DNA reveals new population diversity in Indian Ocean’s tuna stocks

By Catherine NorwoodJune 21st, 2021

New DNA and microchemistry analysis reveals multiple populations among the Indian Ocean’s tunas and will underpin improved fisheries management.

Tuna and billfish are the target species of some of the largest fisheries on the globe and provide a critical source of food for millions of people. DNA-based research is revealing new information about these important species in the Indian Ocean that will help underpin both sustainable fishing and international food security.

Longtail tuna fish in a basket

Longtail tuna samples collected from Indonesia were found to be from one of three separate stocks of this species in the Indian Ocean. Image: Naomi Clear, CSIRO

The Indian Ocean is the second largest provider of tuna and, until now, it has been assumed that most species were part of a single, highly mobile stock within the Indian Ocean basin.

However, new DNA analysis and the chemical analysis of fish “ear bones” – or otoliths – have identified distinct groups of several high priority commercial tuna species within the Indian Ocean.

CSIRO has undertaken this research for the Indian Ocean Tuna Commission (IOTC) in partnership with AZTI Tecnalia (Spain), IRD (France) and CFR (Indonesia), and collaborated with a range of coastal nations to identify the population structure of tuna, billfish and sharks in the Indian Ocean.

“Identifying multiple stocks of several target species is an important starting point for sustainable management and providing sound scientific advice that should help reduce overfishing of any specific fish stock,” said Dr Campbell Davies from CSIRO’s Oceans and Atmosphere, who leads the international fisheries research.

The three-year project was completed in 2020 and findings have already helped to revise aspects of the IOTC stock assessment models, ensuring modelling outputs are more realistic and useful in decision-making.

“The project has helped to improve the basic understanding of population structure and connectivity for tuna, billfish and sharks in the Indian Ocean,” said the IOTC Secretariat’s Science Manager Dr Paul DeBruyn.

“It has also strengthened the scientific advice that underpins stock assessment and management of these species.”

Further research will be needed for some species to identify the characteristics of individual stocks across their full range within the Indian Ocean.

Coastal species

The IOTC project looked at three coastal species: longtail tuna, Spanish mackerel and kawakawa. These species are particularly important for domestic fishing fleets and the food supplies of developing countries bordering the Indian Ocean.

“The project found strong evidence of three genetically distinct populations of longtail tuna and four of Spanish Mackerel,” said Dr Davies.

“It also identified distinct differences in the genetic profiles of kawakawa north and south of the equator, indicating there may be separate breeding populations.”

Many baskets of fish lined up nest to each other with fishers looking at the baskets

Understanding the stock structure of the Indian Ocean’s tuna and related species is critical to sustainable fishing and food security in the region. Image: Craig Proctor, CSIRO

Tropical tunas and billfish

Three tropical tunas were studied: bigeye, yellowfin and skipjack. These are fished equally by domestic fleets and international, industrial vessels.

The research found bigeye tuna appeared to be a single stock across the Indian Ocean. However, it is clearly differentiated from stocks in the Atlantic and South Pacific Oceans.

“Skipjack and yellowfin tuna stocks were found to have distinct genetic signatures north and south of the equator. Otolith chemistry provided further evidence that yellowfin may also have two distinct northern populations,” explained Dr Davies.

“Both yellowfin and bigeye tuna undergo extensive migrations between their spawning grounds in warmer waters near their equator and their colder, sub-tropical adult feeding grounds at northern and southern extremes of the Indian Ocean. However, skipjack remains in tropical and sub-tropical areas year-round, spawning opportunistically. Several genetically distinct groups of skipjack were found intermingling at various locations, but further research is needed to understand the implications of this.”

The results for swordfish indicated a similar pattern to yellowfin tuna, with differences in genetic profiles for fish sampled north and south of the equator, and low levels of connectivity with the Atlantic and Pacific oceans.

“We found distinct genetic differences between albacore tuna in the Indian Ocean and those in the Atlantic and Pacific Oceans. But limited samples from locations within the Indian Ocean made it difficult to identify whether there were separate stocks within the Indian Ocean,” added Dr Davies.

Sampling issues also limited results for three other species researchers had planned to study: striped marlin, sailfish and scalloped hammerhead shark.

Blue sharks

A global analysis of blue shark genetics identified for the first time that the species has a distinct northern Atlantic Ocean population and separate southern population. The southern population is also connected across the Indian and Pacific Oceans.

“Connectivity will require the collaboration of regional fisheries management agencies across the southern hemisphere to further test this finding and to manage blue shark stocks effectively,” suggested Dr Davies.

Collaborative capacity

A major achievement of this project has been the creation of a collaborative network to support what is one of the largest, coordinated studies of fisheries population structure ever undertaken.

International partners and fisheries agencies, universities and fishers from many countries around the Indian Ocean all worked together to contribute, with Pacific and Atlantic Oceans contributors also providing samples for “out locations” for genetic comparisons.

Group of researchers carrying out sampling work

International collaborations provided the foundation for capacity building in fish sampling and analysis techniques. Image: Craig Proctor, CSIRO

In all, 5,767 tissue samples were collected, along with 3,010 otoliths.  Of these, 3,610 tissue samples were genotyped and 689 were processed and analysed for otolith microchemistry.

Samples for each species needed to be collected at similar times of the year so that the ability of these fish to travel long distances quickly – potentially thousands of kilometres in a few months – did not result in a kind of “double counting” that would potentially confound the results.

“The international collaborations, networks and the capacity building in sample collection and analysis have been critical to the study’s success and will support further research into Indian Ocean fisheries,” said Dr DeBruyn.

This project builds on a range of genetic technologies CSIRO is pioneering in its fisheries and conservation management research. Advances in DNA analysis techniques, driven by medical science over the past decade, continue to make the technology cheaper and more precise, allowing just “snips” of genetic code to be quickly sequenced.

“These advances provide increasingly detailed information for analyses of fish population structure, species identification, population estimates and mortality rates – all key information in addressing natural resource management and conservation challenges,” said Dr Davies.

“The evolution of genetic analysis, combined with sophisticated statistical modelling will help to transform monitoring and assessment, supporting a sustainable future for Indian Ocean fisheries, even as these fisheries respond and adapt to climate change and other pressures.”

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