WIOMSA ScienceNews: Genomic tools to address questions in fisheries management

In this week’s edition of WIOMSA ScienceNews, we focus on the “Enabling sustainable exploitation of the coastal tuna species Kawakawa and skipjack in the western Indian ocean” project which is aiming to generate essential information about fisheries in the WIO region and relate this to key economic, biological and environmental information to inform management and development of this sector.

Genomic tools to address questions in fisheries management

A four-country study of small, migratory tunas is expected to generate essential information about fish and fisheries that are growing in importance across the western Indian Ocean region.


Kawakawa (Euthynnus affinis) and skipjack tuna (Katsuwomis pelamis) are small, highly migratory tunas that form an increasingly important part of the catch of small-scale fishers across the western Indian Ocean region. Yet, in spite of their growing importance, very little is known about the population structure of the two species. Nor is there adequate knowledge about the value chains of the fisheries that target Kawakawa and skipjack. This lack of information frustrates African governments that are prioritising the development of national tuna fisheries with a view to securing a larger share of the quotas allocated by regional fisheries management organisations such as the Indian Ocean Tuna Commission (IOTC).

It is against this backdrop that WIOMSA is funding a study of Kawakawa and skipjack tunas in Kenya, Mozambique, Tanzania and South Africa. The project “Enabling sustainable exploitation of the coastal tuna species Kawakawa and skipjack in the western Indian ocean” is led by Rhodes University in South Africa and involves researchers in all four participating countries.

José Halafo, a researcher with the National Institute of Fisheries Research in Maputo, Mozambique, captures the pressing need for a dedicated study of small, migratory tunas when he says that catches of the two species have not been properly recorded in Mozambique.

“In the past, the beach recorders did not distinguish between different species of tunas,” he says. “When we established this project, we got them trained so that they can now easily identify those species.”

Improving the accuracy of catch records represents a very small but vital step in the regional effort to find out more about artisanal fisheries for Kawakawa and skipjack and the four countries participating in the study are making a concerted effort to determine the extent to which the stocks are shared across the western Indian Ocean region.

Gladys Okemwa, a researcher with the Kenya Marine and Fisheries Institute, explains:

“We recognise that tunas in general are a shared stock, they are shared between all the countries in the region. What triggered this study was the need to understand whether there are single stocks, or different stocks of these two species. There have been studies that have tried to do this in the past, but with this study we are deploying more sensitive methods to see if there are actually different sub-stocks of the two species in the region.”

The methods Okemwa is referring to are “next generation sequencing” methods – technology that has revolutionised genetic research. Also referred to as “genomics”, the technology is able to provide unprecedented insight into patterns of population connectivity, or isolation, and therefore represents a highly effective tool for sustainable fisheries management.

Genomic research forms a major component of the WIOMSA-funded study. It is being led and facilitated by the Institute of Biological, Environmental and Rural Sciences at Aberystwyth in the United Kingdom. According to researcher Paul Shaw, the expectation is that the study will identify a single population of both Kawakawa and skipjack tuna across the western Indian Ocean area, but if there are differences between populations, the new genomics techniques will pick them up.

“It’s so important to get the baseline information. If you find there is a single population across the whole region, that has important implications for the management of the stock. Likewise, if there are genetically different or sub-populations, it is important they are managed separately. Whatever the outcome, the study will generate new information that will be of use to fishery managers and the IOTC because at the moment they are working on a lack of information – they’re working on the assumption it’s a single population.”

The collection of biological data, such as the total length, individual weight and stage of maturity of sampled fish is another important component of the study. Unfortunately, this component has been seriously affected by the Covid-19 pandemic and the restrictions on movement that have been introduced by governments across the region in an effort to control the spread of the disease. In many cases, researchers have been unable to regularly sample fish at landing sites and this has delayed the gathering of biological data in all four countries.

In spite of the challenges, in August 2021 Sauer reported that researchers were progressing well with the analysis of genetic material and the working up of the biological and catch data. A first set of results was expected by the end of September 2021.

A third component of the project is a socio-economic analysis of the small-scale fisheries value chain, about which very little is known.

“This is the first time we are looking at this fishery in-depth and in a well-rounded manner,” explains Okemwa. “The socio-economic study is very exciting because we’ll get to understand the fishery across the value chain, right up to the market level. We’ll get to understand the challenges the fishers have on the ground and whether the fishery has been declining on a regional scale. We believe that Kawakawa and skipjack stocks are not overexploited, but there may be localized changes which are not documented and which we may be able to decipher from the socio-economic data analysis.”

A partnership with Solstice WIO, a four-year collaborative project funded by the UK Global Challenges Research Fund, will help researchers to fulfil the objectives of a fourth and final component of the project – the integration of biological and genomic information with environmental data.

“This project represents a first step in improving the management of small species of tuna in the western Indian Ocean,” says principal investigator Warwick Sauer of Rhodes University. “If we find there is a single stock and the fish are moving between countries, then there can be discussions through the IOTC about how to manage these fisheries into the future. In that way we can avoid the kind of overexploitation that has occurred, for example, with yellowfin tuna in the western Indian Ocean region.”

According to the IOTC, very little is known about the status of Kawakawa stocks because catch per unit effort data is highly incomplete, with data available only for short periods of time and for selected fisheries. A lack of catch and effort data for skipjack is a concern for the IOTC, even though the life history characteristics of the species – including low size and age at maturity, a short life and high productivity – mean that it may be fairly resilient to the impacts of fishing with the present level of effort. However, the increasing interest in catching these species necessitates careful monitoring of the fishery, with the introduction of management measures as required.

Please contact Warwick Sauer on w.sauer@ru.ac.za or Gladys Okemwa on gladysokemwa@gmail.com for more information on the project.


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