Abstract:
The dissection of complex traits and the reconstruction of the demographic and selective history of a species requires significant numbers of genetic markers for statistical corroboration and hypothesis testing. Improvement in next -generation sequencing techniques, has recently led to the discovery of hundreds of thousands of SNPs, albeit mostly in commercial pig breeds, of which approximately 60,000 can be efficiently assayed by means of the Illumina 60K beadchip. This assay, although not primarily designed for wild boar population genetics, was found to detect high numbers of segregating loci in European wild populations. We genotyped approximately 500 wild boars from 19 different European countries with the aim of elucidating patterns of diversity and differentiation, investigating hybrid zones and studying the effects of inbreeding, local extinctions and restocking. Various PCA-like methods displayed a high degree of congruence with European geography; twodimensional representations of such analyses can be almost interpreted as virtual maps of Europe. The East-West gradient clearly differentiates the Iberian Peninsula, Italy, and the Balkans, and is likely to be related to the isolation of refugial areas during the last glaciation.These major genetic groups partially include the populations located in the corresponding northern areas, possibly as a consequence of post-glacial northern expansions. The 'Iberian' cluster, for example, encompasses all the Western European populations, and the 'Balkans' cluster includes all the Central-Eastern European populations up to the Finno-Russian border. Some level of genetic divergence along the South-North axis can be identified from the second principal component, which is, however, strongly affected by the populations located in Central-Southern Italy and Sardinia. Sardinia seems to harbor specific genetic wild boar diversity, possibly due to population bottlenecks and/or specific selection pressures typical in insular populations. Local adaptations are further investigated for signatures of selection across the genome. A few European populations showed clear signs of a mosaic origin. The genomic composition of a population in Switzerland, for example, is likely affected by restocking and migration events. These complex patterns of admixture are further analysed using various genome-wide ancestry mapping procedures based both on allele frequency and haplotype sharing. Demographic parameters can be estimated, but caution is required in their interpretation given the ascertainment bias introduced by the SNPs isolation process. Nevertheless, the Illumina 60K SNP chip proved to be an efficient tool for studying genetic variation patterns in wild boar populations.