Category Archives: Planning, monitoring & assessment

The identification and protection of drought refuges for native fish in the Murray-Darling Basin.

Key words: drought, refuge, native fish, Native Fish Strategy

Threats and Impacts: From 1996 to 2009, the Murray-Darling Basin (MDB) experienced severe drought conditions. As the impacts of the drought worsened, the need for improved and co-ordinated management responses became increasingly important to protect key ecological assets and critical aquatic habitats and ecosystems. Within the MDB it was uncertain whether an adequate network of drought refuges (e.g. flowing perennial river reaches, deep waterholes) remained to preserve native fish species/populations through extended drought. This project was established to address this knowledge gap.

Aims: The broad aims of the project were to:

  • define, identify and explore the current status and management of drought refuges in the MDB (Figs 1 and 2); and,
  • develop guidelines and an approach to identify, prioritise and protect drought refuges for native fish that can be implemented across the MDB.
Figure 1: A drying refuge (Photo courtesy of Luke Pearce)

Figure 1: A drying refuge (Photo courtesy of Luke Pearce)

Figure 2: Drought refuge on the Condamine River (Photo courtesy of Michael Hutchison)

Figure 2: Drought refuge on the Condamine River (Photo courtesy of Michael Hutchison)

Methods: The current status and management of refuges were explored using a number of techniques including questionnaires, an expert/management workshop and a review of relevant literature and management programs. This process identified the types of habitats that serve as drought refuges across the MDB, the key native fish species that have been targeted for protection under drought response programs, key threats and the current management responses/actions undertaken for refuge protection. In order to catalogue refuge sites, a preliminary list of critical sites was developed in collaboration with managers and experts.

An approach to identify and protect refuges was developed in conjunction with regional agencies and jurisdictions from two pilot valleys: the Goulburn Broken catchment in northern Victoria and the Moonie catchment in south-eastern Queensland. Under this phase of the project, definitions and criteria for identifying and prioritising refuges were developed in conjunction with management agencies. A management tool was developed for collating refuge values and habitat attributes, as well as threats to the maintenance and improvement of these important characteristics. This approach may be used for the prioritisation of interventions based on key management principles, including: threatened species, protection of habitat biodiversity, water allocation, catchment management actions, fisheries management actions and restoration.

Based on the information elicited from the pilot valley analyses, a template was produced to assist in refuge identification and management across the MDB. This template documents a process that can be integrated into regional natural resource management frameworks across the MDB, acknowledging that different states and regions are subject to various legislative and policy environments and possesses varying levels of information, data, planning structures and intervention opportunities that relate to aquatic habitat protection.                                                                

Findings: A wide range of aquatic habitats were considered important as drought refuges, with unregulated waterways the most commonly identified habitat type, and of the greatest concern to managers. In some instances, key native fish species were used to identify particular drought refuges. The protection and/or management of the refuges for these species either followed a ‘single species’ approach (more common in the drier, southern MDB) or ‘multi-species/community’ approach (more common in the northern MDB).

Refuges were defined and identified at larger spatial scales in the northern MDB and at smaller, site-specific scales in the southern MDB. The reason for these different approaches reflects the varying intensity of drought impacts across the MDB. These different approaches to the management and protection of drought refuges reflect the different aspects of native fish ecology, in terms of resistance versus resilience.

This study concluded that a holistic approach to drought management was required with drought refuge protection plans incorporating enough flexibility to identify and invest in emergency short-term responses during peak drought periods as well as having guidelines in place aimed at broader scales to promote long-term resilience in native fish populations.

Lessons learned and future directions:  This study has reinforced that priority areas which act as drought refuges require adequate management to ensure the long term survival of native fish populations. This study identified the two scales at which drought management operates and the strengths of each scale to address both short and long-term impacts of drought on native fish and their habitats. This information will ultimately lead to better drought management regarding native fish and their habitats, which will minimise the risk of loss of native fish species and populations and preserve native fish habitats.

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contact: Dr Dale McNeil, South Australian Research and Development Institute. Tel: + 61  8 8207 5342, Email:  dale.mcneil@sa.gov.au

Captions

 

Figure 2: A drying refuge (Photo courtesy of Luke Pearce)

LINK: http://www.sardi.sa.gov.au/__data/assets/pdf_file/0006/186702/Drought_Refuges_for_Native_Fish.pdf

Assessment of an infrared fish counter (Vaki Riverwatcher) to quantify fish migrations in the Murray-Darling Basin

Key words: infrared, fish counting, VAKI Riverwatcher, fish migration, Native Fish Strategy

A number of fishways have been constructed under the auspices of the NFS to help reinstate passage of fish past a number of barriers in the Murray-Darling Basin (MDB). Because it is too expensive to continuously trap fishways to gather information on migratory behaviour, using an electronic monitoring unit to continuously monitor fish migrations is an attractive option for monitoring fish movement and fishway effectiveness. The Vaki Riverwatcher technology has been successfully used in Northern Hemisphere rivers to count and measure the size, date and shapes of fish which pass through an infrared scanner. Prior to this project, this technology had not been trialled on Australian rivers and species to evaluate utility for monitoring purposes.

Broad aim and specific objectives: This study aimed to perform a field study on the effectiveness of an infrared fish counter, the Vaki Riverwatcher in anticipation of wider application throughout the Murray-Darling Basin. The limitations and advantages of the system were fully explored in both controlled and field environments.

The objectives of this project were to:

  • perform a field assessment of an infrared fish counter in the Basin;
  • determine if turbidity reduces the accuracy of an infrared fish counter; and
  • determine how fish behave in relation to an infrared fish counter and fish trap.

