30 results

Trophodynamics of the GAB: assessing the need for an ecological allocation in the SA pilchard fishery

Project number: 2003-072
Project Status:
Completed
Budget expenditure: $420,690.00
Principal Investigator: Timothy M. Ward
Organisation: SARDI Food Safety and Innovation
Project start/end date: 30 Aug 2003 - 15 May 2005
Contact:
FRDC
SPECIES

Need

PIRSA Fisheries Policy Group and the SA pilchard industry have identified an understanding of the trophodynamic role of pilchards as a key management need for this fishery.

Strategic assessment of the fishery against ESD principles (e.g. Fletcher et al. 2002) is likely to identify the absence of knowledge of the ecological role of pilchards as a significant issue.

Provisions of the Commonwealth Environment and Biodiversity Conservation Act, and Environment Australia guidelines that require strategic assessment of the ecological impacts of fishing, including trophic impacts, are particularly relevant for large fisheries that target an important prey species, such as the SA pilchard fishery.

The potential trophic effects of fishing can be potentially overcome by establishing appropriate ecological allocations.

This project will collect, synthesize and interpret data on trophodynanamic processes in the GAB that are required to assess the need for an ecological allocation in the SA pilchard fishery.

The long-term project will also address the need for principles and guidelines to assessing the need for and size of ecological allocations in fisheries that may influence trophodynamic pathways and ecological interactions in ecosystems with high conservation value.

Objectives

1. To establish methods for estimating of primary and secondary production in eastern GAB.
2. To establish methods for measuring the importance of pilchards in the diets of key predators in the eastern GAB.
3. To establish methods for comparing the growth rates and reproductive success of these predators in areas/periods of high/low fishing pressure and pilchard abundance.
4. To establish a conceptual ecosystem model and develop a preliminary pelagic trophodynamic model for the eastern GAB.
5. To develop a proposal for comprehensive study to assess the need for an ecological allocation in the SA pilchard fishery.

Final report

ISBN: 0-9757182-0-7
Author: Tim Ward
Final Report • 2005-06-20
2003-072-DLD.pdf

Summary

Shelf waters off southern Australia support the world’s only northern boundary current ecosystem. Although there are some indications of intense nitrate enrichment in the eastern Great Australian Bight (GAB) arising from upwelling of Subantarctic Water, the biological consequences of these processes are poorly understood. We show that productivity in the eastern GAB is low during winter, but that coastal upwelling at several locations during the austral summer-autumn results in localised increases in surface chlorophyll-a concentrations and downstream enhancement of zooplankton biomass. Chlorophyll-a concentrations in the eastern GAB during summer-autumn are higher than those recorded in other parts of Australia, but within the lower portion of ranges observed during upwelling events in the productive eastern boundary current systems off California, Peru and southern Africa. Pilchard (Sardinops sagax) and anchovy (Engraulis australis) eggs and larvae were abundant and widely distributed in shelf waters of the eastern and central GAB in shelf waters during summer-autumn, with high densities occurring in areas with high zooplankton biomass. Egg densities and distributions support previous evidence, indicating that the spawning biomass of pilchard in South Australia is an order of magnitude higher than elsewhere in southern Australia and an order of magnitude lower than in the eastern boundary current systems. 
 
Two numerical models of the circulation and upwelling in the South Australian region were constructed. The first, a coarse resolution model (CRM), was designed to capture the equatorward Sverdrup transport that leads to the deep upwelling favourable Flinders Current. The average transports for the model period, December 1998-March 1999 (obtained using daily atmospheric forcing), compare favourably with estimates obtained from a summer-time climatology of a global ocean model. Within the CRM, a fine resolution model (FRM) was developed. This model has a very fine mesh and was able to resolve scales down to 2 km in the primary region of study: the mid-Bight to Robe. Along the open boundaries of the FRM, the velocities are specified using daily output from the CRM. In order to represent wind forced energy that is generated on the West Australian shelves, a coastal-trapped wave (CTW) “paddle” was added at the western boundary of the FRM (Esperance). This paddle is modulated using sea level observations from Esperance. A similar CTW paddle was introduced at the eastern boundary of the FRM, using sea level observations from Portland. Good agreement with coastal sea level data was obtained for signals in the 5-20 day (weather) band. These results were obtained using daily averaged atmospheric forcing fields. Preliminary results obtained using 6 hourly atmospheric fields, which include the sea breeze, also indicated that some of the 1-3 day variability could be accounted for and that more realistic, deeper surface mixed layers would result.
 
