The genome of the three-spined stickleback has now been mapped by an international research group led by researchers at Uppsala University and Broad Institute and Stanford University in the US. The results are published in the scientific journal Nature and show how the genes changed to enable the three-spined stickleback to adapt to fresh water after the last ice age. Most of the changes took place through mutations in the regulation of genes.

Since the last ice age, the three-spined stickleback, a very common small fish, has adapted to the innumerable brooks and lakes it wound up in when the level of the seas dropped after the ice receded. This repeated ecological adaptation in many places in the northern hemisphere make this fish interesting to study from an evolutionary perspective.

In the present study the genome of the three-spined stickleback has been mapped, and the genomes of a further 20 marine and freshwater fish have been compared with it. The researchers have managed to identify several hundred regions in the genome that differ between fish that live in seawater and those that live in fresh water.

“Our results indicate that several hundred genes or their regulatory signals have mutated as the stickleback adapted to fresh water,” says Manfred Grabherr, new group leader at SciLifeLab Uppsala and co-lead author of the article. “It’s interesting that the same mutations have been selected in all parts of the world in order for these fish to be able to adapt to similar new ecological environments.”

In the regions of the genome that have to do with adaptation to fresh water there are both previously known and newly discovered genes. For instance, it has long been known that the EDA gene leads to reduced armour formation in freshwater fish. New genes include WNT7B, which in all probability can lead to an altered kidney function in freshwater fish, as the salt balance between the fish and the surrounding water has to function.

In evolutionary biology it has long been questioned whether the changes that take place in the genome when various species adapt to new environments are primarily due to mutations within protein-forming sequences or whether so-called regulatory mutations play a greater role. Regulatory mutations determine how much or little of a protein is to be formed in specific tissues. Since this study looked at the whole genome at the same time, this question could be answered with greater certainty. The findings show that mutations that change the protein itself are unusual, whereas mutations that affect where, when, and how much of the protein is to be formed are considerably more common.

“If the protein itself changed, its function would change in many tissues. Instead, a specific regulatory mutation can occur, allowing, for instance, the kidneys to adapt to a different salt concentration,” says Kerstin Lindblad-Toh, professor and director of SciLifeLab Uppsala and research at the Broad Institute, who directed the study together with Professor David Kingsley of Stanford University.

The study lays the foundation for evolutionary biologists studying the three-spined stickleback to be able to better understand the biological processes. The scientists are now moving on to look for further regions of the genome selected on the basis of adaptation to large and small waterways, for instance.