Methods: Laboratory trials were undertaken to determine the ability of the Riverwatcher (Figs 1-3) to cope with different turbidity and fish migration rates. Silver Perch (Bidyanus bidyanus) were passed through the unit under a range of turbidity between 0 and 100 Nephelometric turbidity units (NTU).

Field trials were undertaken at Lock 10, on the Murray River (near Wentworth), which had been retro-fitted with a vertical slot fishway in 2006. The unit was used in conjunction with a DIDSON sonar unit and a standard fish trap, to assess the ability of the Riverwatcher to distinguish different species, count migrating fish, estimate the size of migratory fish and to assess fish behaviour in and around the unit.

Field trials were also performed to test the Vaki Riverwatcher system under river conditions. The unit was used in conjunction with other electronic monitoring gear, and also fish traps, to assess the ability of the Riverwatcher to distinguish different species, count migrating fish, estimate the size of migratory fish and to assess fish behaviour in and around the unit.

Figure 1. The Vaki Riverwatcher (Photo courtesy of Lee Baumgartner)

Figure 1. The Vaki Riverwatcher (Photo courtesy of Lee Baumgartner)

Figure 2. Installing the vaki riverwatcher into the lock 10 fishway (Photo courtesy of Lee Baumgartner)

Figure 2. Installing the vaki riverwatcher into the lock 10 fishway (Photo courtesy of Lee Baumgartner)

Figure 3. Manipulating turbidity to quantify vaki effectiveness (photo courtesy of Lee Baumgartner)

Figure 3. Manipulating turbidity to quantify vaki effectiveness (photo courtesy of Lee Baumgartner)

Findings: The Riverwatcher performed well and counted hundreds of migrating fish. Fish counts from the unit roughly corresponded with those caught within a fish trap upstream of the unit. However, the unit tended to underestimate fish size and some fish avoided contact with the unit.

Experimental trials on the impacts of turbidity on the Riverwatcher revealed that the unit generally overestimated fish counts during low turbidity but underestimated during high turbidity. It was also difficult to identify fish that actively avoiding passage through the unit.

Lessons learned and future directions: The Riverwatcher unit provided a powerful mechanism to monitor fish movement but often underestimated fish numbers and lengths which detracted from the quality of the hardware. If these limitations are overcome, or at least quantified, the unit would represent a cost effective mechanism to count and measure migrating fish.

The unit has a range of potential applications including within fishways, at floodplain regulators, within supply channels or other points of suspected fish movement. It is flexible in terms of operation, but is limited by the restricted width of the scanner unit. Where width or depth is an issue, additional scanner units can be linked together to create an array which can give wider spatial coverage of the target area. Provided the site of application is a known point of fish movement, obtaining count and size data on migrants would be possible and should be considered for a long-term deployment at a key site of fish migration in the Basin. Additional trials would help to determine if the gear is suitable for determining trends in fish movement over a longer time period.

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy. 

Contact: Dr Lee Baumgartner, New South Wales Department of Primary Industries. Tel: + 61 2 6958 8215, Email: lee.baumgartner@dpi.nsw.gov.au

LINK: http://www.dpi.nsw.gov.au/__data/assets/pdf_file/0005/322970/AE_2010_Output-1629_Baumgartner-et-all_Vaki-Riverwatcher-report_REPORT.pdf

Scoping study to determine the methodologies and data availability for identifying native fish hotspots in the Murray-Darling Basin

Key words: hotspots, resilience, native fish, Native Fish Strategy

Recent ecological research at the landscape scale suggests that there may be key locations, or “hotspots”, that play a disproportionate role in sustaining species and ecological communities. The identification of native fish “hotspots’ in the Murray-Darling Basin (MDB) would greatly assist managers in protecting biodiversity and maintaining important ecological processes for native fishes.

Broad aim and specific objectives: This scoping study was undertaken to help guide future investment in the identification of “hotspots” in the Basin, by conducting broad reviews of the literature and available data, and consulting extensively with a range of relevant experts to:

  • develop an appropriate definition for what constitutes a native fish hotspot in the MDB;
  • identify the requirements of resource managers and other stakeholder groups including the Authority to maximise utility and adoption of the hotspots project;
  • identify information already available which may be useful to identify native fish ‘hotspots’;
  • determine appropriate metrics/methodologies to identify geographical areas or ‘hotspots’ across the MDB that are significant for native fishes in terms of species diversity, population densities and key ecological processes;
  • develop an appropriate experimental design for a large-scale project to demonstrate the applicability of the hotspots concept and subsequently enable the extrapolation across the whole of the MDB; and,
  • provide a template for similar studies to be undertaken on other fish species in the Basin.
Figure 1. A healthy stretch of the Murrumbidgee with plenty of habitat for native fish (Photo courtesy of Jamin Forbes)

Figure 1. A healthy stretch of the Murrumbidgee with plenty of habitat for native fish (Photo courtesy of Jamin Forbes)

Figure 2. Identification of native fish 'hotspots' would greatly assist in the management of native fish communities (Photo courtesy of Jamin Forbes)

Figure 2. Identification of native fish ‘hotspots’ would greatly assist in the management of native fish communities (Photo courtesy of Jamin Forbes)

Methods:  The first stage of the scoping study was to define the hotspots concept and management applicability of the project for key stakeholders within the MDB. This was achieved through an extensive review of the background literature of the hotspots concept (both within Australia and globally) and an expert panel workshop to:

  • clearly define the hotspots concept for use in the MDB and within the project, with particular reference to types of criteria;
  • explore spatial and temporal variability within existing datasets for identifying hotspots; and,
  • explore the management applicability and use of MDB hotspots for native fish.

