Project Tiger: understanding past and present population dynamics using genetics

This project dissects the role played by movement compared to adaptation in the survival strategies of large marine vertebrates in response to environmental change. DNA is being extracted from historic tiger shark material from museums and private collectors and contrasted to modern specimens. Genetic analyses such as exome capture of neutral and selective genes, microsatellite genotyping and sequencing of the mitochondrial genome will illuminate past and present patterns of gene flow among populations, as well as highlight temporal changes in gene frequencies that can be linked to adaptation.

Disregarding the effects of environmental changes could lead to weak or erroneous predictions regarding species distributions and abundance. The project intervenes by understanding the genomic mechanisms that have been used by large marine vertebrates in response to change. The project provides a pathway to similar studies of Australian fauna where historic remains are available, and forges strong links with research groups from Europe and USA.

Leader: Jenny Ovenden

Co-investigators: Bonnie Holmes, Einar Nielsen, Safia Maher, Julian Pepperell, Mike Bennett

Funding bodies: Supported by funding from The University of Queensland, The Danish Technical University, New South Wales (including the New South Wales Recreational Fishing Trust) and Queensland State Governments, , The Mohammed Bin Zayed Species Conservation fund and the Wildlife Preservation Society of Queensland. We greatly appreciate the support of members of Game Fishing Clubs around Australia.

Shark Futures: Research for the sustainable management of the NSW whaler shark fishery

The main outcome planned for this project is to improve the ability of managers to set sustainable total allowable catch limits for whaler shark species off NSW while still enabling a profitable industry. Through completing the final pieces of the fisheries management puzzle, this project will act as a test-case to apply risk-based methods for data-poor species that may lead to development of suitable models for future national and/or international data-poor shark fisheries.

The objectives are

  1. Genetically resolve the effective population size of dusky and sandbar sharks targeted in the fishery
  2. Determine the short-term and distance movements of sandbar and dusky sharks to assist in the development of potential spatial management options like time-area (spatio-temporal) closures
  3. Develop a fishing technique that will decrease mortality of unwanted species, particularly threatened and protected species, to minimize environmental impact of the fishery
  4. Assess the effectiveness of the I&I NSW shark field ID-guide through ground-truthing on-board shark identification between fishers and observers, plus via genetic testing
  5. Educate the fishers targeting sharks about field identification of the shark species they are catching to ensure an accurate long-term database to monitor fishing of the shark populations in NSW
  6. Evaluate assessment methods and management indicators for the main shark species that may provide a model for future national and/or international data-poor shark fisheries
  7. Provide scientific data-based advice for management to ensure the future sustainability of shark populations.

Leader: Victor Pedemors

Co-investigators: Jenny Ovenden, Dean Blower, Paul Butcher, Shane McGrath

Funding body: Supported by funding from the Fisheries Research and Development Corporation (FRDC) on behalf of the Australian Government ( 2010/062)

Population units of Chilean skates

Research to identify demographic and evolutionary units of the yellownose skate (Zearaja chilensis) and the roughskin skate (Dipturus trachyderma) between the regions of Valparaiso (33° S) and Magallanes (53° S), Chile

Zearaja chilensis and Dipturus trachyderma are the most commercially valuable batoids that inhabit the continental slope of southern South America from Uruguay (south-western Atlantic Ocean) to central Chile (south-eastern Pacific Ocean) and to the east of the Falkland Islands. The first recorded landings of Z. chilensisin Chile were made in the early 1970s. Since then, the catch effort for both species has gradually intensified especially in the small-scale coastal fleet located between Valdivia (40°S) and Aysen (45° S), which is considered an artisanal fishery by local management authorities and as by-catch in two industrial trawl fisheries: the southern hake Merluccius australis  fishery and the common hake Merluccius gayi (Guichenot 1848).

Resilience to fishing pressure varies among skate species. Some populations have decreased dramatically and others have not. In some cases, other have increased because of reorganization of ecological niches. The vulnerability of batoid populations is mostly assessed through the examination of fisheries catch trends, but in many South American countries, including Argentina, Brazil and Chile, skates and rays have generally been recorded as a single unidentified category (e.g. rays, including rajoids and Myliobatiformes) in official fisheries records for several decades. From 2003, however, landings of the target species, the yellownose skate Zearaja chilensis (Guichenot 1848) and the roughskin skate Dipturus trachyderma (Krefft & Stehmann, 1975) and by-catch (a combination of six other skate species) in the Chilean skate fishery have been recorded separately.

This project on Chilean skates focuses on the use of genetics to identify population structure, and how that information can be used in new ways to investigate the extent of the movement and interbreeding between populations. New ways of producing connectivity estimates of movement and interbreeding across different data-types fine-tune fisheries models and promotes further collaboration and mutual understanding between geneticists and fisheries scientists.

