77,994 results

TSGA IPA: understanding broadscale impacts of salmonid farming on rocky reef communities.

Project number: 2014-042
Project Status:
Completed
Budget expenditure: $74,900.00
Principal Investigator: Sam Ibbott
Organisation: Aquenal Pty Ltd
Project start/end date: 2 Jan 2015 - 11 May 2016
Contact:
FRDC

Need

The monitoring of salmon farms in Tasmania is more comprehensive than that in most other parts of the world and is based on rigorous and broad-ranging research and monitoring that has been ongoing for over 20 years. The success of this integrated research framework has been enhanced through very strong links between government, industry and researchers. Robust regulatory controls have been used to manage benthic impacts from salmon farming activities, and through the adoption of adaptive management strategies, organic loading effects from marine farming operations have been effectively managed using the environmental monitoring framework administered by the Tasmanian Government. The salmon industry-funded Broadscale Environmental Monitoring Program (BEMP) for the D'Entrecasteaux Channel region (which commenced in 2009) has further enhanced the understanding of impacts to include the detection of broadscale impacts to water quality and sediment health. The only marine habitats not subject to broadscale assessment of potential impacts from salmon farming are rocky reef communities. As the Tasmanian salmon industry expands, both in terms of production and growing areas, commercial and recreational fishing groups are concerned that their targeted fishing grounds, which are predominantly based around rocky reef systems, may be impacted by nutrient emissions released through marine farming activities.

This proposal seeks to provide an immediate response to characterising reef community health prior to the development of new growing areas in south eastern Tasmanian waters.

Objectives

1. Undertake analysis of subtidal macroalgal community survey data (2003-2014) at the Ninepin point and Tinderbox Marine Protected Areas
2. Characterise macroalgal community assemblages within south eastern Tasmanian waters to determine potential broadscale impacts from salmon farm developments in south eastern Tasmanian waters.
3. Communicate the status and health of rocky reef communities (based on objective 2) to broad industry and recreational stakeholder groups

Final report

ISBN: 978-0-646-96251-1
Author: Sam S. Ibbott
Environment
PROJECT NUMBER • 2014-040
PROJECT STATUS:
COMPLETED

Oysters Australia IPA: Pacific Oyster Mortality Syndrome (POMS) – closing knowledge gaps to continue farming C. gigas in Australia

The present project is part of a continued program of epidemiologic investigations of OsHV-1 in Australia. Sufficient understanding of POMS is required to provide information for farmers and to direct policy so that profitable farming can continue despite increasing distribution and devastating...
ORGANISATION:
University of Sydney (USYD)

Review and assess stock assessment methods used in Australia

Project number: 2014-039
Project Status:
Completed
Budget expenditure: $152,339.00
Principal Investigator: Richard Little
Organisation: CSIRO Oceans and Atmosphere Hobart
Project start/end date: 4 Jan 2015 - 29 Jun 2016
Contact:
FRDC

Need

Stock assessment is a set of tools and methods generally used to assess the status of wild capture fisheries stocks. They range from complex statistical and mathematical models, to simple, almost back of the envelope, methods. They are used to predict population size, quantify the impact of fisheries on the population and in some jurisdictions, provide key outputs needed in harvest strategies. There is a diverse range of methods in a field where practitioners have tended to produce home-grown tools in their favourite code languages (R, Fortran, C++, Visual Basic, ADMB etc.). The use of a specific model or method is often historical rather based on an objective evaluation of options e.g. the risk-cost-catch framework (see Method references). In recent years changes have occurred allowing some shift away from previous approaches:
• More off-the-shelf methods, with a diverse range of flexible features, have become available and some uptake has occurred e.g. Stock Synthesis (SS) (http://nft.nefsc.noaa.gov/SS3.html)
• There has been some convergence of language tools using the open source model (e.g. ADMB, Gnu and R)
• Stock assessment tool kits have become freely available e.g. the NOAA fisheries toolbox (http://nft.nefsc.noaa.gov/index.html)

However, in many cases it is still standard practice in Australia to develop home-grown models. Although this is not in itself an issue, it does not always allow for synergies and more cost effective practices. For example, it has become standard practice in the USA to have a model developed and maintained by a team, have it independently tested and then made available as an off-the-shelf GUI driven tool. Many stock assessment scientists now use these tools. In Europe, ICES also tends to use standard approaches.

There is a real need for a more strategic view of which framework Australia should adopt in the present climate of:
• Fewer finance and capability resources
• Data rich to data poor fisheries
• Small and large fisheries.

This review does not preclude the use of specific modelling.