During a period of upwelling favourable winds, the model results indicated that water is drawn shorewards across the 200 m isobath in the SA Gulfs region. The coldest water (13oC) is upwelled from depths of 200 m and at sites to the south of Kangaroo Is and off Robe. Through bottom advection this water eventually spreads to the north-east and north-west of Kangaroo Is. The upwelling off the Eyre peninsula is identified to result from water upwelled to the south of Kangaroo Is. The surface signature of the upwelling compares favourably with satellite derived sea surface temperature (SST): plumes of cold 16oC water were advected to the north-west. For other regions the model SST was also in general agreement with the data except near the mid-Bight coastal region, where the model temperatures were too cool. The latter result supports the analysis above, that the coastal heating here is under-represented by the forcing fields.
 
A review of the literature has shown that population, breeding success and foraging patterns of land breeding marine predators such as seals and seabirds, are sensitive to changes in their marine environments and can be used as appropriate monitoring tools of ecosystem change, and fishery impacts. To undertake such studies, however, is not a simple exercise. It requires an understanding of the spatial and temporal variability in the ecosystem, trophic relationships between predators and prey and the distribution of foraging effort of predators so that discontinuities between the areas of potential anthropogenic impact and other areas can be understood and assessed. A suite of appropriate species, parameters and sites were identified to focus future research in this area.
 
We examined the potential suitability of a range and seal and seabird species to provide data on the spatial and temporal variability of their prey resources within and outside the main pilchard-fishing zone (PFZ) within the eastern GAB ecosystem. For each of these species we also assessed a range of population status, reproduction success and foraging parameters that could potentially be monitored at sites within and outside the PFZ. Each of these was discussed with respect to previous studies that had demonstrated their use, and the practical/logistic feasibility of undertaking such monitoring in a systematic fashion at a range of suitable sites.
 
A preliminary conceptual and trophodynamic model for the pelagic waters in the eastern GAB ecosystem was developed to describe and facilitate an understanding of the structure and dynamics of the food web in the region. An Ecopath model was developed that incorporated all available data. A preliminary conceptual food-web model was also developed, based on trophic levels and interactions. There was considerable uncertainty in many of the parameters and dietary profiles entered into the Ecopath model and as a consequence considerable adjustments were required in order to balance it. Most notable were adjustments to the dietary composition of fur seals (highest trophic level), and the biomass of little penguins and shearwaters. Additional modifications had to be made to the biomass of the tuna and kingfish/samsonfish groups, and it is likely that the modified parameters used were unrealistic. In addition, due to paucity of data, some species were amalgamated into groups that in future should be separated. Groups such as benthic and pelagic sharks have not been included. 
 
As this model is only in the developmental stage, it is not yet capable of providing quantitative predictions. It does, however, provide a useful framework within which the complex nature of trophic interactions between species groups can be conceptualised and importantly help to identify data-poor components. Already, this approach has revealed major gaps in data on the biomass of species groups and their trophic interactions, which will form the focus of studies to be undertaken as part of the long-term project, detailed in an FRDC proposal for funding 2005.

Optimising at-sea post harvest handling procedures for the pilchard (Sardinops sagax)

Project number: 2002-236
Project Status:
Completed
Budget expenditure: $261,534.00
Principal Investigator: John Carragher
Organisation: SARDI Food Safety and Innovation
Project start/end date: 29 Jun 2002 - 1 Aug 2006
Contact:
FRDC
SPECIES

Need

Two factories that process pilchards for bait and human consumption have recently been established in Port Lincoln, however a large proportion of the current harvest is still used to feed caged tuna (Ward et al. 2000; Davidson et al. 2000).

Over the last two years, considerable progress has been made towards the development of a manufactured feed for tuna mariculture. Skretting Australia has obtained successful outcomes from a pilot scale commercial trial. Research is increasingly focussing on matters relating to refinement (improved acceptance, better conversion rates) rather than on the identification of suitable feeds (S. Clarke, SARDI, pers. comm.). Over the next 2-3 years it is expected that the commercial use of artificial diets will increase, with a concomitant decrease in the use of fresh/frozen pilchards. The Tuna Industry has recently discussed bringing a pelleting plant on line in Port Lincoln in 2004/05. Such developments will result in a contraction of the market for South Australian pilchards and may impede further development of the industry.

Future development of the South Australian pilchard industry must involve increased utilisation of inter-state and inter-national markets for recreational bait and human consumption (Ward et al. 2000; Davidson et al. 2000).

