Human mitochondrial DNA and population structure of the Western Mediterranean Islands

This thesis reconstructs the maternal genetic history of the major western Mediterranean islands, Sardinia, Sicily, and Corsica, through a comparative analysis of ancient and modern mitochondrial DNA (mtDNA). By integrating high-resolution mitogenomic data, the study aims to explore how migration, colonization processes, and long-term geographic isolation have shaped the genetic structure of insular populations over time. A total of 27 newly generated complete ancient mitogenomes (17 from Sardinia and 10 from Sicily), spanning from the Neolithic to the 16th century, were analyzed together with 105 modern mtDNA genomes from Sardinia, Sicily, and Corsica. These data were combined with published sequences to build a comprehensive database of 2,272 individuals (538 ancient and 1,734 modern). Haplogroup assignment, phylogenetic network reconstruction, and genetic distance analyses were performed to investigate patterns of continuity, differentiation, and demographic change across the islands and within the broader Mediterranean context. The results suggest that Sardinia may represent a case of notable maternal genetic continuity, with observable affinities between ancient individuals (especially from the Early Bronze Age) and modern populations from historically isolated inland regions such as Gallura, Sassarese, and Barbagia. Haplogroup diversity is substantial, with H as the predominant lineage, alongside persistent branches of HV, J, K, T, and deep-rooted components such as U5, suggesting long-term preservation of ancient maternal lineages. In contrast, Sicily displays a more dynamic and heterogeneous maternal history. Modern populations show variable affinities across chronological phases and a marked discontinuity from Eneolithic samples, indicating that prehistoric maternal lineages are not the dominant component of the present-day population. Provincial patterns reveal broad Mediterranean-scale connections, with affinities to ancient Ibiza, Greece, Sardinia, and episodic links to the Eastern Mediterranean. The near disappearance of rare haplogroups such as U8 highlights the progressive loss of ancient maternal diversity through drift or later demographic replacements. Corsica, represented by modern data only, shows strong maternal proximity to Sardinia and western Sicily, supporting a shared central Mediterranean genetic background shaped by long-term mobility and contacts. Overall, this study emphasizes the value of combining complete ancient mitogenomes with modern datasets to reconstruct the evolutionary and demographic history of Mediterranean islands. Future research should test alternative demographic scenarios using approaches such as ABC and integrate autosomal and Y-chromosome data to clarify sex-biased migration, genetic replacement, and insular population dynamics.