Objectives

1. Review existing stock assessment methods used in Australia.
2. Review Australian stock assessment needs, and model developer and user capacity.
3. Review methods used and reviews undertaken elsewhere in the world.
4. Assess the relative merits of off-the-shelf versus case-specific assessments.
5. With input from the different jurisdictions, provide recommendations for a possible set of investment models.

Final report

ISBN: 978-1-4863-0997-9
Authors: Cathy Dichmont Roy Deng Andre Punt Rich Little
Final Report • 2018-06-25 • 1.31 MB
2014-039-DLD.pdf

Summary

Stock assessments provide scientific advice in support of fisheries decision making. They involve fitting population dynamics models to fishery and monitoring data to provide estimates of time-trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as BMSY (the biomass corresponding to Maximum Sustainability Yield, MSY) and FMSY (the fishing mortality rate corresponding to MSY), along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We reviewed the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages were considered, five based on surplus production models (“A Stock Production Model Incorporating Covariates”; “Bayesian Surplus Production Model-1”; “Bayesian Surplus Production Model-2”; “Depletion-Based Stock Reduction Analysis”; “Extended Depletion-Based Stock Reduction Analysis”), one based on a delay-difference model (“Collie-Sissenwine Analysis”), and the remainder based on age-structured models (“Assessment Method for Alaska”, “Age Structured Assessment Program”, “Beaufort Assessment Model”, “MULRIFAN-CL”, “Statistical catch-at-length”, “Stock Synthesis”, ”Simple Stock Synthesis”, “Extended Stock Synthesis”, “Virtual Population Analysis”, “VPA-2BOX”, “).

This report highlights the benefits and disadvantages of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use.

Final Report • 2018-06-25 • 1.31 MB
2014-039-DLD.pdf

Summary

Stock assessments provide scientific advice in support of fisheries decision making. They involve fitting population dynamics models to fishery and monitoring data to provide estimates of time-trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as BMSY (the biomass corresponding to Maximum Sustainability Yield, MSY) and FMSY (the fishing mortality rate corresponding to MSY), along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We reviewed the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages were considered, five based on surplus production models (“A Stock Production Model Incorporating Covariates”; “Bayesian Surplus Production Model-1”; “Bayesian Surplus Production Model-2”; “Depletion-Based Stock Reduction Analysis”; “Extended Depletion-Based Stock Reduction Analysis”), one based on a delay-difference model (“Collie-Sissenwine Analysis”), and the remainder based on age-structured models (“Assessment Method for Alaska”, “Age Structured Assessment Program”, “Beaufort Assessment Model”, “MULRIFAN-CL”, “Statistical catch-at-length”, “Stock Synthesis”, ”Simple Stock Synthesis”, “Extended Stock Synthesis”, “Virtual Population Analysis”, “VPA-2BOX”, “).

This report highlights the benefits and disadvantages of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use.

Final Report • 2018-06-25 • 1.31 MB
2014-039-DLD.pdf

Summary

Stock assessments provide scientific advice in support of fisheries decision making. They involve fitting population dynamics models to fishery and monitoring data to provide estimates of time-trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as BMSY (the biomass corresponding to Maximum Sustainability Yield, MSY) and FMSY (the fishing mortality rate corresponding to MSY), along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We reviewed the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages were considered, five based on surplus production models (“A Stock Production Model Incorporating Covariates”; “Bayesian Surplus Production Model-1”; “Bayesian Surplus Production Model-2”; “Depletion-Based Stock Reduction Analysis”; “Extended Depletion-Based Stock Reduction Analysis”), one based on a delay-difference model (“Collie-Sissenwine Analysis”), and the remainder based on age-structured models (“Assessment Method for Alaska”, “Age Structured Assessment Program”, “Beaufort Assessment Model”, “MULRIFAN-CL”, “Statistical catch-at-length”, “Stock Synthesis”, ”Simple Stock Synthesis”, “Extended Stock Synthesis”, “Virtual Population Analysis”, “VPA-2BOX”, “).

This report highlights the benefits and disadvantages of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use.

Final Report • 2018-06-25 • 1.31 MB
2014-039-DLD.pdf

Summary

Stock assessments provide scientific advice in support of fisheries decision making. They involve fitting population dynamics models to fishery and monitoring data to provide estimates of time-trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as BMSY (the biomass corresponding to Maximum Sustainability Yield, MSY) and FMSY (the fishing mortality rate corresponding to MSY), along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We reviewed the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages were considered, five based on surplus production models (“A Stock Production Model Incorporating Covariates”; “Bayesian Surplus Production Model-1”; “Bayesian Surplus Production Model-2”; “Depletion-Based Stock Reduction Analysis”; “Extended Depletion-Based Stock Reduction Analysis”), one based on a delay-difference model (“Collie-Sissenwine Analysis”), and the remainder based on age-structured models (“Assessment Method for Alaska”, “Age Structured Assessment Program”, “Beaufort Assessment Model”, “MULRIFAN-CL”, “Statistical catch-at-length”, “Stock Synthesis”, ”Simple Stock Synthesis”, “Extended Stock Synthesis”, “Virtual Population Analysis”, “VPA-2BOX”, “).