As South Australian pilchard fishing grounds are often located 12-24 hours steaming away from local ports (cf 2- 3 hours in WA), the quantity and quality of product supplied to processing factories and markets for bait and human consumption will be largely determined by nature and quality of the at-sea post-harvest handling procedures (Ward et al. 2000; Davidson et al. 2000).

This project will occur in three phases:

Phase 1 (a) An audit of the SA pilchard fleet to assess current practices, quantify on-board processing gear, determine the capacity for improving the latter and assess onshore facilities capacity to process pilchards.
(b) An assessment of the marketing issues as they relate to the capacity of the Industry to develop new processes/products.

Phase 2 Once these are completed, the following will be carried out to optimise the handling procedures used in the South Australian pilchard fishery:
(a) An investigation of the biological and ecological factors that affect the rates of deterioration in pilchard quality in the immediate post-harvest period (i.e. net to processing factory); and
(b) Development of options for alternative handling procedures that optimise pilchard quality and economic return.

To achieve these objectives, information is needed on spatial and temporal variation in the biochemical composition of South Australian pilchards, especially with regard to the lipid:protein ratio and the free fatty acid content. These components are useful indicators of fish condition and the deterioration rate in fish quality during post-harvest handling (Fitz-Gerald and Bremner, 1994, NSC project 6). Knowledge of the taxonomic composition and biochemical characteristics of the gut contents of the South Australian pilchard is needed as these factors have been shown to affect the rates of deterioration of planktivorous pelagic fishes in the immediate post-harvest period (Stenstrom, 1965, Goldberg and Raa, 1980, Dr Bjordal Asmund, Norwegian Institute of Marine Research, pers. comm..; Mr Ian Wells, Seafood Services Australia, unpub. data).

Phase 3
A Cost-Benefit Analysis of the various processing options will have to be undertaken to assess the potential benefit of any changes in gear/practices. In order to do this a financial survey of licence holders, including measures of financial performance for the “average licence holder” will have to be carried out, and measures of economic performance of the fishery derived (i.e. gross value of production (GVP), economic rent, etc). This will be used to develop a model of the fishery linking biological and management parameters (CPUE, days fished, etc.) with the economic characteristics of the fishery. The model will be used to derive a baseline scenario, reflecting existing operator and fisheries management practices which will then be compared with scenarios reflecting the various processing options developed during the study.

Objectives

1. To assess current on-board and on-shore processing practices and equipment used by the SA pilchard fleet and to determine the capacity for improvement.
2. To assess marketing issues as they relate to the capacity of the industry to develop new processes/products
3. To investigate biological and ecological factors that affect rates of deterioration in pilchard quality in the immediate post-harvest period.
4. To examine and compare the effects of at-sea post-harvest handling procedures on the rates of deterioration in pilchard quality.
5. To develop options for alternative handling procedures that optimise pilchard quality and economic return
6. To undertake a Cost-Benefit analysis of the various processing options including any changes in gear requirements and fisheries management requirements.

Final report

ISBN: 0-7308-5348-9
Author: John Carragher

Aquatic Animal Health Subprogram: pilchard herpesvirus infection in wild pilchards

Project number: 2002-044
Project Status:
Completed
Budget expenditure: $283,659.00
Principal Investigator: Brian Jones
Organisation: Department of Primary Industries and Regional Development (DPIRD) WA
Project start/end date: 30 Dec 2002 - 30 Jul 2006
Contact:
FRDC
SPECIES

Need

This proposal seeks to continue the work begun at AAHL and Department of Fisheries. There is a need to independently validate the available tools from Western Australia and AAHL and to put them to use in elucidating the biology of the virus, including a survey of wild pilchards for the virus. This is especially important as a number of modeling papers have made inferences about the latency and infectivity of the virus which need to be verified. There is also a need to continue the sequencing of the viral genome which has been carried out both at AAHL and in WA, in order to design more specific tools and also to compare the virus obtained in 1995 with that collected in 1998. This work was identified as a national priority in 1998 and the need has not diminished. It was also recognised by the JPSWG, from the outset, that progress would be slow.

Objectives

1. To improve the sensitive and specific diagnostic assays (polymerase chain reactions (PCRs) and in situ hybridization (ISH) which are based on current limited sequence data. This will include the generation of further sequence data from the available stocks of virus.
2. To independently establish the sensitivity and specificity of the PCRs and ISH at other laboratories, including AAHL.
3. To then investigate basic aspects of the virus and the disease eg. the tissue distribution of virus in infected fish, and the correlation between disease in fish and the presence of virus.
4. To survey wild pilchard populations to determine whether the virus is still currently detectable and causing disease.
5. To compare the herpesvirus strains from 1995 & 1998, and to compare, at the molecular level, this herpesvirus and this disease with two other similar herpesvirus fish diseases which have been reported elsewhere in the world.