A second expert panel workshop was held to review relevant ecological information for the priority species and communities, sampling methodologies and the spatial and temporal coverage of existing data and with the aims of:

  • determining appropriate sampling methodologies for identifying hotspots of priority species and communities; and,
  • using this methodology and data availability to develop an appropriate study design which could be used in Stage II of the of the project to identify ‘hotspots’ across the MDB that are significant for native fish.

Findings: The study mainly focussed on four high priority native fish species; Murray Cod (Macculochella peelii), Silver Perch (Bidyanus bidyanus), Golden Perch (Macquaria ambigua) and Freshwater Catfish (Tandanus tandanus), though some consideration was also given to some other species of conservation concern. The study defined a “hotspot” as being “areas within riverscapes that have extraordinary importance for fish or processes that sustain native fish populations”.

The study highlighted the importance of understanding the processes underlying hotspots in order to maximise the efficiency of management actions and conservation measures to ensure cost-effective return on interventions. To achieve this, a suite of suitable metrics were developed which encompassed both direct measures of fish and measures of the ecological drivers supporting them for each of the priority species and communities.

The study concluded that insufficient data currently exists to adequately identify hotspots across the MDB. However, this project provided an approach and suitable methods to collect relevant data that could then be used with current data to determine and describe hotspots in the MDB.

It was recommended that the next step should be to investigate large-scale patterns in focus species abundance using existing datasets, determine the applicability of the hotspots concept for all metrics in a subset of river valleys, then expand on observed trends to other valleys to identify hotspots throughout the MDB.

Lessons learned and future directions:

The identification of “hotspots’ in the Murray-Darling Basin (MDB) would greatly assist managers in protecting biodiversity and maintaining important ecological processes for native fishes. This study provides a pathway by which to engage the next step in the process of validating the hotspot concept in the MDB. This will identify critically important habitat required for protecting or rehabilitation to support priority native fish species.

Stakeholders and Funding bodies:  This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contacts: Zeb Tonkin, South Australian Research and Development Institute. Tel: + 61 3 9450 8600, Email: zeb.tonkin@depi.vic.gov.au.

Using hydroacoustics to monitor fish migration

Key words: split beam, hydroacoustics, sound waves, fish counting, fish migration.

Understanding how effective a new fishway is at providing passage for migratory fish is an important part of the design process. Most methods for sampling fish communities to understand movement rely on capture-based methods, which have issues with affecting fishes behaviour and thus biasing the results. Remote monitoring that is not based on capture removes such bias. Hydroacoustics (underwater sound waves) is one method of monitoring fish migration.

Project aim and methods: This project aimed to investigate a hydroacoustic method for counting fish migrating at the Murray River fishways. A 200 kHz split-beam hydroacoustic system was installed at the Lock 10 fishway in November 2007 to detect fish moving through the fishway exit channel. A dual-frequency identification sonar (DIDSON) acoustic system was also installed to provide video-quality images able to be used as a comparison with the split-beam acoustic data.

Figure 1: MD823 Fig 3 Echogram showing a fish (encircled in red) swimming out of the fishway exit channel at Lock 10 fishway (Photo courtesy of Andrew Berghuis)

Figure 1: MD823 Fig 3 Echogram showing a fish (encircled in red) swimming out of the fishway exit channel at Lock 10 fishway (Photo courtesy of Andrew Berghuis)

Figure 2: DIDSON laptop display. Photo courtesy of Lee Baumgartner

Figure 2: DIDSON laptop display. (Photo courtesy of Lee Baumgartner)

Figure 3 - Trial of acoustic and didson sounders set within fishway looking out at exit. (Photo courtesy of Mick Bettanin, Fisheries NSW.)

Figure 3 – Trial of acoustic and didson sounders set within fishway looking out at exit. (Photo courtesy of Mick Bettanin, Fisheries NSW.)

Findings:  The DIDSON system appeared to have several advantages over the split-beam system, but both were suggested to have merits for fish counting. The split-beam hydroacoustic system gave an automated fish count of up to 3.96 fish per minute moving through the fishway, but verification using the DIDSON indicated that nearly half of these fish were not detected. Data from the DIDSON system were also analysed, and an automatic fish count of up to 1.09 fish per minute was established. Visual verification over the same one-hour portion as the split-beam data found that over twenty five percent of fish recorded by the DIDSON system were not detected.

Automatic fish length detection consistently underestimated fish length, most likely due to the poor orientation of fish to the acoustic beams. However there did appear to be some relationship between acoustic target strength of fish detected with the split beam acoustic system and fish size, suggesting that this may require further investigation. The DIDSON appeared to provide fairly accurate fish measurement of fish and ongoing data collection and analysis may further improve estimates.

The project highlighted a major limitation of hydroacoustics, being an inability to discriminate between fish species, though it was noted that further experiments might assist in species recognition.

Low rates of fish migration and reduced river levels precluded the ongoing collection of data beyond the initial sampling period.

Lessons learned and future directions: The current study found that despite some limitations, use of hydroacoustics may assist in assessing migrating fish at man-made barriers, and assist in informing future fishway designs, which will have follow on benefits for the long term recovery.

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contact: Andrew Berghuis, Aquatic Biopassage Services, 0407 559 908, andrew@aquaticbiopassage.com.au.

