Spatial-genetic structure and relatedness
In total, 135 alleles were detected across 16 analysed loci. All loci were polymorphic with the number of alleles per locus ranging from 3 to 18 (mean ± SE: 8.4 ± 0.94). Missing data (i.e. % of missing alleles) amounted to 2.4 % of the dataset and no individual was typed at less than 13 loci. Expected and observed heterozygosity averaged 0.61 ± 0.06 and 0.56 ± 0.06, respectively. Following sequential Bonferroni’s corrections, the overall population showed deviation from HWE at eight loci and from linkage equilibrium in 2 out of 120 pairs of loci. Such deviation from equilibrium was most likely attributed to the inherent substructure of the population (i.e. presence of kin groups) and all loci were retained for statistical analyses.
Spatial autocorrelation analysis revealed the presence of genetic structure, as indicated by an autocorrelation coefficient (r) greater than at random, at a distance of up to 20 km at the population level and up to 10 km among ASF-positive individuals, with genetic similarity between individuals declining from the smallest distance (Fig. S1). Genetic structuring was stronger among ASF-positive individuals compared to ASF-negative ones within each distance class up to 10 km (0-2.5 km distance class: rpos = 0.078 ± 0.003 and rneg = 0.033 ± 0.001, p < 0.001; 2.5-5 km distance class: rpos = 0.028 ± 0.002 and rneg = 0.015 ± 0.001, p < 0.001; 5-10 km distance class: rpos = 0.019 ± 0.001 and rneg = 0.011 ± 0.0004, p < 0.001; Fig. S1).
Considering the entire study area, the coefficient of relatedness in the population averaged 0.0003 ± 0.002 and relatedness among individuals with paired infections was much higher than among those without paired infections (0.049 ± 0.009 and -0.003 ± 0.002, respectively, p<0.001). The differences were influenced by the distance between pairs (Fig. 2). Relatedness among animals with paired infections was highest in the 0-2 km and 2-5 km distance classes (0.129 ± 0.054 and 0.129 ± 0.055, respectively) and lower in the subsequent classes (5-10 km: 0.018 ± 0.017; >10 km: 0.042 ± 0.009). Relatedness between individuals with paired infections was consistently higher than among those without paired infections, except within the 5-10 km distance class (Fig. 2).