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).