Link: http://www.depi.vic.gov.au/__data/assets/pdf_file/0014/204251/ARI-Technical-Report-177-Performance-of-a-single-frequency-splitbeam-hydroacoustic-system.pdf

 

 

 

Sea to Hume Fishways – lessons from monitoring

Key words: Fish migration, fishways, monitoring, barriers, River Murray, Native Fish Strategy

Native fish species move along rivers for breeding, dispersal, to access habitat, escape threats and establish new territories. In 2001 the then Murray-Darling Basin Commission approved the construction of fishways (Figs 1 and 2) on all of the Locks and Barrages from Hume Dam to the mouth of the River Murray, thus ensuring continuous fish passage for 2,225 km. It was also vital to undertake monitoring at appropriate scales to determine whether constructed fishways were successfully restoring connectivity along the river for native fish species.

Project aims and methods: In order to assess whether the fishways were being effective, researchers sought to answer four questions:

  1. Are the fishways allowing passage of a full range of size classes and species of fish?
  2. Are the fishways reducing accumulations of fish downstream of the barrier?
  3. Are the fishways contributing to positive changes in the abundance and diversity of native fish in the river?
  4. Are the location, design and operation of the fishways optimised?

To answer these questions, two types of monitoring were performed – compliance monitoring to see if each fishway was working optimally and long-term monitoring to see if the fishway program was having a positive impact on native fish populations. 

Electrofishing and fishway trapping were used to sample fish communities and determine whether they were successfully ascending fishways. Sampled fish were identified and counted, and subsamples measured to enable species/size-specific trends to be identified. Environmental variables such as water temperature, river flow etc. were also recorded for analysis. 

Fig 1. Lock 3 Vertical Slot Fishway 3. (Photo Jarrod McPherson NSW DPI)

Fig 1. Lock 3 Vertical Slot Fishway 3. (Photo Jarrod McPherson NSW DPI)

Fig. 2. Lock 10, vertical slot fishway, assessment cage. (Photo Lee Baumgartner NSW DPI)

Fig. 2. Lock 10, vertical slot fishway, assessment cage. (Photo Lee Baumgartner NSW DPI)

Findings:

  • From sampling at Lock 8, the original aim for the passage of all fish, for each species, from a minimum of 31 mm long, all medium sized fish from 90 to 600 mm long, and adult Murray Cod (Macculochella peelii) to a maximum of 1000 mm long, was achieved.
  • Young-of-year (less than 1 year old) Bony Herring (Nematalosa erebi), and the juvenile size classes of Un-specked Hardyhead (Craterocephalus stercusmuscarum), Murray Rainbowfish (Melanotaenia fluviatilis) and Australian Smelt (Retropinna semonii) were unable to ascend the fishway.
  • several species smaller than the minimum target design size (40 mm), such as Carp Gudgeon (Hypseleotris spp.), Murray Rainbowfish and Unspecked Hardyhead, previously thought not to be migratory were, in their thousands, unsuccessfully attempting to gain upstream passage through the fishways.
  • Small-bodied fishes numerically dominated the total catch at the Lock 8 fishway and during spring and summer the bulk of these were juveniles and young-of-year. This highlights a need for an additional fishway design criterion that includes seasonal changes in fish sizes and migratory biomass, rather than simply aiming to pass a minimum length criterion alone.
  • At Lock 8 few non-native fish species were captured in the fishway, with the exception of adult Carp (Cyprinus carpio), which had an 87% success rate of negotiating the fishway.
  • Although the new vertical slot fishways at Locks 7, 9 and 10 performed to design specifications, there were species-specific variations in the minimum size of successfully ascending fish. In particular, many smaller Bony Herring and Golden Perch (Macquaria ambigua) could not negotiate the fishways.
  • At fishways constructed at the Barrages at the mouth of the Murray, over 98% of fish collected were small-bodied species which were attempting to use the fishways but were unsuccessful due to the design hydraulics, particularly at the vertical-slot fishways. Nevertheless, some small-bodied species were observed using the fishways during periods of low flow between the Lower Lakes and Coorong.
  • Large-bodied estuarine species such as Black Bream (Acanthopagrus butcherii), Mulloway (Argyrosomus japonicas) and various species of Mullet were noticeably absent from the fishways but were present in the vicinity of the Barrages. A large-scale acoustic tracking program was initiated to determine fish passage success for these species.

Longer term monitoring (at Locks 1-3) showed that:

  • Catches were dominated mostly by small and medium bodied species during low flow conditions. Murray Cod were rarely encountered but the captured population was dominated by large individuals, suggesting that recruitment (survival of fishes from eggs to reproductive stage) opportunities for this species in the lower reaches of the River may be limited.
  • Surveys consistently showed large downstream aggregations of fish, dominated by small-bodied native fish and Carp.
  • Australian Smelt, Bony Herring, Flat-headed Gudgeon (Philypnodon grandiceps), Unspecked Hardyhead, Murray Rainbowfish and Carp Gudgeon remain common in the main channel of the lower River Murray.
  • Differences were observed in the diel (daytime vs night-time) composition of the fish community. Some species and sizes were moving exclusively at night.

Lessons learned and future directions:  While many overseas fishways are designed to pass only a few large-bodied economically important fish species, the Murray River fishways are able to restore passage for the majority of migratory species.

The attempted upstream movement of small-bodied threatened species such as Carp Gudgeons, Murray Rainbowfish and Unspecked Hardyhead was not known before the ‘Sea to Hume’ program, highlighting the need to identify the migratory community prior to fishway construction. The subsequent passage of Carp Gudgeons through modified fishways will assist in restoring the ecological processes of dispersal and recolonisation for this species.