Final report

Development of a fisheries habitat suitability model utilising a geographic information system

Project number: 2000-157
Project Status:
Completed
Budget expenditure: $226,332.00
Principal Investigator: David Ball
Organisation: Agriculture Victoria
Project start/end date: 16 Oct 2000 - 29 Jun 2005
Contact:
FRDC

Need

The FRDC Review of Fisheries Habitats stated that “we must know where and what must be conserved for sustainability of fisheries and mariculture, before we determine why and how to do it”. At present key uncertainties exist concerning both the relative values of fisheries habitats and the effects of human disturbances at both regional and local scales. As a result, the FRDC Review found that strategic R&D is needed to overcome the poor ability to predict and manage such disturbances. Specifically, the collection, interrogation and extension of new and existing fisheries and habitat data at scales useful to management are required.

While it is generally known which habitats fish are found in association with, the critical factors which govern fish-habitat usage are poorly understood. In the absence of knowledge about why fish are utilising specific habitats, techniques are required to provide managers with information about the relative importance of different habitats and an ability to predict the impact of different pressures on these habitats. A Habitat Suitability Modelling approach is an effective means that can be employed to enable fisheries managers to identify the spatial component of fish-habitat links and make informed decisions on the management of habitats.

Objectives

1. Develop a fisheries habitat suitability model for Victorian bays, inlets and nearshore waters utilising a Geographic Information System (GIS).
2. Integrate a wide range of existing spatial and non-spatial data for habitat types, environmental parameters, species distribution, species life histories and habitat requirements in the GIS through a relational database.
3. Develop a customised ArcView GIS user interface for querying the fisheries habitat suitability model and producing habitat suitability maps.

Final report

Regrowth of pilchard (Sardinops sagax) stocks off southern WA following the mass mortality event of 1998/1999

Project number: 2000-135
Project Status:
Completed
Budget expenditure: $508,065.00
Principal Investigator: Dan Gaughan
Organisation: Department of Primary Industries and Regional Development (DPIRD) WA
Project start/end date: 9 Oct 2000 - 30 Jul 2008
Contact:
FRDC
SPECIES

Need

There is a need to assess the regrowth of pilchard stocks in southern Australia because of (1) the socioeconomic problems associated with fishery declines and the associated need to provide sufficiently detailed information so that management can proceed with the appropriate balance between sustaining the fishery and allowing recovery of the stocks, and (2) the potential for causes of wide ranging ecosystem affects to go unrecognized if there is no baseline data (i.e. abundance) for this key pelagic species.

In order to provide a time-series of the regrowth of S. sagax stocks in WA the biomass size of each adult assemblage needs to be assessed over the next few years. Because the ecosystem-based goal of this project is to provide a baseline of pilchard abundance which may relate to other species, the longer life spans, slower growth etc. typical of these higher trophic levels necessitates a long time series of surveys. Changes in biomass of the four pilchard assemblages should be assessed for a period of at least five years. Although this is a relatively short period of time over which to examine the recovery of a pelagic stock, such a routine will provide a solid basis for assessing the rebuild of pilchard abundance and thereby pro-actively collect data which could subsequently assist our understanding of other ecosystem affects of the Herpesvirus mortality event. This project will compliment the annual DEPM surveys intended for SA pilchard stock.

Collection of a continuous, albeit short-term, series of estimates of spawning biomass will permit the age structured simulation model being developed by Hall and Gaughan (in prep.) to be fitted to a likewise continuous series of these estimates. This should improve the fitting of the model, thereby making it more useful for predicting impacts of further mortality events involving S. sagax in southern Australia and facilitating the decision -making process in the ongoing management of pilchards in WA.

Objectives

1. Document changes in the biomass of the four exploited adult assemblages of S. sagax in WA during the six year period following the 1998/99 mass mortality event.
2. Integrate results of biomass surveys into the age structured model for each assemblage of pilchards. Further develop the age-structured simulation models for S. sagax and investigate ongoing behaviour of these under conditions of different levels of information
3. Determine if there is a measurable change in biological parameters of pilchards important to ongoing development of the simulation models, in particular growth rate, in response to the decrease in stock size.

Final report

ISBN: 1 921258 26 8
Author: Dr Daniel J Gaughan
Final Report • 2008-07-07
2000-135-DLD.pdf

Summary

This project produced time series of estimates of spawning biomass for pilchards in four purse seine management zones in Western Australia, three on the south coast and one on the west coast. The pilchard stocks in Western Australia have recovered strongly since the 1998/99 mass mortality.

