Different Paths, Similar Pressures: Divergent Drivers of Genetic Diversity Despite Convergent Genomic Signatures of Selection in Response to Urban Intensity in Two Oligolectic Bee Species

Urbanisation is a pervasive form of anthropogenic environmental change and a driver of contemporary evolution. Yet, it remains unclear how demographic processes and environmentally associated genomic variation shape genomic patterns in cities and whether these responses depend on species-specific ecological traits. Here, we addressed this gap using whole-genome sequencing of two related, diet-specialised solitary bees (Andrena florea and Andrena vaga) that differ in dispersal-related traits, rarity and host-plant distribution, sampled along an urban intensity gradient. By integrating population and landscape genomic analyses, we quantified genetic diversity, demographic history, population structure and genotype-environment associations. Neutral genomic patterns differed strongly between species: A. florea showed lower genetic diversity, higher differentiation and a recent population decline, whereas A. vaga maintained higher diversity, connectivity and demographic stability. Genetic diversity was associated with species-specific landscape features (edge density in A. florea and semi-natural habitat in A. vaga), rather than with urban intensity per se. Despite weak population structure, genotype-environment association analyses identified loci associated with urban intensity, and haplotype-based scans detected genomic regions showing patterns consistent with positive selection. Functional annotation and cross-species comparisons revealed partial convergence in candidate genes and functional pathways. Together, these results show that genomic responses to urbanisation cannot be explained by urban intensity alone, but instead emerge from the interaction between gene flow, genetic drift and selection, mediated by species-specific ecological traits. This leads to divergent demographic trajectories but partly convergent genomic responses across species.