At the Barrages, fishway types identified as being suitable to facilitate small-bodied fish passage include small fish locks (mechanical elevator-style fishways), low-head vertical-slot fishways (which use a sequence of pools and baffles to control water depth and velocity) and rock-ramp fishways (which are more natural looking fishway designs constructed of rock in such a way as to create a sequence of pools separated by rocky ridges to control flow). To be effective and efficient at facilitating the passage of small-bodied fish over a long migration season (potentially August to March) these fishways will need to operate over a broad range of flow and headloss conditions. Securing environmental water allocations and delivering these in a manner that resembles natural seasonal cycles will potentially deliver the greatest ecological benefit.

Observed changes in diel abundance patterns of fish assemblages in the lower Murray River

has important implications for future fish passage studies: both day and night samples are required to adequately describe the migratory community.

Remote passive integrated transponder (PIT) tag reader systems, which have been installed at most of the new fishways, continually monitor for any of the 30,000 fish PIT tagged in the Murray River. Upon completion of the program a tagged fish can now be tracked up and down the River for its whole lifetime, providing important ecological data and also offering community stakeholders the opportunity to be involved in the program.

Restoring fish migration in over 2000 km of river is likely to have flow-on benefits. These will maximise the potential success of other management practices such as habitat restoration and threatened species protection for the rehabilitation of native fish populations in the Murray-Darling Basin.

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contacts: Dr Lee Baumgartner, Fisheries NSW, + 61 2 6958 8215, lee.baumgartner@dpi.nsw.gov.au,

 Link: http://www.mdba.gov.au/sites/default/files/archived/mdbc-NFS-reports/2179_Sea_to_Hume_Dam_final_report.pdf

Evaluating use of chemical marking in monitoring stocked fish

Key words: fish tagging, fish marking, chemical marking, stocking effectiveness, Native Fish Strategy

More than three million native fish are produced in private and government hatcheries and stocked into waterways of the Murray-Darling Basin each year. To date, little has been known of the fate of stocked fish or their impact on wild populations, in part because of a lack of suitable methods for marking small juvenile fish. The increasing use of wild fish populations as indicators of river ‘health’ was also potentially compromised by the inability to distinguish between hatchery-bred and wild fish.

Objectives and methods: A sequence of projects funded through the Native Fish Strategy sought to develop techniques for marking hatchery bred fish.

Three marking methodologies were trialled and developed using Golden Perch (Macquaria ambigua) as the model fish species:

  • Osmotic induction marking of fingerlings (which enhances uptake of the marker chemical by immersing fish in a 5% saline solution) with alizarin red S and calcein. (Figs 1 and 2)
  • Marking of otoliths (ear bones) via immersion of fingerlings in enriched stable isotopes of strontium and barium.
  • Transgenerational marking of otoliths through the injection of enriched stable isotopes of barium into maternal broodfish

The feasibility of each of the methods was examined with particular emphasis on practicality and economic considerations for government and private hatcheries.

A range of experiments were conducted to investigate marking effectiveness, assess the influence of immersion times and chemical concentrations on mark intensity, and test for impacts of marking on growth and mortality. Experiments were also conducted to assess whether enriched stable isotopes could be used to induce multiple unique marks, which could then be used as batch marks.

Consultation took place with the Australian Pesticides and Veterinary Medicines Authority (APVMA) and Food Standards Australia New Zealand (FSANZ) to seek clarity on whether marking constituted use of a veterinary chemical product, and the legality of their use in fish that may eventually be consumed as food.

Field-based experiments were undertaken to assess the contribution of stocked fish to fish communities sampled in a number of rivers. Experimental stocking and subsequent fish community surveys took place in the Murrumbidgee River, Edward River and Billabong Creek. The Murray River between Yarrawonga and Tocumwal was also surveyed as an unstocked reference site. Stocked fish were either marked with alizarin complexone or calcein, or were confirmed as stocked fish using otolith chemistry analyses. Electrofishing surveys in experimental and control river reaches enabled assessment and comparison of the contribution of stocked fish to fish communities sampled. 

Figure 1. A calcien marked fish head under natural light. Photo courtesy of Arthur Rylah Institute.

Figure 1. A calcien marked fish head under natural light. Photo courtesy of Arthur Rylah Institute.

Figure 2. A Golden perch fingerling newly marked with calcein. (Photo courtesy of Arthur Rylah Institute.)

Figure 2. A Golden perch fingerling newly marked with calcein. (Photo courtesy of Arthur Rylah Institute.)

Findings: Each of the methods was found to have strengths and weaknesses. Techniques that only marked otoliths (i.e. stable isotopes) require the fish to be killed and the otoliths analysed in a laboratory to determine whether they are marked. However alizarin and calcein leave external marks that can be detected in the field without having to sacrifice the fish, a distinct advantage for most river health monitoring programs or projects involving threatened species.

A field detection kit for calcein marks was developed which included a field fluorometer for quantitative measurement of calcein fluorescence and a specialised torch and glasses set for visual identification of marked fish.

Investigation revealed that there were no registration requirements for any of the marking techniques and chemicals, and that the chemical marking techniques developed during the project can be legally applied in hatcheries provided specific processes are undertaken.

The results of the field stocking experiments showed that at least a proportion of the stocked fish survived to reach the legal minimum size in all three rivers. However, the impacts of stocking on population structure were very different among rivers. In the Edward and Murrumbidgee Rivers, the age classes corresponding to the years of stocking were comprised of 18-38% experimentally stocked fish, and these fish made only a relatively minor contribution to the total catch of Golden Perch. In contrast, stocked fish comprised up to 100% of age classes in Billabong Creek and stocking resulted in a four-fold increase in the catch rates of Golden Perch.

