Acknowledgements
We thank the Swiss National Science Foundation (SNF grant 31003A_165826) for financial support to DB; the Freiwillige Akademische Gesellschaft Basel (FAG) for financial support to QH; Louis Bernatchez, Jenny Boughman, Jacquelin DeFaveri, Bart Hellemans, Jun Kitano, Joost Raeymaekers, Mark Ravinet and Florent Sylvestre for providing marine stickleback samples; Walter Salzburger for sharing web lab infrastructure; Brigitte Aeschbach and Nicolas Boileau for faciliting lab work; Christian Beisel, Ina Nissen-Naidanow and Elodie Vogel Burcklen for Illumina sequencing at the Quantitative Genomics Facility, D-BSSE, ETH Zürich; the developers of Novocraft for sharing their sequence aligner, and Nicolás Lichilín Ortiz for help with cluster scripting. Computation was performed at the sciCORE scientific computing center of the University of Basel (https://scicore.unibas.ch).