Fish fingerprints point the way to the future

Over the past few years, Dr Maren Wellenreuther and her group at Plant & Food Research in Nelson have developed innovative methods using image-based technologies to ‘fingerprint’ individual snapper, opening the way to transfer this technology to other species like Chinook salmon.

“A snapper’s ‘fingerprint’ is its unique patterns of iridescent blue spots – no two snapper have the same spots. So we can take a photo of a baby fish and find it again as an adult years later based on its fingerprint,” says Dr Wellenreuther.

“Other species like salmon and trevally have unique patterns around their body, distinctive enough to be a fingerprint.”

The fingerprints mean that the team can repeatedly measure a fish’s performance traits as it grows – such as its body shape and size.

This work was part of a larger $5.5 million Ministry of Business, Innovation and Employment (MBIE) funded project led by Dr Wellenreuther to develop new aquaculture-ready species in New Zealand. This will help diversify the sector, with a focus on species such as snapper that thrive in warmer ocean waters.

“In any population of captive-raised fish there will be some that do better than others – they have desirable traits for aquaculture,” Dr Wellenreuther says.

Combining the fingerprinting of individuals with methods in fish genetics, Plant & Food Research scientists can then identify some of the important genes responsible for desirable traits. This is invaluable information for a selective breeding programme to help raise fish that carry these naturally occurring genes that ensure they will not only survive but thrive in aquaculture conditions.

With the demonstrated success in identifying snapper based on their spots, the image-based and AI-enabled methodology has exciting applications for surveying and wild-capture stock monitoring.

In 2022, Dr Wellenreuther’s team imaged the fingerprints of more than 2,000 snapper in the Plant & Food Research finfish facility in Nelson. Those fish were then relocated to a sea pen in the Marlborough Sounds and were successfully re-imaged after two years.

Dr Wellenreuther explains the image-based AI method is more efficient.

“If you used video to try and record thousands of fish in a sea pen, and then measured each fish caught on video, you might be taking hundreds  of measurements of the same fish that has repeatedly swum into view.

"This does not give you good data. But if you know exactly which fish you are getting images of and measuring, then you can account for this in your data analysis.”

“Catch, tag and release is an expensive method because you need people on vessels to tag and release, and because the rates of recapturing a tagged fish are so low it takes a lot of time and resources to find enough tagged fish to estimate things like survival and growth,” Dr Wellenreuther says.

This is where the new methodology can be applied. A camera can be used in many places – onboard a vessel, underwater attached to the hull of a vessel or mounted over a conveyor belt in a factory – to recognise a species like snapper.

When the camera recognises a snapper it will automatically store a photo. That information can then be evaluated by the software.

“It means we can identify an individual fish based onits unique fingerprint, then extract the traits that belong to this individual from the images rather than having to handle and measure the fish by hand. This means we don’t have to take the fish out of the water and handle it, which is great for animal welfare and for reducing the overall footprint of such work. "

"Fisheries scientists can then draw conclusions from the data about how a population is aging and growing in a certain environment.”

As at November 2024, the method and technology is in the process of being commercialised, with an announcement due that will be of interest to the commercial seafood sector. 

Epigenetic clocks could replace aging fish by otolith

Dr Wellenreuther’s team are using a recentbreakthrough in epigenetics to develop ‘clocks’ used to estimate the age of fish and shellfish species.

Epigenetics is the study of changes in gene expression that do not involve any changes to the underlying DNA sequence; the gene activity (expression) has changed but the DNA code (sequence) has not. Epigenetic changes occur naturally in all living organisms – it is a normal biological process.

While different species undergo different epigenetic change over time, there are some common patterns in the epigenetic changes that occur as animals age (for example, the loss of histones – a type of protein). And because some of these changes occur in a predictable clock-like nature with age, a unique clock can be developed for some species. Clocks have been developed and are in use for humans and other mammals.

The epigenetic signature of an individual animal is defined by which genes are switched on and off and how that changes with age. The signature, obtained by taking a tiny and usually non-lethal biological sample from an animal, can then be measured against that clock to estimate its age.

Dr Wellenreuther says that epigenetic clocks are used for mammals to about 99% accuracy and have been proven for about 10 finfish species – including the snapper clock her own team has developed. With a new 2024 Smart Ideas MBIE government grant, she is now developing an epigenetic clock to age pāua in wild fisheries. This will be the first clock developed for a mollusc and Dr Wellenreuther’s team already has a prototype clock working to 97% accuracy.

The novel (unique) epigenetic clocks have caught the attention of the Ministry of Primary Industries (MPI) for their potential use in fisheries management and quota setting.

“It will be interesting to explore whether our clock can replace otolith reading, as it may prove to be more accurate and cost-effective. MPI uses otolith reading for more than 5,000 hoki each year – cutting into the head to extract the otolith before putting it under a microscope to count the rings,” Dr Wellenreuther says.

“It’s a very labour-intensive process but it has to be done in order to assess the age structure in a population. This is important to understand variability in recruitment strengths across years and to make sure a stock has enough mature breeders to support the next generations to come.

“These are all the things you need to know for sustainable fisheries management and regulators and fisheries managers are interested in knowing if they can use epigenetic clocks on a commercial scale for fisheries management.”