Human demographic insights from paleogenetic studies of American and Iberian skeletal remains

Abstract

The study of the past through the examination of preserved genetic material from ancient remains has revolutionised the fields of archaeology, anthropology, and evolutionary biology. Ancient DNA can be used as a tool to tackle several questions from a narrow to a broad view, i.e., from a specific archaeological context to global demographic processes. Indeed, in this thesis I covered a large range of projects following this perspective, grouping them according to their respective geographical area: Iberia, Mesoamerica, and the Southern Cone of South America. Part I focuses on the Iberian Peninsula, the westernmost edge of Eurasia and probably one of the most distant regions during the peopling of the continent. In Chapter I, I describe a 1,000- year-old case of Klinefelter’s Syndrome, from an individual unearthed at the mediaeval archaeological site of Torre Velha (Portugal). This work provides an unprecedented integration of morphological, osteological, and genetic evidence to confirm the clinical diagnosis. It also introduces a novel statistical implementation that allows to probabilistically assign individuals to karyotypes based on the number of reads mapping to the X, Y, and autosomal chromosomes. In Chapter II, I investigate the genetic context of the Mas d’en Boixos (MDB) archaeological site—located in the central Pre-littoral depression of Catalonia, Spain—analysing two individuals from the Middle Neolithic, nine from the Early Bronze Age and three previously published from the Iron Age. I infer kinship relationships between individuals buried in close proximity, determine diachronic genetic changes at MDB, contextualise MDB within the rest of Iberia and investigate the Bronze Age transition in Iberia. Part II focuses on the study of pre-Columbian Mesoamerica, a historical and cultural region in Central America whose people probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. In Chapter III, I review previously published ancient DNA studies in pre-Columbian Mesoamerica. Despite a rich archaeological record and Indigenous cultural diversity, aDNA studies are limited and have thus far focused on the study of mitochondrial DNA regions. In Chapter IV, I investigate the past genetic history of pre-Columbian Mesoamerica by analysing 25 newly sequenced ancient genomes from five different archaeological sites across Mesoamerica spanning the time periods between 320 and 1,400 CE. Despite the small sample size, this chapter offers the first (and ongoing) Mesoamerican aDNA genetic screening that includes full mitogenomes and nuclear data. Part III focuses on the Southern Cone of South America (SCSA), a key study region to build a comprehensive picture of the peopling of the Americas as it is geographically the most distant location from the entry point, Beringia. In Chapter V, I investigate the early peopling of the SCSA analysing eighteen ancient human mitochondrial genomes—seven of which are novel— from three Early to Late Holocene (10,000–1,500 years ago) archaeological sites from the understudied Argentinian Pampas and assessing its influence in the southernmost regions.