Duplication, recombination and weak selection shape evolution at the MHC class II SLA-DRB1 locus in wild boars from the western Balkans

The Eurasian wild boar (Sus scrofa), having faced a population size reduction during the nineteenth and early twentieth centuries, is now experiencing a remarkable population recovery, not only confined to natural habitats alone, but also thriving in human-dominated environments. Previously, studies on wild boars predominantly relied on the analysis of supposedly neutral molecular markers (e.g., microsatellites and single nucleotide polymorphisms). In this study, a next-generation sequencing approach was used to examine the adaptive variation at the second exon of the SLA-DRB1 locus in 116 wild boars from the western Balkans. A total of 17 functional SLA-DRB1 alleles were detected which translated into 14 different amino-acid sequences. In 12 individuals, we observed alleles at duplicated SLA-DRB1 loci. Spatial analysis revealed the presence of three genetic clusters, albeit with relatively low overall differentiation (an average F_ST value of 0.012). Positive selection was detected on only one codon, as indicated by multiple tests, while the presence of shared alleles among related species suggested signals of trans-species polymorphism. Our results indicate the high MHC diversity at the SLA-DRB1 locus in wild boars from the Balkan Peninsula, shaped by a complex interplay of several non-exclusive mechanisms, including balancing selection, recombination, and gene duplications.