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Objectives: Punta Arenas is a Chilean city situated on ancestral Aönikenk territory. The city was founded by 19th-and 20th-century colonists from Chile (Chiloé) and Europe (Croatia). This work uses uniparental and ancestryinformative markers (AIMs) to explore the effects of historic migratory and admixture patterns on the current genetic composition of Punta Arenas. Methods:We analyzed mitochondrial DNA (mtDNA), Y-chromosome singlenucleotide polymorphisms (SNPs), and 141 AIMs obtained from 129 DNA samples from male residents with regional ancestry. After characterizing uniparental lineages and ancestry proportions, multivariate analysis was used to explore relationships among the various types of data.Results: Punta Arenas has an admixed population with three main genetic components: European (56.5%), northern Native (11.3%), and south-central Native (28.6%). The Native component is preponderant in the mtDNA (83.76%), while the foreign component predominates in the Y-chromosome (92.25%). Non-Native mtDNA lineages are associated with European genetic ancestry, and Native mtDNA lineages originated mainly in the southern and southernmost regions of Chile. Most non-Native Y-chromosome SNPs originated in Spain, and secondly, in Croatia. Conclusions:The population of Punta Arenas is mainly of Chilote origin with south-central Native and Spanish ancestral components, as well as some Croatian components. The persistence of local Native lineages is notable, suggesting continuity with the ancestral populations of the region such as the Kawésqar, Aönikenk, Yámana, or Selknam peoples. This study contributes to our knowledge of local history and its links to national and global developments in genetic ancestry.

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.

Objectives Northern Chile is an area characterized by a complex cultural and demographic trajectory. During the last few centuries, this complex trajectory has become the destination of intra‐ and intercontinental migratory waves. In this study, we analyzed the Y chromosome to evaluate how migratory and admixture patterns have affected the genetic composition of the populations in northern Chile compared with other populations of the country. Methods A total of 311 people from urban (Antofagasta and Calama), rural (Azapa and Camarones), and Native (Aymara and Atacameño) populations from northern Chile were characterized by 26 SNPs and the STR DYS393 of the Y chromosome, along with 69 individuals from Native populations (Mapuche, Pehuenche, and Huilliche) from southern Chile. In addition to characterizing the paternal lineages, multivariate analyses were performed to compare with published data from other Chilean populations. Results Both the Antofagasta and Calama populations show differences compared with the rest of the Chilean population. On one side, Antofagasta shows a high diversity of non‐Amerindian lineages, including the highest value for haplogroup I (12%) for all Chileans populations. Otherwise, Calama has the highest value of any Chilean urban population (31.9%) for Amerindian lineages, including the only Q‐M3 sub‐lineage detected in the entire sample. Regarding the Native population, Aymara presents the highest percentage of Q‐M3 (94.4%). Conclusions The Y chromosome haplogroup distribution allowed us to identify recent migratory processes typical of the northern populations studied. These have shaped the demographic and cultural dynamics of local and migrant groups in the territory.