Acknowledgements

We would like to thank Anssi Laurila, Dennis Hasselquist, Ane Timenes Laugen, Björn Rogell and Markus Zöttl for discussion and comments on an earlier version of the manuscript, and everyone who helped us by collecting and proving samples. Peter Söderling, Carl Tamario, Kristofer Bergström and Per Koch-Schmidt for Harfjärden, Lervik, Okne and Kosta, Pär Byström and Rickard Linderot for Ängerån, Staff at DTU Aqua, and in particular Henrik Dalby Ravn for the Danish samples, Henrik C Andersson for Yngern and Snäckstavik, Marcus Hall for Hamnaryd, and Olof Engstedt and Tobias Berger for Vambåsa. We would also like to thank Emelie Nilsson and Diego Brambilla for help with the bioinformatical analyses. The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure, NGI, and Uppmax for providing assistance in massive parallel sequencing and computational infrastructure. Funding was provided by the Linnaeus University (to AF), The Swedish Research Council FORMAS (to AF and PT grant Dnr. 2017-00346), and Nilsson-Ehle-donationerna Kungliga Fysiografiska Sällskapet i Lund (to JS and YY grant Dnr 39409).