The objectives are

  1. Perform a literature review focussing on the identification of evolutionary and demographic units in cartilaginous fishes.
  2. Design and evaluate a general sampling plan, which is temporally and geographically appropriate, to achieve the following objectives.
  3. Genetically identify and characterize the main evolutionary units of the yellownose and roughskin skate along the Chilean coast.
  4. Genetically identify and characterize the main population units of yellownose and roughskin skate present along the Chilean coast.
  5. Estimate the number of sources (eg. spawning and nursery grounds) and their relative contribution to each demographic unit in the main capture zone.

Leader: Julio Lamilla, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile.

Co-investigators: Jennifer Ovenden, Carolina Vargas-Caro, Michael Bennett, Carlos Bustamante

Funding body: Council of the Fisheries Research Fund, Chilean Government

Project Black Marlin: Population genetic structure in the Indo-Pacific

The black marlin (Istiompax indica), one of the largest finfish in the world, belongs to the billfish Family Istiophoridae. Black marlin are more commonly caught within Australian waters than anywhere else. However, they are not a commercial species, but have significant value to the catch-and-release recreational fishery. Their status as a highly migratory marine fish gives them a cosmopolitan distribution in all of the world’s tropical and sub-tropical regions. As the world’s oceans generally lack physical barriers, the use of molecular genetic techniques are critical for understanding population structure. Even low levels of population subdivision can have major implications for the scale of fisheries management.

Project ‘black marlin’ attempts to investigate the population structure of black marlin within Australian waters by examining young-of-the-year cohorts using molecular population genetics.

Leader: Jenny Ovenden

Co-investigators: Mike Bennett, Julian Pepperell, Samuel Williams

Funding body: Supported by funding from the Queensland Game Fishing Association Inc. and SeaWorld Research and Rescue Foundation.

Stock structure of tropical reef fish

Optimising the management of tropical reef fish through the development of indigenous scientific capability

This project addresses two key needs in northern Australia. The first is to fill in knowledge gaps on the ecology of key coastal reef fish species which have suffered significant declines across the tropics. Recent stock assessments in the Northern Territory have identified current harvest levels to be unsustainable. Managers have been unable to apply appropriate arrangements due to a lack of knowledge on the stock structure of these species. The second need is related to the indigenous community’s aspirations to develop their scientific research capability and to increase their involvement in co-management of their sea country fisheries resources with the aim of developing sustainable indigenous fisheries whose management is underpinned by scientific information collected by indigenous community members.

The three target species are the Golden Snapper (Fingermark Snapper, Lutjanus johnii), Grass Emperor (Lethrinus laticaudis) and Black Jewfish (Protonibea diacanthus). The biological stock structure of the species will be described using three techniques: genetic techniques, otolith microchemistry and parasite species composition.

Leader: Thor Saunders

Co-investigaotrs: Di Barton, Robert Carne, David Crook, Chris Errity, Stephen Newman, Jenny Ovenden, Richard Saunders, Laura Taillebois, Mike Travers, David Welch, Simon Xuereb

Funding body: Supported by funding from the Fisheries Research and Development Corporation (FRDC) on behalf of the Australian Government (project 2013/017)

Better understanding of gemfish stocks in the Great Australian Bight

Research to underpin better understanding and management of western gemfish stocks in the Great Australian Bight

Western gemfish (western stock of gemfish) are caught predominantly in the Great Australian Bight Trawl Sector (GABTS) and Commonwealth Trawl Sector (CTS) of the Southern and Eastern Scalefish and Shark Fishery (SESSF). Western gemfish have historically been an important stock for both fisheries and they remain an important component today. Eastern gemfish have been heavily exploited with peak catches approximately 25 times greater than GABTS catches and approximately 18 times larger than those in the CTS. The high level of exploitation in the eastern stock resulted in a reduction of spawning biomass to below the harvest strategy policy (HSP) limit of 20% of unfished biomass. Targeted fishing for eastern gemfish ceased in 1998, but recovery has not ensued. The western stock is managed via a total allowable catch (TAC) in the CTS, and catch triggers in the GABTS, however the majority of the stock may reside within the GABTS. Adequate management strategies that are based on the biology and ecology of biological stocks are required to underpin sustainable management of this resource.

Leader: Andy Moore (ABARES, Commonwealth Government)

Co-investigators: Jenny Ovenden

Funding body: Supported by funding from the Fisheries Research and Development Corporation (FRDC) on behalf of the Australian Government ( 2013/014) and Australian Bureau of Agricultural and Resource Economics and Sciences (ABARES).