Objectives To report a modern mitogenome akin to the one retrieved from an ancient Patagonian and to analyze the presence of putatively related lineages among available datasets.Materials and Methods We surveyed an in-house database of mtDNA sequences of Native American/First Nation origin and an unpublished dataset of Chilean populations for relevant matches to any haplogroup B sequence carrying 16409C. We also queried EMPOP, a database from the forensic scientific community. A phylogenetic analysis was performed with five available B2b15 complete mtDNA sequences.Results Two relevant matches, including one complete mtDNA sequence, were found in the in-house database while three control region-only matches were found among Chileans. The new complete mtDNA sequence allowed us to define a new branch of B2b15, to which all the control region matches are inferred to belong.Discussion Increased availability and diversity of complete mtDNAs may lead to a revised definition of haplogroups and subhaplogroups. The newly defined branch B2b15b, previously known only by one ancient Patagonian haplotype, can now be interpreted as being present among extant Chileans.

Smallpox was a major driver of population collapse in the Americas after European contact, yet the genetic identity of the causal strains remains unknown. Here, we report the first ancient smallpox genomes in the Americas, dating to approximately 1492-1631 common era (CE), recovered from two Inca-Colonial individuals in northern Chile. These genomes form a now-extinct lineage that diverged around 1296 CE, after the splitting of early medieval European strains but before the emergence of modern variola lineages, providing direct molecular evidence for smallpox introduction through European colonization. We further identify a constant tempo of gene inactivation until the late 16th century, followed by a phase of constraint and a subsequent rebound in substitution rates, linking variola virus evolution to major shifts in human demography and epidemiology.

OBJECTIVES:This study aims to delve into mobility patterns and demographic movements in the Andes Altiplano, based on mitochondrial DNA analyses, by reviewing the phylogeny for two previously published lineages, B2ag and B2aj and an analysis of control region sequences to discuss the dynamics of the migratory processes that have shaped the maternal genetic variability in the Andean region. While many articles have focused on population dynamics in the Altiplano, all lack meaningful Chilean sequences. MATERIALS AND METHODS:We sequenced the complete mitogenomes of B2ag1a and B2aj haplogroups (13 and 16 samples, respectively), constructed phylogenies, calculated TMRCAs, and performed frequency maps for both haplogroups. We also sequenced the D-loop of 170 individuals from three populations and performed networks, principal coordinate analysis (PCoA), and multidimensional scaling (MDS) for 1135 individuals from 24 published populations from Argentina, Peru, and Bolivia. RESULTS:We describe the B2ag1a sub-lineage, from the Chilean Altiplano, and reanalyze the B2aj. The temporal depth of both lineages, B2ag1a (9.538 BP) and B2aj (11.838 BP), is consistent with an early occupation of the Andean Altiplano. D-loop analysis shows a strong relationship between Bolivia, Chile, and Argentina, with Peru being more isolated. DISCUSSION:The results support intensive mobility patterns between populations from different areas of the Altiplano, with a critical flux center in Tiwanaku. Moreover, the Chilean Altiplano appears to be an important migration source, mainly to Bolivia and Argentina, as well as to the Chilean north coast, while the influence of the Inca Empire, at least at the population level, seems to be minor.

The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.

Distinctive cultural systems converged during the Late Holocene in the northern Patagonian Archipelago (similar to 41 degrees 30'-47 degrees S), connecting groups with ceramic-bearing cultural traditions and economies based on food production (horticultural) with groups of marine hunter-gatherer-fishers established since the Middle Holocene. This article evaluates changes and continuities in the subsistence and dietary patterns of the groups that occupied this archipelago throughout its occupation sequence, based on the results of delta C-13 and delta N-15 value analysis of 27 individual human remains (similar to 4400-150 cal yr BP) from the Chiloe Archipelago (similar to 41 degrees 30'-43 degrees S). These data are integrated with information previously obtained from 36 individuals (similar to 2000-300 cal yr BP) from the Chonos Archipelago (similar to 43 degrees-47 degrees S), as well as complementary samples of algae and archaeofauna. From the estimated diet of 63 individuals, we suggest a low intensity of interaction between these cultural trajectories over time in the northern Patagonian Archipelago, and continuity of hunting, fishing, and marine gathering systems. After European contact, significant changes in the subsistence of these human groups would be reflected, particularly in the Chiloe Archipelago.

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: Yarnana, Kawesqar, 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 Kawesqar 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 Concepción (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 Concepción (~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 = -0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepción, and other southern populations. Finally, we found lineages from Concepción 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 Concepción 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.

Durante el Holoceno tardío en el archipiélago patagónico septentrional (~41°30′-47°S), convergerían sistemas culturales diferenciados, interrelacionándose grupos con tradiciones culturales portadoras de cerámica y economías basadas en la producción de alimentos (hortícolas) con grupos de cazadores-recolectores-pescadores marinos presentes desde el Holoceno medio. En este trabajo se evalúa los cambios y continuidades en los patrones de subsistencia y dieta de los grupos que ocuparon este archipiélago a lo largo de su secuencia de ocupación, de acuerdo a los resultados del análisis de los valores de δ13C y δ15N correspondiente a restos humanos de 27 individuos (~4400-150 años cal aP) del Archipiélago de Chiloé (~41°30´-43°S), los que son integrados con la información obtenida anteriormente de 36 individuos (~2000-300 años cal aP) provenientes del Archipiélago de los Chonos (~43°-47°S), así como con muestras complementarias de algas y arqueofauna. A partir de la dieta estimada de 63 individuos, se sugiere una baja intensidad de la interacción de estas trayectorias culturales a lo largo del tiempo en el archipiélago patagónico septentrional con continuidad de los sistemas de caza, pesca y recolección marina. Luego del contacto europeo, se reflejarían los mayores cambios en la subsistencia de estos grupos humanos, especialmente en el Archipiélago de Chiloé.

The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.

Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2–4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha’a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua ‘Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately ad 1200 via Mangareva. Analysis of genomic networks from 430 modern individuals across 21 Pacific island populations reveals the human settlement history of Polynesia.

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 ancestry-informative 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 single-nucleotide 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.

Studies of the current Chilean population performed using classical genetic markers have established that the Chilean population originated primarily from the admixture of European people, particularly Spaniards, and Amerindians. A socioeconomic-ethno-genetic cline was established soon after the conquest. Spaniards born in Spain or Chile occupied the highest Socioeconomic Strata, while Amerindians belonged to the lowest. The intermediate strata consisted of people with different degrees of ethnic admixture; the larger the European admixture, the higher the Socioeconomic Level. The present study of molecular genomic markers sought to calculate the percentage of Amerindian admixture and revealed a finer distribution of this cline, as well as differences between two Amerindian groups: Aymara and Mapuche. The use of two socioeconomic classifications - Class and Socioeconomic Level - reveals important differences. Furthermore, Self-reported Ethnicity (self-assignment to an ethnic group) and Self-reported Ancestry (self-recognition of Amerindian ancestors) show variations and differing relationships between socioeconomic classifications and genomic Amerindian Admixture. These data constitute a valuable input for the formulation of public healthcare policy and show that the notions of Ethnicity, Socioeconomic Strata and Class should always be a consideration in policy development.

The possibility of voyaging contact between prehistoric Polynesian and Native American populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1–6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially suggested that prehistoric South American populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8–12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian individuals with Native American individuals (around ad 1200) contemporaneous with the settlement of remote Oceania13–15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia. Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled.

Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT), CONICYT FONDECYT: 7787889. University of Chicago

Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.