Ancient mitochondrial genome diversity in South America: Contributions from Quebrada del Toro, Northwestern Argentina.

OBJECTIVES: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina). MATERIALS AND METHODS: We analyzed teeth from four individuals from the site Ojo de Agua (970 ± 60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina® MiSeq™ platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset. RESULTS: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669 ya. DISCUSSION: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.

OBJETIVOS: El objetivo de este estudio fue contribuir a mejorar la comprensión del poblamiento de Sudamérica, específicamente del Noroeste Argentino, mediante el análisis de mitogenomas antiguos completos de individuos del sitio arqueológico Ojo de Agua (970 AP), Quebrada del Toro (Salta, Argentina). MATERIALES Y MÉTODOS: Se analizaron dientes de cuatro individuos del sitio Ojo de Agua (970 ± 60 AP), ubicado en la Quebrada del Toro (región andina del Noroeste Argentino). A partir de los extractos de ADN se armaron librerías doble cadena y se indexaron utilizando combinaciones únicas de pares de cebadores. Las librerías fueron luego enriquecidas en ADN mitocondrial, llevadas a concentraciones equimolares y secuenciadas en una plataforma Illumina® MiSeq™. Las lecturas de las librerías de alta calidad fueron recortadas, fusionadas y, posteriormente, alineadas con la Secuencia de Referencia de Cambridge revisada. Se evaluaron los patrones de daño del ADNa y se estimó la contaminación. Por último, se identificaron las variantes, se filtraron y se construyó el mitogenoma consenso, que se utilizó para la asignación de haplogrupos. Además, se recopilaron secuencias de mitogenomas disponibles para poblaciones pre-hispánicas y actuales de los Andes Centrosur y otras regiones adyacentes de Argentina. Utilizando el conjunto de datos generado, se obtuvieron reconstrucciones filogenéticas mediante Máxima Verosimilitud y estimación Bayesiana. RESULTADOS: Se obtuvo la secuencia completa del mitogenoma de un individuo con una profundidad media de 102X. Esta secuencia corresponde a un nuevo haplotipo que fue asignado al haplogrupo D1. Las reconstrucciones filogenéticas sugirieron que este haplotipo se encuentra dentro del grupo hermano del linaje D1j, conformando un clado bien soportado. La datación estimada para este clado que contiene a D1j y a todo su grupo hermano fue de entre 12.535 y 18.669 años atrás. DISCUSIÓN: La secuencia analizada en este estudio representa el primer mitogenoma antiguo de la región valliserrana del Noroeste Argentino. Se halló que un representante de un linaje altamente asociado con D1j ya estaba presente hace aproximadamente 1000 años AP en la región. Nuestros resultados concuerdan con un origen de D1j en otras regiones al norte de la Patagonia, e independientemente de la ruta migratoria rápida por la costa del Pacífico, en contraposición a lo planteado inicialmente. Este estudio pone en evidencia la falta de información que se tiene actualmente sobre la diversidad genética en tiempos prehispánicos y contribuye al conocimiento del proceso de poblamiento de Sudamérica.

Ancient DNA reveals temporal population structure within the South-Central Andes area.

OBJECTIVES: The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina. MATERIALS AND METHODS: We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru. RESULTS: Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre-Hispanic history: pre-Inca and Inca. All pre-Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y-chromosome analyses. We mainly found a clearly different haplotype composition between clusters. DISCUSSION: Population structure in South America has been mostly studied on current native groups, mainly showing a west-to-east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South-central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio-political changes occurred in the evermore complex pre-Hispanic Andean societies.

Pre-Hispanic Mortuary Practices in Quebrada de Humahuaca (North-Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave.

Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA.

Genetic diversity of a late prehispanic group of the Quebrada de Humahuaca, northwestern Argentina.

This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies whose cultural but especially biological diversity is still poorly understood. We analyzed the DNA extracted from 39 individuals who populated this upper valley during the Regional Development period (RDP) (between the 11th and 15th centuries CE), to determine their maternal and paternal genetic ancestry. Some mitochondrial and Y-chromosomal haplotypes specific to the Andean region are consistent with an origin in the highlands of Central Andes. On the other hand, a significant genetic affinity with contemporary admixed communities of the Chaco area was detected. Expectedly, recent demographic events, such as the expansion of the Inca Empire or the European colonization, have changed the original mitochondrial gene pool of the ancient Humahuaca Valley community. Finally, we identified a particular geographical organization of the prehispanic populations of Northwestern Argentina. Our results suggest that the communities of the region were divided between two different spheres of interaction, which is consistent with assumptions made by means of craniometric traits.