Urbanisation Drives Microevolution in the Egyptian Fruit Bat (Rousettus aegyptiacus)

Urbanisation is a pervasive global phenomenon that exerts strong influence on biodiversity and ecosystems. Many species can thrive in urban landscapes by capitalising on generalist traits and environmental resilience; however, this does not safeguard against potential biases exerted by urban environments on population processes. The Egyptian fruit bat (Rousettus aegyptiacus) is a species with both urban and rural distribution across its range, and some populations show behavioural and physiological differences. Using reduced representation genome sequencing (ddRAD-seq), we tested for genetic underpinnings of these differences between urban and rural bat populations sampled across Israel. Despite a genetically homogenous landscape presenting no population structure, we show clear isolation by distance and landscape effects on genetic connectivity, where open areas, but not urbanisation, constitute a barrier to movement. Using genotype-environment association analysis, we identify 59 candidate SNPs spanning 56 genes potentially associated with urbanisation. This suite of genes entails wide-ranging functions including neurotransmission, metabolism, gene expression regulation, reproductive biology, and retinoic acid and sensory function. Gene Ontology enrichment analysis revealed non-random functional clustering with exceptional enrichment in GABAergic synapse components (98.6-fold), monoatomic ion transport (122.2-fold), and ATP-dependent chromatin remodelling (68.6-fold), evidencing coordinated selection across interconnected neural, metabolic, and regulatory systems. A predominance of intronic variants within this candidate SNP suite (51/59) is suggestive that adaptation in response to urbanisation proceeds primarily through changes in gene regulation, rather than protein-coding modifications. This study shows how a highly mobile species may undergo microevolutionary shifts in response to urban pressures despite ongoing gene flow, elucidating the complex interplay between genetics and the urban environment in a non-model organism.