oxytetracycline in pond water were higher than those of oxolinic acid at the beginning of the simulation. Dissipation rate of oxytetracycline is also higher as it is more readily available for degradation in the water. For the long term, oxolinic acid was present at higher concentration than oxytetracycline in pond water as well as pond sediment. The simulated results were expected to be conservative and can be useful for the lower tier assessment of exposure risk of veterinary medicine in aquaculture industry but more data are needed for the complete validation of the model.

Kissing fish: Rex Hunt, popular culture, sustainability and fishing practices

Natural resource managers and scientists focus on the behaviour of individual recreational fishers to understand environmental problems associated with this leisure activity. They do this in an effort to identify ways to change attitudes in order to facilitate environmentally friendly choices. This applied use of ABC psychology (attitude, behaviour, choice) has not delivered the expected results. This article offers a different approach by investigating an emergent practice in diverse fishing communities, rather than looking to the responsibility of the individual recreational fisher. Using practice theory, I trace the change from take-all to catch-and-release fishing in Australia by analysing the texts of celebrity fisher Rex Hunt, who is an advocate for releasing fish. I combine this with oral history testimony from a sample of recreational fishers from the broader Australian community to show how change happened. The practice of catch-and-release fishing emerged through the combination of sociotechnical and historically specific elements present in popular culture, including the media. Paying attention to the way different elements catalyse provides a rich account of the changing modes of sustainability in recreational fishing communities.

Managing the impacts of sugarcane farming on the Great Barrier Reef: An evaluation of the implementation of the Polluter Pays Principle

This report provides an evaluation of the implementation of the Polluter Pays Principle (PPP) – a principle of international environmental law – in the context of pollution from sugarcane farming affecting Australia’s Great Barrier Reef (GBR). The research was part of an experiment to test methods for evaluating the effectiveness of environmental laws. Overall, we found that whilst the PPP is reflected to a limited extent in Australian law (more so in Queensland law, than at the national level), the behaviour one might expect in terms of implementing the principle was largely inadequate. Evidence of a longer term, explicit commitment to the PPP was particularly weak.

An extended regression approach to estimating loads and their uncertainties in Great Barrier Reef catchments

There are numerous load estimation methods available, some of which are captured in various online tools. However, most estimators are subject to large biases statistically, and their associated uncertainties are often not reported. This makes interpretation difficult and the estimation of trends or determination of optimal sampling regimes impossible to assess. In this paper, we first propose two indices for measuring the extent of sampling bias, and then provide steps for obtaining reliable load estimates by minimizing the biases and making use of possible predictive variables. The load estimation procedure can be summarized by the following four steps: - (i) output the flow rates at regular time intervals (e.g. 10 minutes) using a time series model that captures all the peak flows; - (ii) output the predicted flow rates as in (i) at the concentration sampling times, if the corresponding flow rates are not collected; - (iii) establish a predictive model for the concentration data, which incorporates all possible predictor variables and output the predicted concentrations at the regular time intervals as in (i), and; - (iv) obtain the sum of all the products of the predicted flow and the predicted concentration over the regular time intervals to represent an estimate of the load. The key step to this approach is in the development of an appropriate predictive model for concentration. This is achieved using a generalized regression (rating-curve) approach with additional predictors that capture unique features in the flow data, namely the concept of the first flush, the location of the event on the hydrograph (e.g. rise or fall) and cumulative discounted flow. The latter may be thought of as a measure of constituent exhaustion occurring during flood events. The model also has the capacity to accommodate autocorrelation in model errors which are the result of intensive sampling during floods. Incorporating this additional information can significantly improve the predictability of concentration, and ultimately the precision with which the pollutant load is estimated. We also provide a measure of the standard error of the load estimate which incorporates model, spatial and/or temporal errors. This method also has the capacity to incorporate measurement error incurred through the sampling of flow. We illustrate this approach using the concentrations of total suspended sediment (TSS) and nitrogen oxide (NOx) and gauged flow data from the Burdekin River, a catchment delivering to the Great Barrier Reef. The sampling biases for NOx concentrations range from 2 to 10 times indicating severe biases. As we expect, the traditional average and extrapolation methods produce much higher estimates than those when bias in sampling is taken into account.

Tropical prawn trawl bycatch of fish and seasnakes reduced by Yarrow Fisheye Bycatch Reduction Device

Reducing unwanted trawl bycatch is actively encouraged in Australia, particularly in prawn trawl fisheries. We tested the performance of a Bycatch Reduction Device, the Yarrow Fisheye, during two periods of commercial fishing operations in Australia's Northern Prawn Fishery, by comparing the catches of paired treatment and control nets. We compared the catch weights of the small fish and invertebrate bycatch, and the commercially important tiger prawns, from 42 trawls in 2002. The Yarrow Fisheye reduced the weight of small bycatch by a mean of 22.7%, with no loss of tiger prawn. We also compared the numbers of seasnakes caught in 41 and 72 trawls during the spring trawling seasons of 2004 and 2005, respectively. The Yarrow Fisheye reduced the catches by a mean of 43.3%. Flume-tank tests of the Yarrow Fisheye showed that this device created a slow water-flow region extending over 2 m downstream from its position in the net, and close to where the catch accumulates. Finfish and seasnakes may be exploiting this slow water-flow region to escape via the eye, Although the reductions in fish and seasnake bycatch were excellent, we think they could be further improved by relating differences in fisheye position and localised water displacements, to design and rigging changes.