Lessons learned and future directions: Osmotic induction marking with calcein had no detectable effects on fish health and was found to be relatively quick and easy – taking only 15 minutes to mark up to 20,000 fingerlings. The simplicity and cost-effectiveness of osmotic induction marking make it feasible for widespread adoption in hatcheries.

Large-scale calcein marking of hatchery fish commenced in 2009, and agencies from all State and Territory jurisdictions within the MDB have initiated processes to incorporate calcein marking into their stocking and/or research programs. The results of the experimental stocking study demonstrate that stocking has the potential to strongly affect population structure and abundance of the stocked species.

Stakeholders and Funding bodies:     This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Developing a population model for Murray Cod (Macculochella peelii) to address key management actions

Key words: Population model, Murray Cod, fisheries management, Native Fish Strategy

Threats and Impacts: Murray Cod (Macculochella peelii) is a key recreational fishing target species as well as being a nationally listed threatened species (Fig 1). Management action is required to rehabilitate populations of this species in the Murray-Darling Basin. Fish population models are a simple description of a fishes life cycle and try to incorporate any external factors that may affect the individual and population. The main use of these models is to hypothetically assess the impacts (negative or positive) of different management or environmental scenarios to provide managers with predictive power to better manage fish populations. Prior to this project no such model had been created for any species in the Murray-Darling Basin.

Broad aim and specific objectives: The objectives of this project were to:

  • Develop a computer model (or models) to represent the population dynamics of Murray Cod under alternative management options.
  • Develop various management scenarios in relation to size and bag limits and potential recovery times from overfishing, fish kills and other management or environmental scenarios which may affect Murray Cod populations.
  • Document the findings of this work, and the implications for developing management options for Murray Cod and the research on Murray Cod biology and ecology required for improving the model (or models).

Methods: A review was undertaken initially to summarise relevant scientific, management, angler and aquaculture literature on:

  • Murray Cod biology and ecology;
  • Management options for Murray Cod and similar fish in the Murray-Darling Basin and elsewhere; and,
  • Population and other (climate and GIS) models for fish or other fauna which will allow alternative management options to be tested;

Conceptual models of Murray Cod biology and ecology were then developed, and information gaps which needed to be addressed were identified. A workshop was also held to bring together a range of technical experts and jurisdictional representatives (SA, QLD, VIC, NSW, ACT and Commonwealth) to determine the key management actions to address the sustainable management of Murray Cod as well as the knowledge requirements necessary to develop the appropriate model(s) to assess the key management actions.

A population model for Murray Cod was developed as a key output of this project, which would enable different management actions/scenarios to be assessed and compared on the basis of their relative benefit and level of risk.

Figure 1 - This project developed a population model for Australia's largest freshwater fish species, Murray Cod . (Photo courtesy of Jamin Forbes)

Figure 1 – This project developed a population model for Australia’s largest freshwater fish species, Murray Cod . (Photo courtesy of Jamin Forbes)

Figure 2 - An example of graphical outputs from a fishing scenario. (Courtesy of Charles Todd.)

Figure 2 – An example of graphical outputs from a fishing scenario. (Courtesy of Charles Todd.)

Findings: Modelled management scenarios for Murray Cod indicate that the risk to populations can be reduced substantially by appropriate changes to the size limits on angler take. The  implementation of a slot size (minimum and maximum size limit) that protects both smaller and larger fish reduced population risk considerably. While habitat changes are difficult to quantify, it was illustrated that reductions in amount of habitat can place additional risk on populations, particularly when combined with angler take. Importantly, the collective impacts of less recognised threats such as thermal pollution, fish kills and mortalities to larvae over weirs and losses into irrigation off-takes can be explored and need to be recognised as having the potential to contribute significantly to mortalities at certain sites.

Lessons learned and future directions: The methods outlined in this study offer a formalised, rational, modelling approach that can form the basis for the assessment and prioritisation of management options for Murray Cod to minimise the risk to populations. Such modelling also highlights data gaps and monitoring requirements and can become an integral part of the conservation and fishery management process (Fig 2) and provides a tool for exploring the outcomes of management scenarios at both the regional and local scale. The modelling process has helped facilitate interagency Murray Cod management and emphasises the need for coordination between fishery managers and water/environmental protection/conservation agencies.

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contact: Dr. Charles Todd, Arthur Rylah Institute, (02) 60519920, Charles.Todd@depi.vic.gov.au, 23 Brown St, Heidelberg, Victoria, Australia, +61 3 9450 8600.

Link: http://www.mdba.gov.au/sites/default/files/pubs/MC-Final-Report.pdf

Counting Murray-Darling fishes by validating sounds associated with spawning

Key words: fish counting, spawning, Murray-Darling Basin, Native Fish Strategy

Over 700 fish species worldwide produce sounds, and the unique sounds made by fish species can often detected using underwater microphones. Most sounds are produced during courtship, for communication or identification, and they can be useful if attempting to locate fish, make abundance estimates, or direct habitat management. Prior to this project however, there had been little consideration given to use of sounds produced by fish for these purposes in Australian rivers.

Broad aim and methods: The specific objectives of this project were:

  • To trial a bioacoustic (fish noises) technology to determine whether captive large-bodied native fish (Murray Cod (Maccullochella peelii), Golden Perch (Macquaria ambigua), and Silver Perch (Bidyanus bidyanus) produce sounds associated with artificial or pond spawning, and whether spawning population counts can be obtained.
  • To isolate individual spawning sounds produced by each fish species and its associated behaviours, for example, do individual species produce unique, distinguishable sounds for male dominance, courtship, spawning or distress?
  • To test for soniferous sounds in wild collected adult carp spawned in captive conditions.
  • To scope passive bioacoustics as a tool for measuring the relative abundance of fish in key habitats and potentially in fishways.

