When isolation is only apparent: Disentangling the genetic make-up of the Sardinian wild boar by different classes of genetic markers

M. Scandura, L. Iacolina, D. Biosa, A. Cossu, H.J. Megens, R. Crooijmans, L. Rund, M. Groenen, L. Schook, G. Bertorelle, M. Apollonio
8th International Symposium on Wild Boars and Other Suids, September 1-7, 2010, York, United Kingdom


Human-mediated translocations can cause the loss of genetic distinctiveness of island populations. However, valuable native variation can still be distinguished if many individuals and appropriate markers are analysed. We investigated wild boar populations from the Mediterranean island of Sardinia, Italy. This can be considered as a case study to evaluate the performance of different genetic markers in detecting admixture events related to the introduction of continental wild boars and to crossbreeding with domestic pigs. The Sardinian wild boar, seems to have appeared in the island during the Early Neolithic. The geographic isolation likely favoured the genetic divergence from the continental groups, and the Sardinian boars are now classified as a distinct subspecies (Sus scrofa meridionalis). We analysed a sample of individuals from throughout the island using three different classes of molecular markers: 1) sequences of the Dloop region of the mitochondrial DNA, 2) 16 autosomal microsatellites, and 3) genome-wide scan of 60,000 porcine SNPs. Data for the Sardinian sample were compared with reference data obtained for continental populations from several areas in Europe and with a sample of domestic pig breeds. Dloop data showed that the Sardinian population shares a mtDNA lineage that elsewhere is only found in peninsular Italy. A high percentage of private haplotypes was also remarked, while no haplotype of Asian origin was detected. Microsatellite data showed a clear genetic divergence of the island populations from all mainland populations and from domestic pigs. In addition, signatures of genetic introgression from Italian and non-Italian wild boars, and from local domestic breeds were identified. A sharp genetic structure was also found within the island. Two geographically constrained sub-populations showed very high levels of genetic purity. Finally, SNPs data acquired using the Illumina 60K beadchip revealed  i) a considerable divergence of most Sardinian individuals from continental wild boars,ii) their likely origin in the Italian peninsula, iii) the ancestry of some individuals in other European populations, possibly due to translocations that occured in the recent past.