Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.

OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia. MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network. RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established. DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.

OBJETIVOS: El objetivo principal de este estudio es discutir los procesos migratorios y la dinámica de poblamiento que moldearon la variabilidad genética de las poblaciones durante el poblamiento del Cono Sur, a través del análisis de mitogenomas completos de individuos del sur de Patagonia. MATERIALES Y MÉTODOS: Se obtuvieron mitogenomas completos mediante secuenciación masiva de dos individuos del Holoceno tardío (SAC 1-1-3 y SAC 1-1-4) enterrados en el mismo chenque en la Cuenca del Lago Salitroso (provincia de Santa Cruz, Argentina). Para evaluar las afinidades matrilineales con otros haplotipos, se realizaron reconstrucciones filogenéticas de máxima verosimilitud y bayesianas, así como una red mediana de haplotipos. RESULTADOS: Los mitogenomas fueron asignados a los haplogrupos B2 y B2b, exhibiendo una profundidad de secuenciación promedio de 54X y 89X (cobertura ≥1X de 98,6% y 100%), y un elevado número de diferencias nucleotídicas entre ellos. Los análisis filogenéticos mostraron una relación relativamente estrecha entre el haplotipo encontrado en el SAC 1-1-4 y los recuperados de un individuo del Holoceno Medio de Laguna Chica (provincia de Buenos Aires), y de un grupo de individuos de la costa peruana. Para el SAC 1-1-3, no se establecieron relaciones claras con ningún otro haplotipo. DISCUSIÓN: La gran divergencia entre los haplotipos presentados en este estudio sugiere gran variabilidad en el acervo genético fundador, o bien un enriquecimiento posterior por contacto biológico frecuente con otras poblaciones. Nuestros resultados destacan la persistencia de señales genéticas relacionadas con las primeras oleadas de poblamiento de Sudamérica, lo que sugiere que el poblamiento regional del extremo sur del continente ha sido mucho más complejo de lo que se pensaba inicialmente.

Distribution of maternal lineages in hunter-gatherer societies of the southern coast of Tierra del Fuego, Argentina.

OBJECTIVES: The aim of this work is to explore the maternal genetic diversity of hunter-gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis. MATERIALS AND METHODS: The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined. RESULTS: The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre-Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results. DISCUSSION: Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre-Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel.

First analysis of mitochondrial lineages from the eastern Pampa-Patagonia transition during the final late Holocene.

OBJECTIVE: Studies on population genetics have become highly relevant for understanding the evolutionary history of human settlement in southern South America. The eastern Pampa-Patagonia transition is an area that stands out due to its complex population dynamics, especially during the last about 1,000 years BP. The aim of this work is to characterize the maternal lineages of individuals buried in the Paso Alsina 1 archaeological site (ca. 500 years BP) through the analysis of mitochondrial genetic variability, in order to discuss the population models previously proposed for the southern cone of South America. METHODS: Mitochondrial HyperVariable Region I sequences were analyzed on teeth belonging to 20 adult individuals. Statistical analyses were carried out to compare the interpopulation and intrapopulation molecular variability between the results obtained in this work and those previously published data from pre-Hispanic human groups. D1 haplotype network was constructed drawing from data on ancient and extant population group samples. RESULTS: Thirteen sequences (65%) were obtained from the 20 analyzed samples. The maternal lineages or subhaplogroups identified were D1g (69.24%), C1 (15.38%), D1 (7.69%), and D1j (7.69%). There was low haplotype variability within the site; some individuals could be matrilineally related. DISCUSSION: The subhaplogroups registered in Paso Alsina 1 site are in accordance with those reported for ancient and contemporary Patagonian populations. The results suggest that an initial nucleus of individuals carrying mostly subhaplogroup D1g settled in northern Patagonia, from which local diversity of this matrilineage could have arisen. The existence of gene flow in the final late Holocene with groups from Northern Andean Patagonia, as well as from Central Argentina, is proposed. The D1j variant probably developed in the latter region.

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.

Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina).

Ancient DNA recovered from 21 individuals excavated from burial sites in the Pampa Grande (PG) region (Salta province) of North-Western Argentina (NWA) was analyzed using various genetic markers (mitochondrial DNA, autosomal STRs, and Y chromosomal STRs). The results were compared to ancient and modern DNA from various populations in the Andean and North Argentinean regions, with the aim of establishing their relationships with PG. The mitochondrial haplogroup frequencies described (11% A, 47% B, and 42% D) presented values comparable to those found for the ancient Andean populations from Peru and San Pedro de Atacama. On the other hand, mitochondrial and Y chromosomal haplotypes were specific to PG, as they did not match any other of the South American populations studied. The described genetic diversity indicates homogeneity in the genetic structure of the ancient Andean populations, which was probably facilitated by the intense exchange network in the Andean zone, in particular among Tiwanaku, San Pedro de Atacama, and NWA. The discovery of haplotypes unique to PG could be due to a loss of genetic diversity caused by recent events affecting the autochthonous populations (establishment of the Inca Empire in the region, colonization by the Europeans).

