Urbanisation drives parallel genomic divergence across cities and bumble bee species

Urbanisation imposes pervasive environmental change, yet it remains unclear whether evolutionary responses to cities are largely idiosyncratic or whether similar selective pressures across cities repeatedly generate predictable genomic outcomes.

Here, we analyse whole-genome data from 524 individuals of three widespread bumble bee species sampled across nine independent urban-rural pairs in Central Europe to test whether urban environments drive parallel evolutionary responses across cities and species. Genetic diversity responded idiosyncratically to urbanisation, with two species showing no detectable urban-rural differences and one species exhibiting reduced diversity in cities, consistent with species-specific ecological traits and habitat requirements. Despite weak population structure and high gene flow in all species, we detected consistent and replicated genomic divergence associated with urban environments. Genome-environment association analyses revealed parallel allele-frequency shifts at the same loci across independent cities for each species, while selective sweep scans identified repeated signals of positive selection in urban populations. Across species, urban-associated divergence was highly polygenic and occurred predominantly in non-coding regions with potential regulatory roles. Although the specific genes involved were largely species-specific, functional enrichment analyses revealed strong convergence across species, particularly in pathways related to physiological stress responses, neurocognitive and behavioural processes, metabolism and immunity.

Together, these results suggest that urban environments can impose recurrent selective pressures, generating predictable and parallel genomic responses across cities and species despite ongoing gene flow. More broadly, our findings highlight polygenic, potentially regulatory adaptation as an important component of evolutionary responses to urban environments.