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

ABSTRACT 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.