Effects of fish density distribution and effort distribution on catchability

The effects of fish density distribution and effort distribution on the overall catchability coefficient are examined. Emphasis is also on how aggregation and effort distribution interact to affect overall catch rate [catch per unit effort (cpue)]. In particular, it is proposed to evaluate three indices, the catchability index, the knowledge parameter, and the aggregation index, to describe the effectiveness of targeting and the effects on overall catchability in the stock area. Analytical expressions are provided so that these indices can easily be calculated. The average of the cpue calculated from small units where fishing is random is a better index for measuring the stock abundance. The overall cpue, the ratio of lumped catch and effort, together with the average cpue, can be used to assess the effectiveness of targeting. The proposed methods are applied to the commercial catch and effort data from the Australian northern prawn fishery. The indices are obtained assuming a power law for the effort distribution as an approximation of targeting during the fishing operation. Targeting increased catchability in some areas by 10%, which may have important implications on management advice.

Sampling accuracy of reef resource inventory technique

A new technique called the reef resource inventory (RRI) was developed to map the distribution and abundance of benthos and substratum on reefs. The rapid field sampling technique uses divers to visually estimate the percentage cover of categories of benthos and substratum along 2x20 in plotless strip-transects positioned randomly over the tops, and systematically along the edge of reefs. The purpose of this study was to compare the relative sampling accuracy of the RRI against the line intercept transect technique (LIT), an international standard for sampling reef benthos and substratum. Analysis of paired sampling with LIT and RRI at 51 sites indicated sampling accuracy was not different (P > 0.05) for 8 of the 12 benthos and substratum categories used in the study. Significant differences were attributed to small-scale patchiness and cryptic coloration of some benthos; effects associated with sampling a sparsely distributed animal along a line versus an area; difficulties in discriminating some of the benthos and substratum categories; and differences due to visual acuity since LIT measurements were taken by divers close to the seabed whereas RRI measurements were taken by divers higher in the water column. The relative cost efficiency of the RRI technique was at least three times that of LIT for all benthos and substratum categories and as much as 10 times higher for two categories. These results suggest that the RRI can be used to obtain reliable and accurate estimates of relative abundance of broad categories of reef benthos and substratum.

Assessment of an environmentally friendly, semi-pelagic fish trawl

Minimising catches of non-target animals in a trawl fishery reduces the impact on a marine community and may help to sustain the fishery resource in the long term. Hence the desirability for trawls that minimise impacts on non-target species while maintaining catches of target species. This study resulted from a need to further develop easily handled, semi-pelagic style trawls for Australia's Northern Fish Trawl Fishery. In November 1993 we compared catches from three differently rigged versions of a demersal wing trawl: one fished in a standard demersal configuration with its footrope on the sea bed, and two fished semi-pelagically, with their footropes raised to either 0.4-0.5 or 0.8-0.9 m above the sea bed. At two sites in the northeast Gulf of Carpentaria, each trawl type was used on the same combination of sites, grids within sites and times of day. Catches of the main target species (Lutjanus malabaricus and Lutjanus erythropterus) by the three trawl types were not significantly different. However, the mean catches of both these species and of other commercially important snappers, were highest in the semi-pelagic trawl raised 0.4-0.5 m above the sea bed. This increase could be due to a larger trawl spread or to the whole rig fishing higher in the water column. Of the 107 species of fishes analysed, 61 were caught in greater abundance in the demersal trawl. Seven species were caught more effectively in the semi-pelagic trawl with the footrope 0.4-0.5 m above the substrate; none was caught most effectively with the footrope set at 0.8-0.9 m. Epibenthic byproduct species (squid and Thenus orientalis), fish bycatch, sponges and other epibenthic invertebrates were also caught in lower numbers in the semi-pelagic trawls. The semi-pelagic trawls convincingly caught less (in both numbers and biomass) of the unwanted species which are normally discarded. Semi-pelagic fish trawls of the types tested would be suitable for Australia's Northern Fish Trawl Fishery and probably other demersal trawl fisheries that would benefit from the conservation of non-target epibenthic communities.

Oh Holly, The Fish is Dead

From Kurt Vonnegut to Stephen King, many novelists use metanarrative techniques to insert fictional versions of themselves in the stories they tell. The function of deploying such techniques is often to draw attention to the liminal space between the fictional constructs inherent in the novel as a form, and the real world from which the constructs draw inspiration, and indeed, are read by an audience. For emerging writers working in short form narratives, however, the structural demands of the short story or flash fiction make the use of similar techniques problematic in the level of depth to which they can be deployed. ‘Oh Holly, the fish is dead’ is the fourth in a series of short stories that work to overcome the structural limitations of a succinct form by developing a fractured fictional version of the author over a number of pieces and published across a range of sites. The accumulative affect is a richer metanarrative textual arrangement that also allows for the individual short stories to function independently.