Acknowledgements

Financial support for this study was provided by Bundesamt für Landwirtschaft BLW (Swiss Federal Office for Agriculture FOAG) Grant No. 627000708, by Labogena and FranceAgriMer (Programme d’Investissements d’Avenir), the Alabama Agricultural Experiment Station, and the USDA NIFA Multi-state Hatch Project NC1173. We thank Lucie Genestout (Labogena) for coordinating the Beestrong project, Christina Sann and Yannick Poquet (Labogena) for organising the sampling in Savoie, and Alice Revel (Agroscope) for her help in organising the sampling in Switzerland. We thank Rachid Mahla (Labogena) for DNA extraction and Olivier Bouchez (GeT-PlaGe) for sequencing. Sequencing was performed in collaboration with the GeT platform, Toulouse (France), a partner of the National Infrastructure France Genomique, thanks to support by the Commissariat aux Grands Investissements (ANR‐10‐INBS‐0009). Sequence alignments and allele frequencies estimations were performed on the computer cluster of the Genotoul bioinformatics platform Toulouse Midi‐Pyrénées (www.bioinfo.genotoul.fr). We are grateful to all of the experts for colony evaluation and to all of the beekeepers for supporting the sample collection. This study was performed in collaboration with the Beestrong Consortium. Beestrong Consortium: Sonia Eynard, Alain Vignal, Bertrand Servin (INRAE, GenPhyse, 31326 Castanet-Tolosan, France), Lucie Genestout, Rachid Mahla, Christina Sann, Yannick Poquet, Yves Agez (LABOGENA DNA, Laboratoire d’Analyses Génétiques pour les Espèces Animales, Domaine de Vilvert, 78353 Jouy-en-Josas, France), François Guillaume (Evolution XY, rue Eric Tabarly, 35538 Noyal-Sur-Vilaine, France), Benjamin Basso, Yves Le Conte, Fanny Mondet (INRAE, Abeilles et Environnement, 84914 Avignon, France & UMT PrADE, 84914 Avignon, France), Benjamin Basso, Axel Decourtye (ITSAP, 84914 Avignon, France), Florence Phocas, Jean-Pierre Bidanel (Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France), Olivier Bouchez (GeT-PlaGe, Genotoul, INRAE Auzeville, 31320, Castanet-Tolosan, France).