Genetag Tools and Methods

The following snippets provide an insight into the many components of the Genetag Research Project. New snippets are continuously added as the project evolves.

The concept of genetagging fish
Important partnerships
Why Spanish mackerel?
Collecting the tissue samples: A special hook for a special job
Collecting the tissue samples: A different tagging pole for a different job
Collecting the tissue samples: Collecting fins for a wide coverage
Processing the tissue samples: Developing a screening strategy
Processing the tissue samples: Extracting DNA from the tissue samples
Processing the tissue samples: Genotyping Spanish mackerel
Producing results: Checking for recaptures
Adding value: Sonic tagging

Adding value: Sonic tagging

Posted: March 2006

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Producing results: Checking for recaptures

Posted: August 2005

We have previously explained how fish were given a genotype from their fin tissue and what a genotype was like. After we determine the genotype, we store them in the computer.

The next step is to see if any of these genotyped fish have been 'genetagged' or recaptured. A genetagged fish is one that was caught on a genetag lure or tagged by volunteer recreational fishers using the combination tagging method.

To find genetagged fish we cross check the genotypes from the fins with genotypes from tissue obtained from the lures and combination tagging samples. If the genotypes match, then we know that we have captured the same fish twice.

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Processing the tissue samples: Genotyping Spanish mackerel

Posted: May 2005

The previous snippet explains how the DNA was extracted from mackerel fins. The next step is to 'genotype' the DNA collected from each fish. A genotype is a numerical description of individual fish in genetic language.

Each fish has a different genotype. For example, one fish may have a genotype of 124 126 252 254, another may have a genotype of 124 128 250 254. The genotype remains the same for the fish from birth to death.

Each set of numbers is established using a combination of lab methods such as polymerase chain reaction (PCR) and capillary DNA electrophoresis, followed by computer analysis. In the next snippet, we will explain how genotypes are used to search for recaptures.

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Processing the tissue samples: Extracting DNA from the tissue samples

Posted: February 2005

In the previous snippets we introduced the concept behind genetic tagging, and the methods we have adopted in this project to collect the tissue samples. In this snippet, Dr Jenny Ovenden explains how the DNA in each sample is extracted.

The tissue samples are transported on dry ice to the Molecular Fisheries Laboratory in Brisbane, where they are defrosted and washed. A minute piece of tissue is placed in solution containing an enzyme that removes the protein from the sample. The DNA is released into the solution and stored at -200C.

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Processing the tissue samples: Developing a screening strategy

Posted: February 2005

The tissue samples are screened for the presence of genetagged fish, so that we can establish a harvest rate estimate.

Genetag Research Project staff from Queensland's Department of Primary Industries and Fisheries have developed a clever system that minimises costs and facilitates high throughput.

The screening strategy they have developed identifies potential recaptures in a process that involves the fewest number of microsatellite loci possible. Subsequent genotyping with additional loci leads to further elimination, and only a few fish are genotyped at all available loci.

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Collecting the tissue samples: Collecting fins for a wide coverage

Posted: February 2005

One of the greatest advantages of genetagging fish is that it allows you easily screen the commercial and recreational catch for tagged fish. By doing this, we should be able to maximise the return rate and increase the accuracy of our harvest rate estimates.

To screen the catch, all we need to do is collect small tissue samples from the fins of landed fish. Currently, commercial and recreational fishers assist us greatly with this task, but in the future this task could be undertaken at the wholesaler or the marketplace.

The fin samples are frozen and sent to the Molecular Fisheries Laboratory in Brisbane, where the extraction of the DNA and cross-checking for matches occurs. The samples are stored at the lab for future reference.

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Collecting the tissue samples: A different tagging pole for a different job

Posted: February 2005

Tissue sample can also be collected using a modified tagging pole. These tagging poles allow the fish to be genetagged and conventionally tagged at the same time. Combination tagging allows the advantages and disadvantages of the two tagging approaches to be compared.

Using a tagging pole is advantaged in that the fish do not need to be removed from the water, thereby reducing potential stress on the fish. Tagging in this manner is also attractive to recreational fishers who prefer to catch and release their catch.

