Historical and contemporary genetic structure reveals recent fragmentation without loss of diversity in Mediterranean House Sparrow populations

Understanding how human-modified environments shape long-term genetic diversity is crucial for conservation, particularly in species experiencing widespread population declines. The House Sparrow Passer domesticus has declined markedly across Europe, yet its long-term genetic dynamics remain poorly understood, especially in Mediterranean landscapes. We assessed spatiotemporal patterns of neutral genetic variation by integrating contemporary samples from 13 populations distributed along an agricultural–urban gradient in Catalonia (NE Spain) with historical museum specimens collected between 1919 and 1950. Using twelve short-amplicon microsatellite loci suitable for degraded DNA, we quantified changes in genetic diversity, population structure, and demographic signals, and evaluated their association with recent population trends. Historical populations were genetically homogeneous and formed a single cluster, consistent with larger effective population sizes and higher connectivity in the past. In contrast, contemporary populations exhibited increased genetic structuring, positive inbreeding coefficients, and heterozygote deficiencies, with subdivision into multiple clusters not clearly associated with habitat categories. Signals of recent demographic bottlenecks were detected in several contemporary populations, particularly in urban areas, indicating localized population contractions linked to landscape intensification. Despite these changes, overall neutral genetic diversity remained largely stable across the past century, and genetic diversity metrics were not associated with recent population trends. Together, our results suggest that Mediterranean House Sparrow populations have experienced recent fragmentation and demographic contractions without pervasive genetic erosion, consistent with historical population declines followed by demographic stabilization or adjustment to novel anthropogenic environments. This study highlights the value of historical DNA for reconstructing long-term genetic baselines in conservation genetics.