This project has shown that the fishery independent and fishery dependent methods applied to Western Australia’s pilchard fisheries cannot provide precise estimates of the size of the pilchard spawning biomass in each management region. Although the trends indicated by the age-structured simulation model are reliable and provide good evidence for a strong recovery of pilchard stocks, the magnitude of changes in stock size from year-to-year are not known with sufficient certainty to allow high rates of exploitation.

The demonstrated increases in pilchard spawning biomass has lead to optimism for the future of the purse seine industry in southern WA, which in turn has encouraged this industry to be proactive in ensuring that exploitation rates were not set at levels that were too high to impede the recovery of the stock or put undue pressure on the long term viability of the stocks. Tracking the progress of estimating of pilchard biomass in each region over the duration of this project was a crucial factor that assisted industry members to better appreciate the need to examine factors additional to the point estimate of biomass generated in any one year.

The project also determined that the growth rates of pilchards in WA can be highly variable, sometimes changing markedly from year to year while at other times exhibiting more gradual changes over several years. The tendency for a negative relationship between annual growth rates and stock size suggests density dependence, which in turn supports the contention that that pilchard stocks in this region are limited in size by the biological and oceanographic characteristics of the continental shelf waters of southern WA. The magnitude and variability of pilchard biomass observed during this project builds on the knowledge obtained during the 1990s, providing a strong basis against which the purse seine industry can expect future quota levels to be set.

Keywords: pilchard (sardine), recruitment, age-structured model, spawning biomass, daily egg production method, stock recovery, fisheries management.

Implementation of an age-structured stock assessment model for pilchards (Sardinops sagax) in South Australia

Project number: 2000-125
Project Status:
Completed
Budget expenditure: $196,311.50
Principal Investigator: Timothy M. Ward
Organisation: SARDI Food Safety and Innovation
Project start/end date: 12 Nov 2000 - 30 Nov 2005
Contact:
FRDC
SPECIES

Need

1. Implement an age-structured stock assessment model. Stock assessment models that incorporate catch-at-age data and annual fishery-independent estimates of spawning biomass are powerful tools for optimising management strategies for fisheries resources that undergo large inter-annual fluctuations in abundance (Cochrane 1999). The need to implement the WA age-structured stock assessment model in SA is pressing (Fletcher 2000) as there is considerable pressure to further expand the rapidly growing fishery and a clear responsibility to ensure the resource is managed sustainably.

2. Develop a reliable and accurate age-determination method. Knowledge of patterns of age and growth is central to the development of strategies for the sustainable management of clupeoid populations (Cochrane 1999). The major factor limiting current understanding of the age and growth of SA pilchards is the absence of a reliable and accurate age-determination method (Fletcher 2000). The development of a valid ageing protocol has been impeded by lack of data from juveniles (Ward et al 1998). A reliable and accurate method for determining the age of SA pilchards is needed to implement the WA model.

3. Estimate the age structure of the commercial catch. Age-structured stock assessment models require reliable estimates of the age structure of the commercial catch and/or population (Cochrane 1999). Otoliths collected from the SA fishery since 1995 and by the fishery-independent means since 1998 provide an opportunity to assess (1) the validity of the age-determination method developed in objective 2 and (2) the degree to which catch-at-age data reflects the age structure of the population. Reliable estimates of the age structure of the commercial catch and/or the population are needed to implement the WA model.

Objectives

1. To implement an age-structured stock assessment model for the SA pilchard fishery.
2. Todevelop a reliable age-determination method for SA pilchards.
3. To determine the age structure of the SA pilchard fishery/population.
4. To assess the potential for using data on the abundance of pre-recruits in catches as an index of recruitment.

Final report

Pilchard mortality events in Australia and related world events

Project number: 1999-227
Project Status:
Completed
Budget expenditure: $59,025.44
Principal Investigator: Will Zacharin
Organisation: Department of Primary Industries and Regions South Australia (PIRSA)
Project start/end date: 20 Oct 1999 - 15 Apr 2004
Contact:
FRDC
SPECIES

Need

The lack of a consolidated report on the 1995 pilchard mortality event hampered the Joint Pilchard Scientific Working Group in its investigation of the 1998 mortality event. It remains uncertain that the response to the 1998 mortality was efficient and it poses the risk that should another event occur in the future, it too will be met with a poorly-coordinated response. Such a response may not yield adequate data or appropriate data for researchers and fisheries managers around Australia. There is also a risk that scientific investigations may be duplicated, resulting in an inefficient use of industry and public resources.

