Background Wild boar (Sus scrofa) is a widely distributed ungulate whose success can be attributed to a variety of ecological features. The genetic variation and population structure of Lithuania’s wild boar population have not yet been thoroughly studied. The purposes of this study were to investigate the genetic diversity of S. scrofa and assess the effects of habitat fragmentation on the population structure of wild boar in Lithuania. A total of 96 S. scrofa individuals collected from different regions of Lithuania were genotyped using fifteen microsatellite loci. Results The microsatellite analysis of the wild boars indicated high levels of genetic diversity within the population. Microsatellite markers showed evidence of a single panmictic wild boar population in Lithuania according to STRUCTURE’s highest average likelihood, which was K = 1. This was supported by pairwise Fst values and AMOVA, which indicated no differentiation between the four sampling areas. The results of the Mantel test revealed a weak isolation by distance and geographic diversity gradients that persisted between locations. Motorway fencing and heavy traffic were not an effective barrier to wild boar movement. Conclusions There was limited evidence of population genetic structure among the wild boar, supporting the presence of a single population across the study area and indicating that there may be no barriers hindering wild boar dispersal across the landscape. The widespread wild boar population in Lithuania, the high level of genetic variation observed within subpopulations, and the low level of variation identified between subpopulations suggest migration and gene flow between locations. The results of this study should provide valuable information in future for understanding and comparing the detailed structure of wild boar population in Lithuania following the outbreak of African swine fever.

The emergence of African swine fever (ASF) in Lithuania and its subsequent persistence has led to a decline in the population of wild boar (Sus scrofa). ASF has been spreading in Lithuania since its introduction, therefore it is important to understand any genetic impact of ASF outbreaks on wild boar populations. The aim of this study was to assess how the propensity for an outbreak has shaped genetic variation in the wild boar population. A total of 491 wild boar samples were collected and genotyped using 16 STR markers. Allele richness varied between 15 and 51, and all SSR loci revealed a significant deviation from the Hardy–Weinberg equilibrium. Fixation indices indicated a significant reduction in heterozygosity within and between subpopulations. PCoA and STRUCTURE analysis demonstrated genetic differences between the western region which had had no outbreaks (restricted zone I) and the region with ASF infection (restricted zones II and III). It is concluded that environmental factors may play a particular role in shaping the regional gene flow and influence the genetic structure of the wild boar population in the region with ASF outbreaks.

African swine fever (ASF) is a contagious disease of key importance that occurs in wild boar population and domestic pigs. To date, there is no vaccine or treatment available, hence disease surveillance and stamping out in case of an outbreak is the only way to control it. A duplex ASF-IC real-time PCR assay was optimised using field samples obtained in Lithuania and results of singleplex and duplex real-time PCR assays allowing the identification of the ASF virus were compared. The specificity and sensitivity of ASF virus detection was validated using a reference sample of positive and negative virus nucleic acid and ASF virus positive and negative samples obtained from animals in Lithuania. Results prove that duplex ASF-IC real-time PCR assay provides a rapid, sensitive, and reliable molecular tool for ASF virus detection in wild boar population and domestic pigs. In general, it was found that duplex ASF-IC real-time PCR assay proves to be faster and more sensitive than singleplex real-time PCR and therefore has a high potential to be applied in routine analysis.

Background: Wild boar (Sus scrofa) is a widely distributed ungulate whose success can be attributed to a variety of ecological features. The genetic variation and population structure of wild boar population in Lithuania before the spread of African swine fever has not yet been thoroughly studied. To characterize the amount of genetic variation and population structure of wild boar in Lithuania before the African swine fever outbreak, we genotyped and analyzed microsatellite loci for a total of 96 wild boar specimens from nine locations. Results: In the present study, individuals were genetically typed at fifteen microsatellite loci using multiplex PCR amplification. Our data showed that that 85% of the genetic variation originated from individuals, indicating a high gene exchange between the nine subpopulations of wild boar in Lithuania. Bayesian-based clustering analysis in STRUCTURE identified two inferred genetic clusters and each of the 9 subpopulations had more than 1 cluster. A factorial correspondence analysis confirmed homogeneity and no genetic differentiation between subpopulations of S.scrofa in Lithuania.Conclusions: Our results reveal that wild boar subpopulations of Lithuania before the African swine fever outbreak were still not distinguished and admixed. This study highlights the potential contribution for the future study understanding the detailed structure of wild boar population in Lithuania after African swine fever outbreak.