This report highlights the benefits and disadvantages of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use.

Final Report • 2018-06-25 • 1.31 MB
2014-039-DLD.pdf

Summary

Stock assessments provide scientific advice in support of fisheries decision making. They involve fitting population dynamics models to fishery and monitoring data to provide estimates of time-trajectories of biomass and fishing mortality in absolute terms and relative to biological reference points such as BMSY (the biomass corresponding to Maximum Sustainability Yield, MSY) and FMSY (the fishing mortality rate corresponding to MSY), along with measures of uncertainty. Some stock assessments are conducted using software developed for a specific stock or group of stocks. However, increasingly, stock assessments are being conducted using packages developed for application to several taxa and across multiple regions. We reviewed the range of packages used to conduct assessments of fish and invertebrate stocks in the United States because these assessments tend to have common goals, and need to provide similar outputs for decision making. Sixteen packages were considered, five based on surplus production models (“A Stock Production Model Incorporating Covariates”; “Bayesian Surplus Production Model-1”; “Bayesian Surplus Production Model-2”; “Depletion-Based Stock Reduction Analysis”; “Extended Depletion-Based Stock Reduction Analysis”), one based on a delay-difference model (“Collie-Sissenwine Analysis”), and the remainder based on age-structured models (“Assessment Method for Alaska”, “Age Structured Assessment Program”, “Beaufort Assessment Model”, “MULRIFAN-CL”, “Statistical catch-at-length”, “Stock Synthesis”, ”Simple Stock Synthesis”, “Extended Stock Synthesis”, “Virtual Population Analysis”, “VPA-2BOX”, “).

This report highlights the benefits and disadvantages of stock assessment packages in terms of allowing analysts to explore many assessment configurations and facilitating the peer-review of assessments. It also highlights the disadvantages associated with the use of packages for conducting assessments. Packages with the most options and greatest flexibility are the most difficult to use, and see the greatest development of auxiliary tools to facilitate their use.

TSGA IPA: Understanding Dorvilleid ecology in Macquarie Harbour and their response to organic enrichment

Project number: 2014-038
Project Status:
Completed
Budget expenditure: $87,135.40
Principal Investigator: Jeff Ross
Organisation: University of Tasmania (UTAS)
Project start/end date: 1 Jan 2015 - 29 Jun 2015
Contact:
FRDC

Need

Previous research has shown a clear impact gradient associated with cage salmon farming operations, and that presence of bacterial mats (Beggiatoa) and proliferation of opportunistic species are features commonly associated with high levels of organic enrichment (e.g. Pearson & Rosenberg, 1978). The presence of opportunists, such as Capitellid worms, being classified as representative of “unacceptable impact” (Macleod et al., 2004). This premise has been validated in SE Tasmania and underpins regulatory monitoring requirements statewide (DPIPWE, 2004).

The understanding that proliferation of opportunists represents deteriorating conditions was translated to monitoring protocols in Macquarie Harbour, but the relationship between opportunists and the level of enrichment was not explicitly tested in this region. However, video surveys suggest that in Dorvilleid worms rather than Capitellids were the species most indicative of organic enrichment effects(DPIPWE, 2004). Dorvilleids can tolerate anaerobic sediments and high levels of hydrogen sulphide (Levin et al. 2013) and are known to be indicators of the impacts of finfish aquaculture (e.g. Paxton et al. 2010).

However, Macquarie Harbour is ecologically very different to other farming areas in SE Tasmania; the sediments are inherently depauperate, largely epibiotic and spatially patchy. A recent study in Canada has highlighted the need to better understand the relationships and compliance thresholds for established enrichment indicators (i.e. Beggiatoa sp and opportunistic polychaete complexes) in systems where ecological patchiness may occur (Hamoutene et al 2014); suggesting that, where there is significant potential for small scale spatial variability, normal successional responses may not be as reliable. Consequently, the responses may not be consistent with expectations developed from southern Tasmanian regions.

In this context it is important to identify the relationship between Dorvilleids and sediment condition; determining the reliability of this species as an indicator of sediment condition, and characterising the environmental conditions associated with changes in Dorvilleid abundance.