The lack of a detailed analysis of the events of both 1995 and 1998 and of similar events in other parts of the world compound the difficulties involved in an evaluation of the implications of the mortalities to commercial fisheries and other species which depend wholly or in part on access to pilchards, eg sea lions and penguins.

Objectives

1. Prepare a comprehensive report of pilchard mortality events in Australian waters prior to 1995 and in waters world wide to the present time
2. Provide a summary of the 1995 pilchard mortality event
3. Prepare a comprehensive and competent technical report on the pilchard mortality event in 1998
4. Describe and evaluate the coordinating and managing approaches taken in 1995 and 1998 pilchard mortality events
5. Assess the implications of the pilchard mortality events
6. Evaluate the conclusions which can be drawn from various hypothese as to the cause, origin, trigger and epizootiology of the events
7. Assess options for managing future pilchard mortality events

Final report

ISBN: 0-759-01316-0
Author: Alexandra Gaut

The development of a model of the spread of the pilchard fish kill events in southern Australian waters

Project number: 1999-225
Project Status:
Completed
Budget expenditure: $46,251.00
Principal Investigator: Alexander Murray
Organisation: CSIRO Oceans and Atmosphere Hobart
Project start/end date: 28 Jun 1999 - 16 May 2001
Contact:
FRDC
SPECIES

Need

The mass mortality events are very economically and ecologically damaging. Economic damage occurs acutely in the short-term due to the need to close the fishery during events and damage also occurs in the longer term owing to the removal of large numbers of fish during the event.

No model exists of the spatial propogation of a viral epidemic in an exploited fish population, we will derive such a model. This model will be aimed less at predicting the spread of a particular mass mortality event and more at the understanding of the dynamics of the event. Using the model we will be able to assess hypothesises concerning the factors which control the mass mortality and hence focus future study on the most sensitive processes. The model will also show the conditions under which these events may recur. We will also be able to assess the potential for management intervation to halt an ongoing epidemic or prevent further outbreaks. The model will also integrate all the aspects of the spread of the mass mortality events, showing linkages within the existing data and showing those areas for which adaquate data is lacking.

It should also be noted that damaging epidemics among wild caught and farmed marine fisheries are not infrequent and that modified versions of the model may have future applications to other fisheries.

Objectives

1. We will construct a 1-D SIR (Susceptible, Infected, Removed) model of the spread of the pilchard mass mortality events of 1995 and 1998/9
2. We will analyse the effect of different modes of local transmission on the mass mortality's dynamics.
3. We will produce a literature review of similar mass mortalities and the modelling approaches used to analyse them.
4. We will refine the SIR model to include different transmission process functions and data obtained by other pilchard mortality study projects, in particular the Fisheries WA lead study on viral transmission.
5. We will review the observations, including those obtained in concurrent studies, to provide the tightest possible constraints on the ranges of model parameters.
6. We will analyse the effects of fisheries management strategies on pathogen transmission, in particular we will test the viability of a 'fire break' policy.
7. We will construct a simple model of the recovery of the fishery to investigate the period required for the stocks to become vulnerable to renewed mortality.
8. We will develop a Graphical User Interface (GUI) to display the local and geographical spread of pathogens.
9. We will produce an initial report detailing the approaches used both by us and other modellers of epidemics.
10. We will produce a final report detailing the final form of the model produced and incorporating analysis of model structure, parameters and results.
11. We will present this work at a nationally significant scientific meeting in 2000.

Final report

ISBN: 0-643-06233-5
Author: Alexander Murray

Pilchard (Sardinops sagax) nursery areas and recruitment process assessment between different regions in southern Western Australia

Project number: 1999-150
Project Status:
Completed
Budget expenditure: $124,503.76
Principal Investigator: Dan Gaughan
Organisation: Department of Primary Industries and Regional Development (DPIRD) WA
Project start/end date: 1 Aug 1999 - 11 Jun 2003
Contact:
FRDC
SPECIES

Need

There is an urgent need to determine the relationship between pre-recruit stages from the different stocks of adult pilchards amongst regions of southern WA. In particular, whether pre-recruits which originate in each region largely remain separate or mix together needs to be determined. Following this, knowledge on the rates of mixing of pre-recruits should be investigated so that the relative contribution from any one region to any other region can be estimated.