The Genetag Research Project is utilising the growing number of recreational fishers keen to contribute to the better understanding of our fisheries. A dedicated group of volunteer taggers greatly assist this project, and have combination tagged over 400 Spanish mackerel to date.

Around 150 of these fish where tagged during the Inaugural Spanish Mackerel Tagging Tournament. The event was such as success, we are hosting the 2nd Spanish Mackerel Tagging Tournament in June 2005.

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Collecting the tissue samples: A special hook for a special job

Posted: November 2004

To genetag a fish, a minute amount of tissue is required to establish the animal's DNA genotype (the animal's unique tag).

Project staff from the Northern Territory's Department of Regional Development, Primary Industry, Fisheries and Resources have invented a special biopsy hook that allows fish to be genetagged without even being brought to the vessel.

The shafts of these hooks are made from copper and bend easily to ensure the safe release of the fish. This approach has the potential to minimise tagging-induced mortality or changes in behaviour.

The hollow stainless steel tip of the hook collects a small amount of tissue as the fish strikes, and a special rasp holds the sample in place while the hook is in the water. The amount of tissue collected is so small that the sample is often invisible to the naked eye.

The biopsy hook can be baited to genetag demersal fish (fish found near the substrate). Baited biopsy hooks have already proven capable of tagging deep-water fish that may otherwise face decompression.

The biopsy hook may also be incorporated onto a lure to genetag pelagic fish (fish that inhabit the water column). The Genetag Research Project is currently using the biopsy hook on lures to target Spanish mackerel.

Please note, the design of the hook is protected by an Australian patent.

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Why Spanish mackerel?

Posted: August 2004

Spanish mackerel (Scomberomorus commerson) are prefect candidates for genetagging, and clearly warranted being the first fish in the world to be genetically tagged.

For a variety of reasons, traditional approaches to estimating stock size cannot be applied to Spanish mackerel. For example, as Spanish mackerel aggregate in schools, catch rates are poor indicators of abundance.

Without the benefit of knowing the size of the exploited Spanish mackerel stocks, fishery managers have had to estimate the sustainable harvest levels from previous catch trends.

In northern Australia, catches of Spanish mackerel peaked in the late 1970s when Taiwanese gillnet fishers working in the area. In the early 1980s, catches stabilised at around 450 tonnes per annum; providing the best indication of the sustainable harvest yield.

Uncertainty regarding the accuracy of this catch data, together with recent increases in the annual harvest from the waters managed by the Northern Territory, highlight the need for refined stock size estimates. Genetic tagging may provide the answer.

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Important partnerships

Posted: August 2004

The Genetag Research Project commenced in July 2002, and is funded by the Fisheries Research and Development Corporation. The Northern Territory and Queensland Governments also contribute funding and staff to this project.

Staff from the Northern Territory's Department of Regional Development, Primary Industry, Fisheries and Resources (DPIFM) are responsible for genetagging the fish. To do so, they have had to develop a series of novel sampling tools.

Staff from Queensland's Department of Primary Industries and Fisheries have the task of processing the thousands of genetic samples being collected. To do this in a cost-efficient manner, they have also had to develop some novel processing approaches.

Commercial and recreational mackerel fishers also play an important role in this project. They assist greatly by genetagging fish at-large and collecting tissue samples from landed fish. Without their help this project would not be as successful.

Last, but not least, the Amateur Fisherman's Association of the Northern Territory is contributing to the combination tagging component of this project by collecting information on recaptured fish.

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The concept of genetagging fish

Posted: August 2004

The concept behind genetaggging fish is simple: All fish have a unique DNA genotype that can be used to identify individuals over their entire life span. In other words, genetagging uses the microsatellite DNA profile of each fish as a life-long indelible tag.

With previous genetic tagging studies focussing on the likes of bears and wolves in the Arctic Circle, the Genetag Research Project is quite unlike anything undertaken before. The project represents the first time this new approach has been applied to fish.

The Genetag Research Project has had to re-invent the whole process to be able to apply this method to fish. The series of snippets that follow describe the sampling tools and lab methods that have been developed in the process.

Like any tagging program, if enough tag returns are gained, it is possible to estimate the size of the harvested fish stock. Genetagging may allow this to occur in fisheries where conventional tagging may not be suited (e.g. large pelagic fish and deep water fish).

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