Analysis of relatedness and spatial-genetic structure
Basic parameters of microsatellite polymorphism and genetic diversity were calculated using GENALEX 6.5 (Peakall & Smouse, 2006) and FSTAT (Goudet, 1995). GENEPOP 4.7 (Raymond & Rousset, 1995) was used to test loci for departures from linkage equilibrium and Hardy–Weinberg equilibrium (HWE) using the Markov chain method (parameters: 1000 dememorization steps, 100 batches, 1000 iterations per batch). The significance level was adjusted for multiple testing across loci using the sequential Bonferroni’s correction (Rice, 1989).
Pairwise genetic relatedness (Queller and Goodnight, 1989) was calculated with GENALEX 6.5 among all individuals (n = 323) and subsequently used in all analyses. The Queller and Goodnight estimator is an unbiased measure of relatedness based on population allele frequencies. It ranges from -1 to 1, where positive values indicate pairs more related than average and negative less related than average. We used the Queller and Goodnight estimator to allow comparison with previous studies of wild boar social structure which we build upon (Podgórski et al., 2014a) . We used a dyadic relatedness as continuous predictor in models explaining variation in infection probability. We also dychotomized highly related (hereafter ”kin”) and unrelated (herefater ”non-kin”) pairs of individuals using previously published mean relatedness between social group members of 0.247 (Podgórski et al., 2014a). Analysis of spatial-genetic structure was performed with GENALEX 6.5. Autocorrelation coefficients (r ) between pairwise genetic and geographic distance matrices were calculated for pre-defined Euclidean distance classes (Supplementary Information: Fig. S1) which correspond to spatial genetic structure previously observed in wild boar populations (Pepin et al., 2016; Podgórski et al., 2014a; Podgórski et al., 2018; Poteaux et al., 2009). Spatial-genetic structure was examined among all individuals as well as among ASF-positive and ASF-negative individuals separately. Spatial autocorrelation coefficients were compared across distance classes using randomization tests (10 000 permutations) (Manly 1997). When estimating probability of infection and comparing relatedness within distance classes, we merged the 10+ km classes into one due to weak genetic structure between pairs and negligible contact rates beyond 10 km. We compared relatedness of individuals with paired infections (pairs where both individuals were infected) and with no paired infection (none or one individual of the pair were infected) within the same distance classes as in models estimating probability of infection (0-2 km, 2-5 km, 5-10 km, >10 km) and using the same temporal windows of potential transmission to select pairs for comparison. Relatedness levels were compared using randomization tests (10 000 permutations) (Manly 1997).