The key issues which need to be addressed are:
1. Do specific pilchard nursery areas exist?
2. Do recruits to each region come from a common pool of pre-recruits (e.g. one year olds)?
3. Is there significant eastward and or westward movements of pre-recruits between zones?
4. Does each zone of the fishery contribute similar numbers of recruits or is one zone (or two) more important than other(s)?

Because of the extent of the gap in our knowledge of pre-recruit pilchards this proposal is only for a 15 month pilot study. If results from the pilot study are encouraging, once the initial questions have been addressed a second research proposal will be developed to investigate mixing rates in greater detail through a combination of further otolith analyses and tagging. Also, continuing advances in methods to compare mitachondrial DNA may also permit this method to be used to examine the question of origin of recruits.

Objectives

1. Ascertain if pre-recruit pilchards can be caught on a regular (or even semi-regular) basis at each of the south coast regions or if a "major" nursery area exists for the entire stock.
2. Undertake an analysis of the oxygen and carbon stable isotope ratios for otoliths of pre-recruit and young post-recruit pilchards from each fishing zone to determine if separate groups of pre-recruits can be identified.
3. Undertake an analysis of the oxygen and carbon stable isotope ratios for the central region of otoliths from fully recruited pilchards at each region caught over the past 8 years to determine if separate groups of pre-recruits can be identified consistently over several years.
4. Attempt to tag large numbers of pre-recruit pilchards using tetracycline, calcein and possibly other 'dyes' to mark the otoliths and other calcium based structures such as fin rays to determine if this is a viable research tool for pilchards on the south coast of WA.
5. Assess whether there is a potential to develop a fishery independent index of recruitment.

Final report

Mesoscale oceanographic data analysis and data assimilative modelling with application to Western Australian fisheries

Project number: 1997-139
Project Status:
Completed
Budget expenditure: $462,214.00
Principal Investigator: David Griffin
Organisation: CSIRO Oceans and Atmosphere Hobart
Project start/end date: 22 Jun 1997 - 17 Oct 2001
Contact:
FRDC

Need

Understanding the influence of environmental effects on recruitment is an important aspect of fisheries stock assessment (and hence sustainable management) to help interpret whether fluctuations in recruitment are due to environmental effects or to the impact of fishing on the spawning stock. In many cases, the effect of breeding stock cannot be detected unless environmental effects have been taken into account. At present the measure of variation in the strength of the Leeuwin Current along the WA coast from Shark Bay to Esperance is based on monthly and annual mean sea levels at Fremantle, which are highly correlated with sea levels at other locations and have few missing values. The impacts of this and other environmental factors such as westerly winds are presently being examined in isolation rather than obtaining an overall measure of the impact on the circulation. This project will integrate these separate oceanic and atmospheric processes into circulation models and thus result in improved estimates of ocean currents, water temperature and salinity for regions adjacent to important fisheries, providing a better understanding of the effects of environmental variability on recruitment as well as better prediction of recruitment levels.

The current assessment of the impact of the breeding stock on the level of recruitment in the western rock lobster assumes that larvae hatched from all areas contribute to the settlement at each location. Although extensive mixing of larvae during the larval phase occurs, it is possible that larvae hatched from certain areas may contribute proportionally more to the puerulus settlement in different regions. This project will provide an improved understanding of the relative importance of the breeding stocks from different regions, enabling better assessment of the impact of the breeding stock and an improved stock-recruitment relationship which is fundamental for the proper management of the fishery.

There is therefore a need for a physical oceanographic analysis tool that can be used to test theories on the influence of favourable/unfavourable larval advection, or temperature, or larval mortality. A well understood physical/biological interaction would enable efficient ocean and fisheries observation and monitoring programs to be established to maximize the skill of larval survival predictions.

Objectives

1. To develop algorithms for operational estimation of near-surface currents and temperatures off south-western Australia based on satellite altimetry and thermometry.
2. To develop and test a three-dimensional data-assimilating model of ocean dynamics off Western Australia, to be run in hindcast mode, archiving data for the last ten years.
3. To run tracking scenarios for rock lobster larvae to describe larval behaviour under different environmental conditions (extended to other larvae as time permits).
4. To provide advice on management issues that may be addressed by improved ocean understanding, such as the spawning locations of successful larvae, and correlations between larval success and ocean conditions.