 A series of trials were undertaken initially to benchmark or sound truth ambient noises within the experimental environment. In an initial trial, a hydrophone was placed into a tank with no fish to record noises. A second trial involving the same procedure but with a single fish was undertaken. The final experimental phase was to benchmark the noises from a number of fish (mixed sexes) Four fish that had been injected with hormones (two male and two female) were placed into a tank and recorded for 24 hours (Figs 1 – 2). A DIDSON camera was also set up to provide vision of the spawning fish.

Figure 1 - A sonogram of acoustic signals recorded in a tank with spawning Golden Perch. The noise could not be specifically isolated to the fish. (Courtesy of Ivor Stuart)

Figure 1 – A sonogram of acoustic signals recorded in a tank with spawning Golden Perch. The noise could not be specifically isolated to the fish. (Courtesy of Ivor Stuart)

Figure 2 - Researcher Jonothan Doyle listening to fish. (Photo courtesy of Ivor Stuart)

Figure 2 – Researcher Jonothan Doyle listening to fish. (Photo courtesy of Ivor Stuart)

Findings: Several acoustic noises were isolated during the project and although these were absent from the controls they could not specifically be attributed to the fish. These results demonstrate that some Murray-Darling Basin native fish potentially produce noises. Further research and replication is needed to clarify the mechanism of fish sound production, individual variation in vocalisation and the utility for research and management. The sonogram data did appear to include biological noise, but the DIDSON camera proved unsuitable in hatchery tanks and further work with fixed video cameras is needed to link sound production with fish behaviour.

Murray Cod appear to provide a model species for further acoustic trials as these fish have complex social behaviour that can be observed in the semi-natural conditions of a hatchery pond. The suggested protocol is to set up a DIDSON camera or video recorder and hydrophones within the spawning drum (used by fish as a laying site). This method would allow visual confirmation of fish making noises, and the hydrophone would be placed in an optimal position to capture any vocalisations.

Lessons learned and future directions: The preliminary results of this project suggest that using a hydrophone to detect native fish is plausible, but requires further work. If further trials are successful this technology would be useful for detecting native fish spawning which would be used to determine fish habitat preferences for both conservation and rehabilitation. 

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contacts: Ivor Stuart, Kingfisher Research P/L.,0408 619 126, ivor.stuart@gmail.com

Link: http://www.mdba.gov.au/sites/default/files/pubs/MDBA-13088-Soniferous-Reportv2.pdf

Assessment of a potential to develop population models for priority species in the Murray-Darling Basin

Key words: population models, native fish, Murray-Darling Basin, Native Fish Strategy

Threats and Impacts: Native fish of the Murray-Darling Basin (MDB) have experienced severe contractions since European settlement. Gaining greater insight into the population dynamics of native fishes is critical for long-term conservation. Population models play an important role in identifying underlying factors that may affect population structure and the persistence of species.

Broad aim and specific objectives: This study aimed to assess the potential development of population models for priority species in the MDB and provide an indication of the use of these types of models in natural resource management. 

An initial review of the available literature was undertaken to assess the degree to which populations models developed for Australian freshwater fishes have been adopted to inform decision making by managers or guide data collection and research directions.

A survey was undertaken of fish and fishery managers to identify species of interest. A further survey of managers and researchers provided information on data availability for these species. For each species of interest, a life cycle model was developed to help identify the data required to develop a population model. This process, in conjunction with the information gathered from mangers and researchers and information already available in the literature, identified key knowledge gaps to help guide future research and data acquisition for developing a deeper understanding of population dynamics.

Findings: A review of population models in natural resource management raised a number of concerns in relation to the ability to get appropriate information from the primary literature. The review did also find good examples of where population models have integrated into management and policy, mainly in a fishery context. There are some examples where models have influenced management and policy development in freshwater research such as the trout cod model. Although the review found there was strong interest in the development of models, there needs to be a concerted effort from all interested parties to ensure models are used to influence policy and management outcomes and utilised by the intended stakeholders.

This study also surveyed a number of fish and fishery managers in the Murray-Darling Basin to establish a list of fish species of most concern. Twenty five species were recorded as of most concern and these were scored for priority. A further survey of scientists and managers was conducted to assess data availability that could be used in a model similar to that developed for Murray Cod (Maccullochella peelii). Of the twenty five species reviewed, there was sufficient life cycle information to construct an age population model and data that could be used to estimate the parameters required for an age structured model for eight species (in order of concern with rank number): Silver Perch (Bidyanus bidyanus) (1st); Macquarie Perch (Macquaria australasica) (2nd); Trout Cod (Maccullochella macquariensis) (4th); Murray Hardyhead (Craterocephalus fluviatilis) (6th); Golden Perch (Macquaria ambigua) (7th); Two-spined Blackfish (Gadopsis bispinosus) (14th); Carp (Cyprinus carpio) (17th); Brown Trout (Salmo trutta) (23th); and while no data was held in Australia for Rainbow Trout (Oncorynchus mykiss) (12th), sufficient data is available in the international literature to estimate the required parameters for an age based population model. As a priority, it was recommended that models be developed for the five species ranked in the top 10 of species of most concern: Silver Perch, Macquarie Perch, Trout Cod, Murray Hardyhead and Golden Perch.