[Gene mixture in a population sample from Buenos Aires City]. / Mezcla genica en una muestra poblacional de la Ciudad de Buenos Aires.

The aim of this study is to estimate the gene admixture in the population of Buenos Aires City from samples of blood donors, which come from a public health centre (Hospital de Clínicas). These studies were performed on 218 unrelated people, who donated blood during the year 2002. Eight erythrocyte genetic systems and GM/KM allotypes were analysed. A survey to obtain information about place of birth, present residence and genealogical data of the donors was performed. The gene frequencies were determined using a method of maximum likelihood. The genetic admixture was calculated through the ADMIX program (trihibride). The Amerindian and African contributions were 15.8% and 4.3% respectively. These data were compared with those obtained in a previous study performed in a private centre (Hospital Italiano de Buenos Aires) and significant differences were observed, except in the KM system. The results obtained are in concordance with the demographic and historic information of Buenos Aires City.

Mezcla genica en una muestra poblacional de la ciudad de Buenos Aires / Gene mixture in a population sample from Buenos Aires City

Este estudio tiene como objetivo estimar la mezcla génica en la población de la Ciudad de BuenosAires, a partir de muestras de dadores de sangre provenientes de un centro público de salud (Hospitalde Clínicas). Los estudios se realizaron sobre 218 personas no emparentadas que donaron su sangre duranteel año 2002. Se analizaron 8 sistemas genéticos eritrocitarios y los alotipos GM/KM. Se realizó una encuestacon la finalidad de obtener información sobre lugar de nacimiento, residencia actual y datos genealógicosde los dadores. Las frecuencias génicas se determinaron empleando métodos de máxima verosimilitud. Paracalcular la mezcla génica se aplicó el programa ADMIX (trihíbrido). Se registró un 15.8% de aporte indígena(AI) y 4.3% de africano (AA). Estos datos se compararon con un estudio previo realizado en un centro privado(Hospital Italiano de Buenos Aires), no observándose diferencias significativas salvo en el sistema Km. Los resultadosobtenidos se corresponden con la información histórica y demográfica de la ciudad de Buenos Aires. (AU)

The aim of this study is to estimatethe gene admixture in the population of Buenos Aires City from samples of blood donors, whichcome from a public health centre (Hospital de Clínicas). These studies were performed on 218 unrelated people,who donated blood during the year 2002. Eight erythrocyte genetic systems and GM/KM allotypes were analysed.A survey to obtain information about place of birth, present residence and genealogical data of the donors wasperformed. The gene frequencies were determined using a method of maximum likelihood. The genetic admixturewas calculated through the ADMIX program (trihibride). The Amerindian and African contributions were 15.8%and 4.3% respectively. These data were compared with those obtained in a previous study performed in a privatecentre (Hospital Italiano de Buenos Aires) and significant differences were observed, except in the KM system.The results obtained are in concordance with the demographic and historic information of Buenos Aires City. (AU)

Mezcla genica en una muestra poblacional de la ciudad de Buenos Aires / Gene mixture in a population sample from Buenos Aires City

Este estudio tiene como objetivo estimar la mezcla génica en la población de la Ciudad de BuenosAires, a partir de muestras de dadores de sangre provenientes de un centro público de salud (Hospitalde Clínicas). Los estudios se realizaron sobre 218 personas no emparentadas que donaron su sangre duranteel año 2002. Se analizaron 8 sistemas genéticos eritrocitarios y los alotipos GM/KM. Se realizó una encuestacon la finalidad de obtener información sobre lugar de nacimiento, residencia actual y datos genealógicosde los dadores. Las frecuencias génicas se determinaron empleando métodos de máxima verosimilitud. Paracalcular la mezcla génica se aplicó el programa ADMIX (trihíbrido). Se registró un 15.8% de aporte indígena(AI) y 4.3% de africano (AA). Estos datos se compararon con un estudio previo realizado en un centro privado(Hospital Italiano de Buenos Aires), no observándose diferencias significativas salvo en el sistema Km. Los resultadosobtenidos se corresponden con la información histórica y demográfica de la ciudad de Buenos Aires. (AU)

