Complex population structure and haplotype patterns in Western Europe honey bee from sequencing a large panel of haploid drones

Honey bee subspecies originate from specific geographic areas in Africa, Europe and the Middle East. The interest of beekeepers in specific phenotypes has led them to import subspecies to regions outside of their original range. The resulting admixture complicates population genetics analyses and populations stratification can be a major problem for association studies. As a typical example, the case of the French population is studied here. We sequenced 870 haploid drones for SNP detection and identified nine genetic backgrounds in 629 samples. Five correspond to subspecies, two to isolated populations and two to human-mediated population management. We also highlight several large haplotype blocks, some of which coinciding with the position of centromeres. The largest is 3.6 Mb long on chromosome 11, representing 1.6 % of the genome and has two major haplotypes, corresponding to the two dominant genetic background identified.