Category Archives: Genetic issues

Management of genetic resources within the Murray-Darling Basin

Key words: Murray- Darling Basin, fish, genetic diversity, genetic resources, Native Fish Strategy.

The Native Fish Strategy aims to rebuild all fish stocks within the Murray-Darling Basin (MDB) to 60 percent of pre-European settlement levels within 50 years. To achieve this target, management responses would be assisted by an understanding of the underlying genetic diversity of species. Many species have genetically distinct populations. For example, Murray Cod (Macculochella peelii) are known to have little genetic difference throughout most of the southern range of the MDB, however, several populations (Lachlan, Macquarie and Gwydir catchments) were found to be genetically distinct.

Maintaining genetic diversity is critical to species and ecosystem resilience, particularly in the face of changing environmental conditions. Despite the explicit recognition within legislation that genetic diversity is a key component of biodiversity, until now there remains no consistent or practical guidelines for the management of these resources.

Project objectives and methods: The objectives of this project were to create a resource able to be used to guide the management of genetic diversity within the Basin.

Specific objectives:

  • Review current genetic management practices across the MDB;
  • Review the current knowledge base for genetic structure within native fish species in the MDB and identify knowledge gaps;
  • Hold an international workshop to define the level of genetic management required to maintain distinct evolutionary significance of native fishes within the MDB;
  • Suggest a consistent approach to the management of genetic resources for native fish in the MDB.

A survey of fisheries agencies was conducted to identify current genetic management protocols for hatchery management, restocking, translocations, conservation captive breeding programs, fish rescues and interventions and the monitoring of threatened species. Protocols for the collection, preservation and storage of genetic material (e.g. fin clips, biopsy material, scales, bones, cryopreserved sperm, etc.) were also identified.

Previous and contemporary genetic research of MDB species was reviewed to highlight and map inferred genetic boundaries within the Basin. All available published and unpublished molecular data were compiled to assist in determining genetic structuring, ecologically sustainable units and management units. Strengths, weaknesses and implications of these data were considered, knowledge gaps highlighted and methods for addressing these gaps were discussed.

A workshop was held to determine what level of genetic management is appropriate for fish in the MDB and bring together experts to present the latest thinking on defining conservation units, to help inform development of a framework for prioritising and managing evolutionary distinction. Review findings and workshop outputs were then used to inform development of guidelines for management of genetic diversity in Australian native fish within the MDB which includes:

  • a review of current genetic issues and management practices across the MDB;
  • a review of the genetic structuring for native fish and crustacean species in the MDB including knowledge gaps;
  • guidelines and recommendations for genetic management within the MDB;
  • a genetic management template for fish stocking; and,
  • recommendations from the Management of Genetic Resources for Fish and Crustaceans in the Murray-Darling Basin workshop.
Figure 1. Studies have indicated there may be up to five discrete populations of Golden Perch (Macquaria ambigua) in the Basin (Photo courtesy of Jamin Forbes)

Figure 1. Studies have indicated there may be up to five discrete populations of Golden Perch (Macquaria ambigua) in the Basin (Photo courtesy of Jamin Forbes)

Figure 2. Studies have shown there to be five distinct genetic populations of Murray cod in the Basin  (Photo courtesy of Jamin Forbes)

Figure 2. Studies have shown there to be five distinct genetic populations of Murray Cod in the Basin (Photo courtesy of Jamin Forbes)

Findings and recommendations: Available data on genetic subdivision for 65 fish and crustacean species across the MDB were reviewed and discussed in the context of management for these species. This review highlighted significant genetic differences between populations of native fish and crustaceans within the Basin. These genetically different populations potentially contain unique evolutionary heritage that will require specific approaches to manage.

A number of recommendations were provided from this project:

  • Populations that are defined as distinct genetic management units should be treated as unique populations with limited transfer of individuals between units (Figs 1 and 2).
  • Information provided through this project should be used to develop a unified approach to the management of genetic diversity within the MDB.
  • The substantial knowledge gaps for species with insufficient genetic data (outlined in species profiles) should be addressed to allow the identification of genetic management units for the MDB.
  • Adequate stocking and hatchery genetic protocols should be adhered to for all breeding programs within the MDB.

