The Evolutionary History of Italy from the Mesolithic to the Present: Lessons from Ancient Genomes

In this thesis I outline the work that I carried out for over three years, which so far has led to a scientific publication in a peer-reviewed journal and a manuscript currently accepted for publication and a manuscript to be submitted for publication. These studies focus mainly on reconstructing the evolutionary history of Italy in the last 10,000 years through the analysis of ancient DNA. The Italian Peninsula, a crossroads of Mediterranean cultures, has long been recognized for its pivotal role in European history. Despite extensive genomic studies across Europe, the genetic history of Italy remains largely underexplored due to scarcity of ancient whole-genome data spanning limited geographical regions. In this context, the analysis of ancient genomes is fundamental to uncover these complex genetic and demographic dynamics, through the use of recently developed computational frameworks. Chapter 1 introduces the evolutionary history of Europe and Italy through the analysis of ancient DNA. Chapter 2 focuses on the history of Italy a through comprehensive analysis of 43 ancient genomes from 16 necropoleis across mainland Italy, Sicily, and Sardinia, spanning about 10,000 years of his- tory, alongside hundreds previously published ancient complete genomes covering from the Mesolithic to the Medieval periods. Leveraging Genotype Likelihood computations and imputation of missing positions alongside the genome, I achieved robust statistical reconstructions of past evolutionary dynamics despite the inherent challenges of low-coverage data. These analyses revealed a complex mosaic of external influences shaping the genetic landscape of Italy, highlighting major migrations that have occurred over time. Chapter 3 uncovers the history of the island of Sicily through the analysis of ancient and modern whole mitochondrial genomes, spanning the last 15,000 years. The analysis of ancient mitochon- drial variation revealed the genetic structure of Sicilian populations through time in the context of Mediterranean territories. Integrating the analysis of 236 present-day mitochondrial genomes I was able to reconstruct the demographic history of the island in the last 15,000 years from a maternal perspective.