Exploring ancient and modern genomes of Indigenous populations in the Americas.

The peopling of the Americas refers to the migration, expansion, and settlement of ancient human populations from Asia to the double continent, resulting in the diverse Indigenous American (IA) groups. Archaeological evidence and genetic research are some of the areas that contribute to our understanding of this ancient dynamic. Mitochondrial DNA has initially enabled the detection of founder Indigenous lineages. Nowadays, archaeogenomics enables diachronic comparison and analysis of modern and ancient DNA at the genomic level. The projects presented in this thesis utilize these novel genomic tools to explore the genetic histories of IA populations. The first project centered on the mitochondrial haplogroup X2a. It has a distribution limited to northern North America and a high prevalence in the Great Lakes area. In this study, we analyzed 13 ancient and 55 modern mitogenomes. The ages and distributions of X2a branches have been evaluated through a phylogeographic approach. Our analysis revealed that two major sub-haplogroups, X2a1 and X2a2, exhibit distinct demographic trends and have differentiated into several sub-branches. We classified the most ancient X2a mitogenome, which was found at the Kennewick Man site along the Columbia River in Washington State and dated it to approximately nine thousand years ago. The Bayesian phylogeny places the Kennewick Man mitogenome as part of an ancestral pre-X2a branch. These findings suggest that the initial X2a population (pre-X2a2 and X2a2) migrated along the Pacific coast before moving into the interior of North America. Conversely, only the X2a1 group may have entered directly through the interior corridor. The Ashaninka project pertains to the largest indigenous group in Amazonian Peru, despite their demographic decline after European contact. In this study, we generated 51 genome-wide profiles from Ashaninka individuals uncovering an unexpected high degree of genomic variation and genomic structure. We identified two distinct Ashaninka subgroups with unique genomic compositions. Both were shaped differently by external admixtures, particularly with Indigenous groups from the Andes and the Pacific coast, based on the degree and timing of admixture. On a larger scale, the study indicates that Ashaninka ancestors probably migrated from south to north, entering the Amazonian rainforest from a southeastern region with contributions from the Southern Cone and the Atlantic coast. The research highlights connections between present-day Ashaninka individuals, who belong to the Arawakan language family, and Indigenous groups that migrated northward into the Caribbean. These groups contributed to the early Ceramic (Saladoid) tradition in the islands. The findings provide insights into the intricate genetic history of South America. For my third project, I analyzed human remains from seven different archaeological sites in northeastern Argentina dating back to the late pre-Hispanic period. A total of 20 ancient specimens excavated along the Paraná River basin were processed. The kinship analysis showed no relationship among them. Their mitogenomes were classified into three different IA mitochondrial haplogroups, three A2, one B2 and two C. The genomic profiles were then compared to a large dataset of modern and ancient genomes, confirming the heterogeneity of pre-Hispanic individuals from the southern cone of South America. The purpose of this thesis was to investigate the genetic history of the pre-Hispanic Americas, using ancient and modern genomic data. The analysis of mitogenomes from the Indigenous haplogroup X2a suggests that alternative migration routes to North America may be related to X2a1 and X2a2 sub-haplogroups. Additionally, genome-wide data from the Indigenous Ashaninka group revealed a complex genetic structure and high genetic diversity within this community. Finally, ancient DNA data from Argentina has increased our understanding of the pre-Hispanic Southern Cone.