The aim of this study is to estimatethe gene admixture in the population of Buenos Aires City from samples of blood donors, whichcome from a public health centre (Hospital de Clínicas). These studies were performed on 218 unrelated people,who donated blood during the year 2002. Eight erythrocyte genetic systems and GM/KM allotypes were analysed.A survey to obtain information about place of birth, present residence and genealogical data of the donors wasperformed. The gene frequencies were determined using a method of maximum likelihood. The genetic admixturewas calculated through the ADMIX program (trihibride). The Amerindian and African contributions were 15.8%and 4.3% respectively. These data were compared with those obtained in a previous study performed in a privatecentre (Hospital Italiano de Buenos Aires) and significant differences were observed, except in the KM system.The results obtained are in concordance with the demographic and historic information of Buenos Aires City. (AU)

Mezcla genica en una muestra poblacional de la ciudad de Buenos Aires / Gene mixture in a population sample from Buenos Aires City

Este estudio tiene como objetivo estimar la mezcla génica en la población de la Ciudad de BuenosAires, a partir de muestras de dadores de sangre provenientes de un centro público de salud (Hospitalde Clínicas). Los estudios se realizaron sobre 218 personas no emparentadas que donaron su sangre duranteel año 2002. Se analizaron 8 sistemas genéticos eritrocitarios y los alotipos GM/KM. Se realizó una encuestacon la finalidad de obtener información sobre lugar de nacimiento, residencia actual y datos genealógicosde los dadores. Las frecuencias génicas se determinaron empleando métodos de máxima verosimilitud. Paracalcular la mezcla génica se aplicó el programa ADMIX (trihíbrido). Se registró un 15.8% de aporte indígena(AI) y 4.3% de africano (AA). Estos datos se compararon con un estudio previo realizado en un centro privado(Hospital Italiano de Buenos Aires), no observándose diferencias significativas salvo en el sistema Km. Los resultadosobtenidos se corresponden con la información histórica y demográfica de la ciudad de Buenos Aires.

The aim of this study is to estimatethe gene admixture in the population of Buenos Aires City from samples of blood donors, whichcome from a public health centre (Hospital de Clínicas). These studies were performed on 218 unrelated people,who donated blood during the year 2002. Eight erythrocyte genetic systems and GM/KM allotypes were analysed.A survey to obtain information about place of birth, present residence and genealogical data of the donors wasperformed. The gene frequencies were determined using a method of maximum likelihood. The genetic admixturewas calculated through the ADMIX program (trihibride). The Amerindian and African contributions were 15.8%and 4.3% respectively. These data were compared with those obtained in a previous study performed in a privatecentre (Hospital Italiano de Buenos Aires) and significant differences were observed, except in the KM system.The results obtained are in concordance with the demographic and historic information of Buenos Aires City.

African ancestry of the population of Buenos Aires.

The population of Argentina today does not have a "visible" black African component. However, censuses conducted during most of the 19th century registered up to 30% of individuals of African origin living in Buenos Aires city. What has happened to this African influence? Have all individuals of African origin died, as lay people believe? Or is it possible that admixture with the European immigrants made the African influence "invisible?" We investigated the African contribution to the genetic pool of the population of Buenos Aires, Argentina, typing 12 unlinked autosomal DNA markers in a sample of 90 individuals. The results of this analysis suggest that 2.2% (SEM=0.9%) of the genetic ancestry of the Buenos Aires population is derived from Africa. Our analysis of individual admixture shows that those alleles that have a high frequency in populations of African origin tend to concentrate among 8 individuals in our sample. Therefore, although the admixture estimate is relatively low, the actual proportion of individuals with at least some African influence is approximately 10%. The evidence we are presenting of African ancestry is consistent with the known historical events that led to the drastic reduction of the Afro-Argentine population during the second half of the 19th century. However, as our results suggest, this reduction did not mean a total disappearance of African genes from the genetic pool of the Buenos Aires population.

Genetic variability in Amerindian populations of Northern Argentina

The allelic variability of four dinucleotide microsatellites located in the HLA region (MOGc, D6S265, MIB, and TNFa) was analyzed in 67 individuals representing three Amerindian populations of the Argentine Gran Chaco: Toba, Wichi and Chorote. Genomic DNA was prepared from peripheral blood and DNA was extracted using the standard phenol-chloroform procedure. Alleles were identified by PCR, using an end-labelled reverse oligonucleotide primer (fluorescent 6 - Fam labeling). Despite the low number of samples studied, a high level of gene diversity was observed in each population and for each locus. Moreover, the mean number of alleles was 7.7, 5.3, 10.0, and 7.0 at loci MOGc, D6S265, MIB and TNFa, respectively. Differentiation tests between pairs of populations showed a clear differentiation between the Wichi and the other two groups. However, the proportion of the total genetic variability that is due to differences among populations, estimated by the Gst' index, was relatively low (6 percent). Almost all the genetic variation occurred at the intra-population level (96 percent). The high intra-populational genetic variation suggests the existence of an intensive gene flow among the Gran Chaco tribes. Historical information seems to confirm this result.