European cisco – genetic adaptation to variation in salinity and spawning time

European cisco roe is known as a Swedish delicacy. A new study has shown that there are different types of European cisco in Swedish waters that are each genetically adapted to fresh, saline or brackish water. Genetics also steers when European cisco spawn. The new knowledge from this study can be used in sustainable management of the species, and for investigating whether the spawning environment affects the quality of the roe. The study was conducted by researchers at Uppsala University, the Swedish University of Agricultural Sciences (SLU), the Royal Institute of Technology in Stockholm (KTH), Stockholm University, and the Museum of Natural History, and was recently published in the journal Molecular Ecology.

Peer-review/Observational study/Animals

The European cisco is a small salmonid that has three different variants. As a purely freshwater fish, it is found in Lake Vänern and Lake Mälaren, among other freshwater bodies. As an anadromous fish, it lives in the Gulf of Bothnia and some other parts of the Baltic Sea from where it migrates up rivers and spawns in freshwater just like salmon. The third variant both lives and spawns in the somewhat brackish waters of the Gulf of Bothnia. It is the latter variant of European cisco that produces the most sought-after roe.

“We have developed a reference atlas describing all the genes found in the genome of the European cisco. This work is part of a larger international collaborative project aiming to map the genome of all species,” explains Kerstin Lindblad-Toh, professor at Uppsala University.

“Having a map of different species’ genomes is a useful tool for studying the biology of a species as well as how the species is divided up into different sub-populations within the species’ range of habitats. This information is particularly important for species that we humans use for food production, for example. It gives us the opportunity to monitor how a species is affected by our exploitation of it,” says Leif Andersson, Uppsala University, who led the study.

The study shows that there are two main groups of European cisco in Swedish waters. One main group occurs in some lakes in the southern Swedish highlands and there is another group that occurs in the rest of Sweden. It is very likely that these two types represent European cisco that were separated during the last Ice Age and subsequently colonised different areas of Sweden.

“Our results show clear genetic differences between European cisco that spawn in freshwater and those that spawn in the brackish waters of the Gulf of Bothnia. There are also genetic differences between spring-spawning and autumn-spawning European cisco. The vast majority of European cisco spawn in the autumn, but in Lake Fegen, which is located on the border between the Swedish provinces of Västergötland and Småland, there are both spring-spawning and autumn-spawning populations,” says Bo Delling of the Museum of Natural History in Stockholm.

A number of the genetic differences between the populations that spawn in freshwater and those that spawn in brackish water have previously been identified as important for salinity tolerance in other species, while genes with a known function related to the regulation of circadian rhythm were significantly overrepresented in the genetic differences between spring-spawning and autumn-spawning populations.

“We saw clear genetic differences between the anadromous European cisco that spawn in the Kalix River compared to those that spawn in the brackish waters of the Gulf of Bothnia. It would be interesting to explore whether there is a connection between the quality of the roe and the spawning environment. This could also affect how European cisco in the Gulf of Bothnia are managed in the future,” says Leif Andersson.

Reference Deng Q, et al.; Genetic Adaptation to Brackish Water and Spawning Season in European Cisco. Mol Ecol. 2025 Sep 3:e70094. DOI: 10.1111/mec.70094 ; Epub ahead of print. PMID: 40903929.

For more information:

Leif Andersson, Professor at Department of Medical Biochemistry and Microbiology at Uppsala University,
e-mail: leif.andersson@imbim.uu.se, phone: +46 70 425 02 33

Funding: The research was funded by the Swedish Research Council and the Knut and Alice Wallenberg Foundation.