Author response: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

The Atlantic herring is one of the most common fish in the world and has been a crucial food resource in northern Europe. One school of herring may comprise billions of fish, but previous studies had only revealed very few genetic differences in herring from different geographic regions. This was unexpected since Atlantic herring is one of the few marine species that can reproduce throughout the brackish Baltic Sea, which can be about a tenth as salty as the Atlantic Ocean. This unexpected finding could be explained in at least two different ways. Firstly, perhaps Atlantic herring are flexible enough to adapt to very different environments (i.e. high or low salinity) without much genetic change. Secondly, the previous studies only looked at a handful of sites in the Atlantic herring’s genome and so it is possible that genetic differences at other genes control this fish’s adaptation instead. Now, Martinez Barrio, Lamichhaney, Fan, Rafati et al. have sequenced entire genomes from groups of Atlantic herring and revealed hundreds of sites that are associated with adaptation to the Baltic Sea. The analysis also identified a number of genes that control when these fish reproduce by comparing herring that spawn in the autumn with those that spawn in spring. This is important because natural populations must carefully time when they reproduce to maximize the survival of their young. These new findings provide compelling evidence that changes in protein-coding genes and stretches of DNA that regulate the expression of other genes both contribute to adaptation in herrings. The analysis also clearly shows that variants of genes that contribute to adaptation were likely to evolve over time by accumulating multiple sequence changes affecting the same gene. Furthermore, these gene variants essentially form a rich “tool-box” that underlies the Atlantic herring’s adaptation to its environment, and different subpopulations of herring were found to have their own optimal sets of gene variants. For instance, autumn-spawning herring and spring-spawning herring from the Baltic Sea both have gene variants that favor adaptation to low salinity. However, autumn-spawning Baltic herring also share gene variants that favor spawning in the autumn with autumn-spawning herring from the North Sea, but not with spring-spawning Baltic herring. The next step will be to study how the 500 or so genes identified affect adaptation at the molecular level. This will likely involve experiments with other model fish such as zebrafish and sticklebacks. Finally, these new findings can be directly applied to monitor stocks of herring to make herring fisheries more sustainable.

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