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

Contacts: Dr Andy Moore, Department of Agriculture Fisheries and Forestry. Tel: + 61 2 6272 3090, Email: anthony.moore@daff.gov.au.

Assessing the impacts of native fish stocking on fish within the Murray-Darling Basin (MDB)

Key words: fish stocking, impacts, native fish, Murray-Darling Basin

Fish stocking (i.e. hatchery production of fish to a size or stage so that they can be released into an area) has been practiced worldwide for centuries, but it is only recently that the environmental and ecological risks have been recognized. Stocking has been undertaken largely to enhance recreational angling but also to aid conservation of a species. Regardless of the objectives, appropriate and effective management of stocking activities is required because a number of risks exist, which are not always well understood.

Broad aim and methods: This project reviewed the impacts of native fish stocking on fish within the Murray-Darling Basin (MDB), and also provided a summary of stocking activities within the MDB. Potential impacts on abundance and behaviour, genetics, disease and ecosystem level effects were considered.

A review of literature was undertaken to consider the impacts of native fish stocking on fish within the MDB. Research papers were evaluated using the following criteria: a) whether the research was relevant to native fish stocking; b) whether the design was confounded; and, c) whether the analysis and interpretation of data were correct and the conclusions valid. Studies that did not meet these criteria but provided useful information to generate hypotheses were also considered.

The review focused on four potential impacts of stocking: abundance and behavioural responses; genetic implications; spread of disease; and ecosystem level effects.

There is a need to ensure that potential risks associated with stocking are acknowledged and managed. (Photo courtesy of Michael Hutchison)

Figure 1. There is a need to ensure that potential risks associated with stocking are acknowledged and managed. (Photo courtesy of Michael Hutchison)

Findings: Changes to abundance and behaviour of fish from stocking were reported to arise mainly through competition between stocked and wild fish. These effects can be either direct (for food and habitat) or indirect (habitat alteration, behavioural changes, expansion of species range and displacement of wild stocks). Generally, there has been a lack of research on abundance and behavioural responses to fish stocking on native Australian species.

Genetic impacts of hatcheries and hatchery fish on wild populations were noted to have received a lot of attention, but the literature is mainly theoretical in nature. Genetic effects can be direct (e.g. hybridisation) and indirect (e.g. reduction in population size caused by predation, competition and diseases). Artificial breeding of fish also alters the genetics of captive bred populations. At the time of this project, very little was known about the genetic structure of native fish populations in the MDB.

Impacts of introducing diseases, parasites and exotic organisms unintentionally when stocking fish were noted to have received little attention. The accidental introduction of a disease with the stocking of native species is most likely to have a negative impact on wild populations. Several examples of the spread of pathogens through stocking exist for the MDB.

Ecosystem alteration from stocking fishes is extremely difficult to demonstrate, and has mostly been attributed to introduced species rather than native species.

Figure 2: Fish stocking can assist fish conservation or enhancing recreational fisheries, but can also impact on wild populations and ecosystems if not managed correctly. (Photo courtesy of Lee Baumgartner)

Figure 2: Fish stocking can assist fish conservation or enhancing recreational fisheries, but can also impact on wild populations and ecosystems if not managed correctly. (Photo courtesy of Lee Baumgartner)

Lessons learned and future directions: The review concluded that targeted research on MDB species is needed for all potential impacts and highlighted a need for sound baseline data and monitoring programs. Many species of native fish in the MDB are stocked in some way and the potential impacts outlined in this review should be considered when designing or reviewing stocking programs to maximise desired effects (i.e. boost numbers of stocked species) and minimise negative effects on resident native fish species (Figs 1 and 2). The study identified potential benefits in undertaking a risk assessment of potential impacts prior to stocking and conducting experimental evaluation and monitoring of any stocking program.  Only with such an approach will the success of stocking programs be evaluated and the risks mitigated.

Stakeholders and Funding bodies: This project was funded through the Murray-Darling Basin Authority’s Native Fish Strategy, and conducted by Bronwyn M. Gillanders, Travis S. Elsdon and Andrew R. Munro University of Adelaide and Woods Hole Oceanographic Institution.

Contact: Professor Bronwyn Gillanders, University of Adelaide, bronwyn.gillanders@adelaide.edu.au or +61 8 830 36235.

