Reconstructing the ancestry and history of populations through ancient and modern genomes

Population genetics has been a fundamental discipline in the study of human history since the early 20th century. Over the decades, researchers have employed a range of approaches — beginning with classical markers, followed by uniparental systems such as mitochondrial DNA (mtDNA) and the Y chromosome, and more recently, whole-genome sequencing — to investigate the genetic composition of populations and uncover clues about their past dynamics. More recently, the advent of archaeogenomics has been a game-changer, enabling scientists to unlock the genetic information preserved in ancient skeletal remains and offering unprecedented insights into the origins, evolution, and interactions of human groups across time. Human populations have been shaped by complex processes, including migrations, admixture, and demographic shifts, that occurred over thousands of years. While specialists in archaeology, history, and linguistics have long sought to reconstruct these events, archaeogenomics now provides a powerful complementary tool, allowing for a more integrated and data-driven reconstruction of human history. In this framework, the main aim of my PhD project was to reconstruct the genetic history of populations, as well as of single individuals, through the analysis of ancient human remains. This involved the processing of a total of 60 skeletal elements recovered from different archaeological contexts in Europe, specifically Italy and Greece (Chapters 8-11). In most cases, sampling was performed using a minimally invasive approach to preserve bone integrity while still obtaining sufficient material for genomic analysis. In addition, one project focused on mitogenome variability to elucidate the origin of modern North Africans from a maternal perspective (Chapter 12). This study, recently published in Scientific Reports, contributed 238 newly generated complete modern mitogenomes from North Africa, substantially enriching the available genetic data for this region. My research also extended to the analysis of DNA samples recovered from the Turin Shroud (Chapter 13), adding a unique case study to the broader framework of ancient DNA investigations. Beyond population-level analyses, I also contributed to the development of an R package for the management of huge amounts of ancient DNA metadata (Chapter 14). This tool was designed to streamline data organisation and enhance reproducibility in the study of ancient genomes. Overall, my research encompassed five main projects and two side projects, carried out in collaboration with different institutions, as detailed in the respective chapters.