Whale shark genetics revealed by water samples – University of Copenhagen

21 November 2016

Whale shark genetics revealed by water samples


How many whale sharks can fit into a liter of water? From just a few water samples collected off the coast of Qatar, scientists at the University of Copenhagen in collaboration with the Qatar Ministry of Environment and Maersk Oil Research and Technology Centre have obtained detailed genetic information about the whale shark population. The new environmental DNA method is a breakthrough in the study of marine animals and it does not require an encounter with and direct sampling of the animal itself. Genetic variation in the DNA fragments isolated from water samples can be used to estimate population sizes, as well as investigating relatedness between different populations of the same species. The new results are published in the international journal Nature Ecology & Evolution.

Every year from May to September off the coast of Qatar, one of nature’s most impressive phenomena plays out. Hundreds of whale sharks come together to feed on eggs from the tuna fish that spawn in the area.

Whale shark. (Photo: David. P. Robinson).

Whale shark. (Click on photo to see larger image. Photo: David. P. Robinson).

The whale shark is the world’s largest fish. It can grow to a size of 15 meters and weigh over 30 tons. Nonetheless, the shark is harmless, as it is adapted to a diet of microscopic animals, or zooplankton. The whale shark is endangered globally, and scientists all over the world are following the state of the populations. The species is particularly threatened by overfishing. To make things worse, efficient monitoring methods for large oceanic species are lacking. 

The scientists therefore applied a new approach to the study of marine animals. They collected water samples in the area where the whale sharks aggregate, and carried out a thorough analysis of the DNA fragments in the water. Eva Egelyng Sigsgaard is first author of the study and PhD student at the Center for GeoGenetics, Natural History Museum of Denmark, at the University of Copenhagen. She explains:

”We were surprised to see that even long fragments of DNA from the whale sharks were preserved in the water samples. And it got really interesting when we looked closer at the sequences and found DNA from many different individuals”.

The scientists found that the DNA sequence they were investigating appeared in different versions. Many of the versions were the same as those the scientists could obtain from tissue samples collected from the whale shark aggregation. And like the tissue samples, the water samples indicated that the whale sharks in Qatar are more closely related to populations in the Indian Ocean and the Pacific than to the whale sharks in the Atlantic Ocean.

Population size is revealed by water samples

The genetic diversity in a population is to a large degree controlled by its effective size, which is the number of individuals in the population that are reproducing. This size is crucial for the population’s resilience, and is therefore important knowledge for the management of marine biodiversity. Based on the genetic variation in the whale shark DNA obtained from water samples, the scientists calculated an effective population size of about 70,000 females for the Indo-Pacific population.

Dr. Philip Francis Thomsen sampling for eDNA in Qatari waters. (Photo: Eva Egelyng Sigsgaard).

Dr. Philip Francis Thomsen filtering seawater for environmental DNA (eDNA) in Qatari waters. (Photo: Steffen Sanvig Bach).

A previous estimate for the global population suggested 100,000-200,000 females. The scientists at the University of Copenhagen therefore consider their estimate from the water samples for the Indo-Pacific population reasonable. Philip Francis Thomsen is Assistant Professor at Center for GeoGenetics, and leader of the project. He has worked with DNA analysis of water samples for several years, and together with colleagues demonstrated the applicability of the approach to the marine environment. He says:

The project with the whale sharks was a unique opportunity to test the potential of the DNA method at the population level, as we had a large number of tissue samples at our disposal to compare with, and we can now go beyond the species level and look at individual populations, which provides completely new perspectives for the research field”

Collaborative work

The seasonal gathering of hundreds of whale sharks off the coast of Qatar was documented for the first time in 2007 by an employee at Maersk Oil’s platforms in the Al Shaheen field. Since then the sharks have been studied by satellite tagging and underwater photography, which utilizes the white spot patterns of the sharks to identify individuals. Steffen Sanvig Bach, marine biologist at the Maersk Oil Research and Technology Centre in Qatar, explains:

Whale shark. (Photo: Steffen Sanvig Bach).

Whale shark. (Photo: Steffen Sanvig Bach).

"We use satellite tags and acoustic tags to follow the sharks’ movements around the platforms, but also to see where they go when they leave the area. By using photo identification, we can see whether the same individuals return from year to year and estimate the size of the population. However, the latter method requires that we actually encounter the sharks, which is not always the case. With the new DNA method we have gained a powerful tool for collecting information about the sharks that can be used to protect them”.

Eva Egelyng Sigsgaard and her colleagues decided to investigate whether the sharks’ preference for tuna eggs were reflected in the DNA fragments from the water samples. They measured the concentration of DNA from whale shark and from tuna in the water samples and found a striking correlation between the two. The more tuna DNA there was in a sample, the larger the amount of whale shark DNA. Eva Egelyng Sigsgaard says:

Eva Egelyng Sigsgaard filtering seawater. (Photo: Rafael de la Parra Venegas).

Eva Egelyng Sigsgaard filtering seawater. (Photo: Rafael de la Parra Venegas).

It was really interesting to see a strong correspondence between the concentrations of tuna DNA and whale shark DNA in the water samples, as we know from an earlier study that the sharks feed on tuna eggs. This suggests that the DNA method could potentially be used to study food chains in marine ecosystems”.

The new study on whale shark DNA traces is the culmination of several years of collaboration between Maersk Oil, The Natural History Museum of Denmark and the Ministry of Environment in Qatar, which was initiated by Peter Rask Møller, Associate Professor at the Natural History Museum of Denmark, Philip Francis Thomsen and Steffen Sanvig Bach. The DNA work continues as part of a larger project, which aims at mapping the diversity of fishes, whales, sea snakes and turtles in the waters around Qatar using water samples. The samples are collected from a broad range of habitats including coral reefs to mangroves and seagrass areas. Besides investigating the marine life around Qatar, the project aims to further develop the DNA method, which can hopefully improve monitoring and aid scientific investigation of marine animals.

Paper: “Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA”. Nature Ecology & Evolution 1, Article number: 0004 (2016).


PhD researcher Eva Egelyng Sigsgaard, eva.sigsgaard@snm.ku.dk; phone: +45 20944266

Assistant Professor Philip Francis Thomsen, pfthomsen@snm.ku.dk; phone: +45 27142046

Biologist Steffen Sanvig Bach, steffen.bach@maerskoil.com; phone: +974 66229200

Communications Officer Uffe Wilken, ugwilken@snm.ku.dk; phone: +45 31772016