Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000-20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia ( = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

We observed an important differentiation in their maternal lineages: while Kawéskar shows a high frequency of D (80%), Yámana shows a high frequency of C (90%). The analysis of paternal lineages reveals the presence of only Q1a2a1a1 and little variation was found between individuals. Both groups show very low levels of genetic diversity compared with modern populations. We also notice shared and unique mitochondrial DNA variants between modern and ancient samples of Kawéskar and Yámana.

Background: Within the southern end of South America, Western Patagonia arises as an intricate region of channels, fjords, and islands. This region holds evidence of human occupation since ca. 14,500 cal years BP, with distinctive maritime adaptations developing around 7300 cal years BP. Historically, three major populations were characterized as part of these maritime traditions: Yámana, Kawésqar, and Chono. The arrival of European population had a profound impact in these communities, affecting their lifestyles, territory and population size and health. The northernmost populations, living within the Chonos Archipelago, were the most affected and the least known communities from Western Patagonia. Objectives: This research aims to characterize the mitochondrial DNA diversity of ancient individuals from the Chonos Archipelago, evaluating their genetic affinities with other ancient and present-day populations from Patagonia. Materials and Methods: A total of 46 individuals from the region were sampled for ancient DNA analysis. Mitochondrial DNA haplogroups were characterized and compared with ancient and present-day populations from Southern South America. Results: All individuals from the Chonos Archipelago belong to C and D haplogroups, particularly to C1b, C1b13, D1, D1g, and D4h3a5. As a group, the individuals from Chonos Archipelago lay closer to ancient individuals from Kawésqar territory, immediately south of them. Using mitogenomes, we characterized two new D4h3a5 lineages almost exclusively associated with populations from Western Patagonia. Discussion: Our results contribute to the understanding of the peopling and human interactions in Western Patagonia, suggesting these unique maritime traditions developed within local populations, genetically associated with earlier terrestrial populations.

Objectives:To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population movement to Santiago (capital of Chile). The intensity of migration was quantified using three mitochondrial lineages restricted to South-Central native groups. Methods: D-loop sequences were genotyped in 550 unrelated individuals from San Felipe-Los Andes (n = 108), Santiago (n = 217), and Concepci on (n = 225). Sequence processing, alignment, and haplogroup inference were carried out, and different genetic structure analyses were performed for haplogroup frequencies and D-loop sequences.Results: The Native lineages B2i2, C1b13, and D1g were the most frequent haplogroups, especially in Santiago (71.8%). Despite the distance, this city showed a high-genetic affinity with southern populations, including Concepci on ($500 km distant) and native groups, rather than with those from San Felipe-Los Andes (<100 km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr = À0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepci on, and other southern populations. Finally, we found lineages from Concepci on acting as ancestral nodes in the northern clade.Conclusions: Considering the geographic distances from these cities, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north-to-south migration during admixture onset in Concepci on and in addition, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post-European contact.