Seagrass meadow restoration trial using transplants – Cockburn Sound, Western Australia

Jennifer Verduin and Elizabeth Sinclair

Keywords: marine restoration, seagrass, Posidonia australis, transplant, genetic diversity, microsatellite DNA, provenance

Cockburn Sound is a natural embayment approximately 16 km long and 7 km wide, to the west of the southern end of the Perth metropolitan area. Its seagrass meadows have been reduced in area by 77% since 1967, largely due to the effects of eutrophication, industrial development and sand mining. To answer a range of questions relevant to seagrass restoration, we (i) carried out a transplant trial, (ii) monitored the impact and recovery of the donor site, and (iii) retrospectively assessed genetic diversity in the transplant site.

Methods. (i) The transplant trial was conducted between 2004 and 2008 in an area totalling 3.2 hectares of bare sand at 2.2–4.0 m depth on Southern Flats, Cockburn Sound. Donor material was sourced from a naturally occurring seagrass meadow on Parmelia Bank, north of Cockburn Sound, approximately 16 km away from the transplant site. Sprigs (15–20 cm length) of a dominant local seagrass, Posidonia australis Hook.f., were harvested from donor material and each sprig tied to a purpose-designed degradable wire staples (30 cm in length) and planted and secured into a bare sandy area at 50 cm shoot spacing by SCUBA divers (Figure 1). Sprig survival was periodically monitored in 10 m x 10 m representative sub-plots (15–20 plots per hectare).

(ii) For the meadow recovery study, several plug (a clump of seagrass excavated) extraction configurations were examined in P. australis meadows to monitor shoot growth into plug scars, with metal rings placed into the resulting bare area to monitor shoot growth into it at 3, 10, 13 and 24 months. Rings of 8.3 cm diameter were placed into adjacent undisturbed meadows to act as reference plots. (iii) Shoot material was collected from established plants for microsatellite DNA genotyping from the donor site in 2004, and from the 2007/2008 plantings in the restoration site in January 2012. Genetic sampling from the restoration site was done from mature shoots only, to ensure we were sampling original donor material. DNA was extracted from shoot meristem and genotyped using seven polymorphic microsatellite DNA markers (Sinclair et al. 2009).

Fig1

Figure 1. Transplants in situ, prior to the pegs being covering with sediment (Photo Jennifer Verduin)

Results. (i) The transplants have grown well to fill in gaps and become a healthy, self-sustaining meadow, with first flowering in July 2010, three years after initial transplant in 2007. There has also been considerable natural recruitment in the area through regrowth from matte and new seedlings (Figure 2). (ii) No significant differences in shoot growth between extraction configurations were observed in the donor meadow, and there was an increase in shoot numbers over two years. Based on the number of growing shoots, the predicted recovery time of a meadow is estimated at three years. (iii) Genetic diversity was very high in the restored meadow (clonal diversity R = 0.96), nearly identical to the donor meadow.

Fig2

Figure 2. Aerial view of the restoration site (within yellow markers), with natural recruitment occurring from vegetative regrowth and new seedling recruits (Photo Jennifer Verduin, 2010).

Important considerations for long-term success and monitoring. While several important questions have arisen from this trial, it demonstrated that (i) the transplants achieved a high level of establishment within a few years; (ii) the high genetic diversity in the donor site was captured and retained in the restored meadow; and (iii) surrounding sandy substrate is being colonised by P. australis through regrowth from the matte and natural recruitment from seeds dispersed within and/or from other meadows, (the latter potentially helping to ensure the long-term viability of restored seagrass meadows.)

Partners and Investors: This project was carried out as part of the Seagrass Research and Rehabilitation Program through Oceanica Consulting Pty Ltd, with Industry Partners Cockburn Cement, Department of Commerce (formerly Department of Industry and Resources), WA, Department of Environment and Conservation WA, The University of Western Australia, and the Botanic Gardens and Parks Authority, WA.

Contact: Jennifer Verduin, School of Environmental Science, Murdoch University, Murdoch, WA 6150 Australia Email: J.Verduin@murdoch.edu.au; Elizabeth Sinclair, School of Plant Biology, University of Western Australia, Crawley, WA 6907 Australia Email: elizabeth.sinclair@uwa.edu.au. If you are interested in becoming involved with seagrass rehabilitation through student projects please contact us.