Final report

ISBN: 1 876996 01 3
Author: David Griffin
Final Report • 2001-09-17 • 5.77 MB
1997-139-DLD.pdf

Summary

The more that is understood about the factors controlling the abundance of an exploited fish stock, the more optimally it can be harvested for sustainable yield and profit. It has been known for some time that catches of western rock lobster are closely related to the number of larvae surviving their year at sea and settling as puerulus on the coast, and that the variation in settlement, in turn can be statistically predicted using several types of ocean data. What is not understood is why sea level, for example, should be a predictor of larval survival. This needs to be understood so that insight into reasons why the correlation might break down (as it did in 1998) can be gained, and so that a better predictor can be found. The value of a reliable indicator of the environmental influence on larval survival is that, for example, a year of very poor larval settlement can then be correctly attributed to either over-fishing of the breeding stock, or poor survival rates at sea.

This project addressed the question of why larval survival rates are so variable by taking a process-based, modelling approach, as distinct from the statistical, or correlative approaches taken to date. The modelling approach has only recently become feasible, for two reasons. One is that the computing demands are high, but the more significant recent advance is the advent of satellite techniques for mapping near-surface ocean currents. We used these maps to calculate where winds and ocean currents from 1993 to 1998 carried numbers of individual western rock lobster larvae, from hatching to far offshore, then back to the coast. 

Crucial to the success of this project was that relatively much has been learnt, from decades of sampling from ships, about the behaviour of larval western rock lobsters in the deep ocean. In particular, we needed to know the details of when larvae rise to the surface and when they descend to depth, and how this varies with larval age, time of day, phase of moon, etc. We also needed to know what triggers a late-stage larva to metamorphose to the non-feeding, fast-swimming puerulus stage that is found settling on inshore reefs. This trigger, however, is unknown, so our model simply assumes that all larvae at least 270 days old make this transition if they find themselves over the continental slope near new moon, a behaviour that is consistent with available observations.

In the first phase of the project, many types of ocean data were assembled, and two techniques developed for making accurate maps of the ocean currents. The first technique was relatively straightforward: observations of sea level height and surface temperature were used to estimate the surface currents directly via approximations of the physical equations. The second technique is called data-assimilative modeling. The satellite data were ‘assimilated’ into a hydrodynamic model.

Our data-assimilating model of the ocean currents of Western Australia is the first of its kind in Australia. However, it took somewhat longer to complete than originally planned, and we still consider it to be a work in progress. Work on this model was de-prioritised in favour of using the maps of ocean near-surface currents diagnosed directly from the satellite data, which turned out, fortunately, to be more accurate than hoped for. The accuracy of these ‘altimetric’ current maps was assessed by comparing them with the velocities of satellite-tracked drifting buoys, and animations of ocean thermal imagery. 

The current maps and (also only recently available digitally) daily wind maps were then combined with information on larval behaviour and many simulations were performed of the fate of six year-classes of lobster larvae. The simulations confirm the importance of the summer southerly winds in transporting larvae ‘upstream’ against the mean onshore and southward flows that exist just below the surface, and which help return larvae to the coast. The simulations also highlight the role of energetic eddies, which mix the larvae at velocities much in excess of the larger-scale flows.

It is the vigorous mixing by eddies in our simulations that produce the result that the location of hatching of larvae quickly becomes immaterial to its destiny. To test this hypothesis was one of our primary objectives because of its relevance to the potential benefit of preferentially protecting certain spawning regions.

With regard to explaining the observed correlation of sea level with larval settlement,  our simulations confirm that sea level does serve as an indicator of both the strength of the Leeuwin Current, and the intensity of eddies associated with it, but does not support the hypothesis that the direct (transporting) influence of the currents on the larvae is responsible for the large (ie five-fold) changes observed in how many return to the coast.

So the mystery of why larval settlement correlates with sea level remains, although we now have a clearer picture of how any return at all. 

We concluded our project with a very preliminary study of the potential importance, to larval survival, of the inter-annual variability of food availability. For this we used the recently launched SeaWiFS satellite that senses ocean colour, from which near-surface chlorophyll abundance can be estimated. These data show that there was less phytoplankton in the water in the summer of 1997-98 than in the next two summers, perhaps explaining why the settlement in 1998 was very low, even though the prediction based on sea level was for average settlement. 

The next step to take is to include temperature- and prey field-dependent larval growth and mortality in an advection model such as the one developed here. In addition to explaining the inter-annual variability of settlement, the inclusion of growth and mortality in the model could also change our finding about the importance of hatching location, because of the regional differences that exist in primary production.

To complete this project, we have produced an educational CD-ROM with all the data assembled, along with results of the larval transport simulations, presented in the form of movies that can be viewed on any computer. The CD can be browsed at
www.marine.csiro.au/~griffin/WACD/index.htm.

Keywords: Western Rock Lobster, larval advection, ocean currents, altimetry, data assimilation.

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