Ancient DNA Characterization of Sheep Remains from the Medieval Site of Siponto (Southern Italy)

The archeological site of Siponto is located on the shore of the Gulf of Manfredonia (Apulia, Southern Italy). The site hosts the remains of a town abandoned around the mid XIIIth century after an earthquake. Excavation campaigns carried out from 2000 to 2009 revealed several ovine bones located in different buildings of the last housing phase of the ancient town. Such remains significantly predate the hypothetical introduction of Spanish merino rams claimed by King Alphonse I of Napoli (mid XVth century) and may represent the ancestral gene pool of local southern Italian sheep populations before the beginning of the so-called “merinization” process. To explore such intriguing hypothesis and characterize the molecular variation of this ancient sheep population, a DNA extraction was carried out on 33 bone and teeth remains from the site of Siponto, following stringent protocols for ancient samples within the dedicated lab facility of the BioDNA Research Centre. For ten samples, 311 base pairs of the mitochondrial (mtDNA) control region were characterized through PCR amplification, cloning and direct sequencing. Further, the four best-performing DNA samples were used to construct genomic libraries for a subsequent high-throughput sequencing. MtDNA data highlighted the presence of eight different haplotypes belonging to haplogroup B, the most frequent in Europe. Ancient DNA-specific bioinformatics pipelines were applied to analyze the resulting high-throughput sequencing data, allowing to retrieve ~0.3% of endogenous sheep DNA. A preliminary variant calling investigation identified 2,550 variants, eight of which are predicted to have a major impact on protein structure and functioning.