Objectives

1. Review the international literature to establish the current state of knowledge regarding Dorvilleid ecology, and in particular, their response to organic enrichment. This will include a review of their current use as indicator of the impacts of finfish aquaculture.
2. Carry out targeted field survey at selected leases to identify the relationship between Dorvilleids and sediment condition, characterising the environmental conditions associated with changes in Dorvilleid abundance.
3. Based on the finding of 1. and 2. determine the reliability of this species as an indicator of sediment condition in Macquarie Harbour
4. In conjunction with industry and government stakeholders make recommendations on the future use of Dorvilleids in regulatory monitoring of Salmonid aquaculture in Macquarie Harbour

First implementation of an independent observer program for the Charter Boat Industry of NSW: data for industry-driven resource sustainability

Project number: 2014-036
Project Status:
Completed
Budget expenditure: $209,300.00
Principal Investigator: Charles A. Gray
Organisation: WildFish Research
Project start/end date: 30 Nov 2014 - 14 Apr 2016
Contact:
FRDC

Need

This project was initiated in response to management and scientific needs for greater inclusion of recreational fisheries data for resources assessments of key recreationally caught species and for inclusion in environmental assessments of recreational fishing. This project was deemed a high priority outcome of the NSW DPI Resource Assessment Workshops in 2011, 2012 and again in 2013.

Objectives

1. Deliver independent quantitative observer-based information on the diversity, rates of capture and length compositions of species retained and released from coastal charter boats in NSW
2. Obtain quantitative information and report on the ages and age compositions of catches of key fish species harvested by the coastal charter boat fishery in NSW
3. Provide summaries of analyses of data across appropriate spatial and temporal scales
4. Deliver summary profiles of charter boat cliental to industry
5. Compare on-board observer estimates of species retained and their rates of capture with industry logbooks
6. Provide feedback to industry and management on project objectives

Final report

ISBN: 978-0-9941504-9-3
Author: Charles Gray

Safeguarding commercial fishing in NSW from ciguatera fish poisoning

Project number: 2014-035
Project Status:
Completed
Budget expenditure: $72,639.11
Principal Investigator: Shauna Murray
Organisation: University of Technology Sydney (UTS)
Project start/end date: 31 Oct 2014 - 29 Feb 2016
Contact:
FRDC

Need

CFP is an illness caused by consumption of fish that have accumulated ciguatoxins (CTXs), which are naturally produced by marine microalgae (Gambierdiscus spp), and not degraded by freezing and heating processes. It is well known from Queensland, with more than 1000 cases in the past 15 years, including 2 fatalities, despite only ~20% of cases reported. Around 90 species of fish can be contaminated with CTXs, which accumulate, and are often associated with larger and carnivorous fish. Species of Gambierdiscus may be invasive: internationally, increases in abundance and expansion into new areas have occurred. Our recent work (shown in http://theconversation.com/explainer-what-is-ciguatera-fish-poisoning-21835) has now found Gambierdiscus spp is present in NSW.

No study has been conducted on the presence of CTXs in fish from NSW, and knowledge about its distribution within Australian waters is poor. The recent illnesses at Scotts Head and Evans Head show that CTX may occur in fish caught in NSW. The NSW Food Authority has advised the public not to eat Spanish Mackerel weighing over 10 kg, based on the Sydney Fish Market management plan, which restricts the sale of fish based on size limits, high-risk species and location where fish were caught. However, no data exist regarding sizes, location and risk from Spanish Mackerel in NSW. Smaller Spanish Mackerel may represent a potential risk. However, these guidelines may be excessively restrictive, as some of the fish discarded may be safe for consumption.

We are now able to quantify marine biotoxins in Sydney using a newly obtained LC-MS, and links with a group of collaborating experts. We propose to undertake a thorough sampling and testing program to determine the presence of CTXs in Spanish Mackerel (Scomberomorus commerson) from NSW, to provide the baseline data necessary for the revision of guidelines for the management of CFP in NSW.

Objectives

1. Establish the first testing facility for CTXs in NSW
2. Determine if CTXs are present Spanish Mackerel (Scomberomorus commerson) caught in NSW waters, and if so, generate qualitative and quantitative information
3. If found, analyse data on CTX presence and concentration in relation to: fish size, location that fish was caught, date, water temperature.
4. Liaise with commercial fishing organisations and regulators to inform them of the evidence on CTXs and procedures for testing fish

Final report

ISBN: 978-0-646-95465-3
Author: Shauna Murray
Environment
PROJECT NUMBER • 2014-034
PROJECT STATUS:
COMPLETED

Revision of the existing AQUAVETPLAN: ‘Viral Encephalopathy and Retinopathy Disease Strategy Manual’

Australian aquatic veterinary emergency plan (AQUAVETPLAN) for Viral Encephalopathy and Retinopathy Disease can be accessed from the federal Department of...
ORGANISATION:
University of Sydney (USYD)
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