Significant fine-scale population differentiation in two common bumblebee species (B. pascuorum and B. lapidarius) detected in Northern Europe

Abstract Bumblebees are keystone pollinators which facilitate the reproduction of a wide range of wild and agricultural plants. Their abundance and diversity have been severely reduced by anthropogenic stressors such as widespread land-use change and habitat fragmentation. However, we lack a comprehensive understanding of population structure and local adaptation in bumblebees inhabiting human-altered landscapes. Here, we discover significant fine-scale (e.g. ~300 km) population structure within two common bumblebee species, Bombus lapidarius and Bombus pascuorum , by analysing whole genome data of 106 specimens from 7 sites in northern Europe. While the observed population structure is largely associated with natural oceanic barriers, we also detect significant divergence between populations sampled from anthropogenic landscapes which are not separated by such barriers. Furthermore, whereas genetic divergence in B. lapidarius is spread relatively evenly across the genome, divergence in B. pascuorum is concentrated within several megabase-sized genomic regions—including a putative chromosomal inversion – which may underlie well-known colour polymorphisms across its range. Our observations reveal a distinct genomic architecture underlying population structure within these bumblebee species, and highlight the necessity of increasing our understanding of bumblebee connectivity to design optimal bumblebee conservation strategies.