It was also recommended that research be undertaken on the five other species of concern in the top 10, for which there is insufficient information to construct a model, to improve knowledge and/or data to the model development level and consider model development for these species. 

Figure 1 - Silver Perch was identified as a species for which a population model could be developed, and would be valuable. (Photo courtesy of Jamin Forbes)

Figure 1 – Silver Perch was identified as a species for which a population model could be developed, and would be valuable. (Photo courtesy of Jamin Forbes)

Figure 2 - This study highlighted value of using data on Trout Cod to inform an age structured population model. (Photo courtesy of Jamin Forbes)

Figure 2 – This study highlighted value of using data on Trout Cod to inform an age structured population model. (Photo courtesy of Jamin Forbes)

Lessons learned and future directions: The study has highlighted a short list of native species, which as a priority require population modelling to provide better guidance for future management actions (Figs 1 and 2). Better-targeted management actions will provide increased benefits for native fish populations on a benefit per resource basis. The highlighted species where insufficient data is available to construct population models provide researchers with a shortlist of priority research questions and should better focus attempts at filling knowledge gaps for native fish species of the MDB. 

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contact: Dr. Charles Todd, Arthur Rylah Institute, (02) 60519920, Charles.Todd@depi.vic.gov.au, 23 Brown St, Heidelberg, Victoria, Australia, +61 3 9450 8600.

Link: http://www.finterest.com.au/wp-content/uploads/2013/07/MD1179%20Population%20modelling%20scoping%20study.pdf

Audit of water quality problems arising from land use in the Murray-Darling Basin

Key words: water quality, audit, land use, Murray-Darling Basin, Native Fish Strategy

Aims: This is one of a suite of early projects under the Native Fish Strategy (NFS) that sought to scope the issues and information gaps that the NFS would need to address.  Specifically, this project aimed to: :

  • collate data, identify and map regions , landscapes, land uses and industries that are important causes of water quality (WQ) problems in the Basin (e.g. Fig 1)
  • Determine a meaningful scale/accuracy for reporting based on available data and quantitatively report on land use (distributed and point source) contributions to WQ problems on a third order catchment basis.
Figure 1 - this project sought to collate data on land uses and industries which are important causes of water quality problems. Photo courtesy of Arthur Mostead.

Figure 1 – this project sought to collate data on land uses and industries which are important causes of water quality problems. (Photo courtesy of Arthur Mostead.)

Methods: This project was essentially a desktop review and Geographic Information System data atlas formation exercise that included: developing a classification of land uses/management practices in relation to WQ impacts; identifying existing relevant datasets and projects; evaluating available data for relevance and identify gaps; reporting the findings for a pilot catchment (the Broken River/Creek catchment in Victoria). Mapping was available at a range of scales.

There is a wide range of physical, chemical ecotoxicological and ecological parameters that can be used to provide information on WQ, but no single measure of overall WQ. The WQ parameters selected for the study were considered to have direct effects on native fish as well as direct effects on habitat suitability, food sources as well as fish behaviour and ability to migrate and reproduce. Water quality parameters considered of major importance in the study were temperature (cold water); turbidity, dissolved oxygen, and nitrogen/ammonia. Parameters of moderate importance were salinity, pH, toxicants, and pathogens. Land use has known relationships with the nature of WQ changes that occur as a result of that land use (e.g. mining and acid water drainage), and similarly there are known relationships between point source discharges from particular industries and WQ. A matrix of relationships between land use/point source discharges and the nine WQ parameters informed a spatial model that also included a risk assessment of the likelihood and consequence of a critical WQ impact occurring, including the location of high priority native fish sites (species/habitats/refuges). 

The methodology devised for the project was designed to:

  • Facilitate ease of access and use of a complex array of land use and WQ related datasets
  • Display the data so that it can be used by managers responsible for native fish and their habitat
  • Recognise important WQ parameters for native fish in the Basin
  • Provide insight into areas of the Basin under threat from WQ changes with respect to native fish, and
  • provide a predictive yet easy to understand and utilise spatial model.

Findings: The spatial model when applied to the Broken River catchment with land use mapped at ≤1:100,000 scale clearly identified spatial areas that were at risk of WQ impacts, and the level of the risk involved (low, moderate, high extreme). When compared with land use mapped at the 1:250,000 scale, the coarser scale of mapping led to errors in assessment of risk of WQ impacts. Consequently, the spatial model was not recommended to be used for specific catchment investigations where land use was captured at scales >1:100,000. While the limitations of 1:250,00 scale land use capture are acknowledged, analysis using such data may provide useful information to focus further investigations. Consequently the spatial model was applied across the entire Basin at the 1:250,000 scale and indicated the following catchments had the most land use area with high potential to cause water quality impacts that may affect native fish: Gwydir, Namoi, Murray (Hume Dam to SA Border), Murrumbidgee, Loddon, Broken, Goulburn and Campaspe. 

Lessons learned and future directions: The spatial model provided a useful tool for managers to investigate and visualise areas at risk of WQ impacts to native fish. The ability of the model to discriminate such areas at risk at a specific catchment scale declined above scales of 1:100,000 for land use mapping. The lack of detailed information on fish tolerances to various WQ parameters hampers the precision of the model. Similarly the scarcity of spatial data on WQ and the lack of readily available spatial data for fish distribution was a significant issue.

Stakeholders and Funding bodies:  This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy.

Contact: Earthtech, +61(7) 3343 3166

Link: http://www.mdba.gov.au/sites/default/files/archived/mdbc-NFS-reports/464_execsum_audit_WQproblems_draft.pdf