Population Genetic Changes Associated with Long-Term African Swine Fever-Related Management in a Wild Boar (Sus scrofa) Population from Northern Hungary

Background/Objectives: African swine fever (ASF) has caused substantial wild boar (Sus scrofa) mortality across Europe and prompted intensive density-reduction measures, yet its long-term effects on population genetics remain poorly understood. To our knowledge, this is the first study to compare genetic diversity, population structure, demographic signatures, and wildlife forensic identification parameters in the same wild boar population before ASF emergence and after several years of ASF-related management. Methods: Wild boar samples collected before ASF emergence in Hungary (n = 67) were compared with samples collected after several years of ASF-related management from the same geographic area (n = 65). All 132 individuals were genotyped at 13 tetrameric microsatellite loci. Diversity was assessed using allelic richness, allele number, and heterozygosity; differentiation using F-statistics, analysis of molecular variance, and discriminant analysis of principal components; demographic history using a two-phase mutation model; and forensic performance using probability of identity and probability of identity among siblings. Results: The post-ASF population showed lower genetic diversity and significant temporal differentiation. Paired Wilcoxon tests indicated a significant reduction in the number of alleles, whereas changes in heterozygosity were not significant. Bottleneck analyses provided no robust evidence of a recent genetic bottleneck. Forensic discrimination power declined modestly while remaining sufficient for individual identification. Conclusions: Because no contemporaneous unaffected reference population was available, these changes cannot be attributed specifically to ASF or management rather than to genetic drift or natural turnover, although they are consistent with sustained demographic disturbance. Nevertheless, this study provides the first temporal genetic comparison of a European wild boar population before ASF emergence and after several years of ASF-related management and demonstrates that a routinely used STR marker panel remains suitable for wildlife forensic individual identification despite these genetic changes.