Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database

An overview of the mtDNA diversity across the Colombian Andean region

In Colombia, a country in the northwest corner of South America, populations are highly diverse due to the intercontinental admixture of Native Americans, European settlers, and enslaved Africans. While genetic diversity has been largely assessed based on autosomal markers, studies on mtDNA are much scarcer, allowing only a fragmentary view of the distribution of maternal lineages in the country. In this study the genetic diversity of maternal lineages in Colombian Andean populations was interrogated to infer whether the pattern of structuring was in line with the different colonization histories of the departments within the region. The ultimate goal was to establish a haplotype database for forensic purposes. In a total of 458 individuals born and residing in the departments of the Andean region, haplotypes of the total mtDNA control region were determined and assigned to the corresponding haplogroups. Across the 10 departments, haplotype diversities ranged between 0.9665 and 0.9967, and power of exclusion between 0.9208 and 0.9845. A component ascribed to be of Native American ancestry prevailed in all departments, where 89.27 % of haplotypes in the total sample belonged to mtDNA macro-haplogroups A2, B4, C1, and D. The remaining lineages were of Eurasian (6.65 %) or African (4.08 %) origin. Pairwise FST values showed signs of genetic differentiation, but still only reached statistical significance when Risaralda or Cundinamarca were compared with other populations. Principal component analysis showed that the population structure was mainly due to some differences in Native American substrates. The results obtained highlighted a heterogeneity within Andean populations that must be considered when developing mtDNA haplotype databases for forensic purposes. In this context, the use of specific databases is recommended for the departments of Risaralda and Cundinamarca, while the other departments can rely on a single haplotype frequency database.

Using uniparental genetic profiles to unravel the complexity of Argentine admixed populations

Latin American countries are distinguished by their highly admixed populations, characterized by a significant preservation of Native American matrilineal ancestry. This contrasts with the paternal lineages, which exhibit different patterns due to pronounced sex-biased mating practices during the colonial period. Uniparental genetic markers have been instrumental in population genetics, facilitating the reconstruction of human settlement histories and serving forensic identification purposes. The primary objective of this study was to investigate the diversity and structure of lineage markers in Argentina and compare them with other admixed populations in South America. For this study, we analyzed Y-STR and mtDNA haplotypes from 5202 unrelated individuals, providing a detailed description of the observed variability in both markers. Additionally, we conducted a genetic distance analysis, incorporating data from bibliographic sources across Argentina and South America. In pairwise comparisons among provinces, higher FST values were found in mtDNA haplotypes than in Y-STR haplotypes. This allows for more provinces to be grouped by similarity when using Y-STR data. These differences were also evident in the multidimensional scaling (MDS) analysis between South American countries. Y-STR haplotypes showed greater similarity to European haplotypes, whereas mtDNA haplotypes exhibited greater dispersion. Thus, the comprehensive compilation of haplotypes in this study, including those integrated from our research and those cited in existing literature, provides an in-depth understanding of the inherent genetic complexities within Argentina.

Population analysis of complete mitogenomes for 334 samples from El Salvador

The use of mitochondrial DNA (mtDNA) in the field of forensic genetics is widely spread mainly due to its advantages when identifying highly degraded samples. In this sense, massive parallel sequencing has made the analysis of the whole mitogenome more accessible, noticeably increasing the informativeness of mtDNA haplotypes. The civil war (1980-1992) in El Salvador caused many deaths and disappearances (including children) all across the country and the economic and social instability after the war forced many people to emigration. For this reason, different organizations have collected DNA samples from relatives with the aim of identifying missing people. Thus, we present a dataset containing 334 complete mitogenomes from the Salvadoran general population. To the best of our knowledge, this is the first publication of a nationwide forensic-quality complete mitogenome database of any Latin American country. We found 293 different haplotypes, with a random match probability of 0.0041 and 26.6 mean pairwise differences, which is similar to other Latin American populations, and which represent a marked improvement from the values obtained with just control region sequences. These haplotypes belong to 54 different haplogroups, being 91% of them of Native American origin. Over a third (35.9%) of the individuals carried at least a heteroplasmic site (excluding length heteroplasmies). Ultimately, the present database aims to represent mtDNA haplotype diversity in the general Salvadoran populations as a basis for the identification of people that disappeared during or after the civil war.

Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization

OBJECTIVE

This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.

MATERIALS AND METHODS

We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.

RESULTS

We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP.

DISCUSSION

The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.

Social injustice unveiled by genetic analysis: Argentina as a case study

BACKGROUND

The population of the American countries is genetically heterogeneous, whose genesis result from of recent admixture events. In this process, the transoceanic European component displaced the original inhabitants of the continent.

AIM

To investigate whether socially differentiated cohorts exhibit underlying ancestry components within an urban admixed population, two cohorts of individuals inhabiting Argentina were studied. One cohort included genetically unrelated individuals involved in voluntary paternity testing while the other included sexual or blood-crime suspects.

MATERIALS & METHODS

We analyzed over 2500 unrelated individuals: four Native American maternal lineage mtDNA markers in 1024 samples, five Y chromosome haplogroups in 658 male samples, 24 autosomal ancestry informative markers (AIMs) in 205 samples, and 15 autosomal short tandem repeats (STRs) in 1557 samples; countrywide and divided by regions.

RESULTS

While our results confirm a tricontinental ethnic contribution to both cohorts, their proportions showed statistically significant differences, with a higher proportion of Native American ancestry in the cohort linked to violent crimes compared to those in paternity testing. This hallmark was observed with all the marker sets used and at various levels of analysis.

DISCUSSION

Since paternity tests are costly, socio-economic differences might help to interpret our observations. The effect of discrimination against descendants of Native American minorities, and exposure to violent social environments, might link marginal groups to criminality.

CONCLUSION

Our findings underscore the relevance of proper social management since only by improving living conditions, reducing discrimination, promoting education, and providing job opportunities will it be possible to attain equality in a heterogeneous society. Genetic markers proved to be highly informative in unveiling unexpected social differences.

The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

The Mitochondrial DNA Landscape of Modern Mexico

Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated.

Uniparental origins of the admixed Argentine Patagonia

OBJECTIVES

We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history.

METHODS

The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information. Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers.

RESULTS

Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762-2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region.

CONCLUSIONS

The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed.

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

Maternal ancestry and hematological cancer risk: case-control study in an Argentinean population

Aim: We investigated the role of maternal ancestry in neoplastic hematological malignancies (HMs) risk in a population from Central Argentina. Materials & methods: We analyzed 125 cases with HMs and 310 controls from a public hospital, and a set of 202 colorectal, breast, lung, and hematologic cancer patients from a private hospital. Results: A decreased risk for HMs was associated with the Native American haplogroup B2 (odds ratio = 0.49; 95% CI: 0.25-0.92; p = 0.02). The sub-Saharan African parahaplogroup L was associated with higher susceptibility for disease (odds ratio = 3.10; 95% CI: 1.04-9.31; p = 0.043). Although the mean ancestral proportions in the total studied population was as published (61.7% Native American, 34.6% European and 3.7% African), an unequal distribution was observed between hospitals. Conclusion: We confirmed the tri-hybrid nature of the Argentinean population, with proportions varying within the country. Our finding supports the notion that associated haplogroup is population and cancer specific.

Ancestral genetic legacy of the extant population of Argentina as predicted by autosomal and X-chromosomal DIPs

Aiming to determine their ancestry diagnostic potential, we selected two sets of nuclear deletion/insertion polymorphisms (DIPs), including 30 located on autosomal chromosomes and 33 on the X chromosome. We analysed over 200 unrelated Argentinean individuals living in urban areas of Argentina. As in most American countries, the extant Argentinean population is the result of tricontinental genetic admixture. The peopling process within the continent was characterised by mating bias involving Native American and enslaved African females and European males. Differential results were detected between autosomal DIPs and X-DIPs. The former showed that the European component was the largest (77.8%), followed by the Native American (17.9%) and African (4.2%) components, in good agreement with the previously published results. In contrast, X-DIPs showed that the European genetic contribution was also predominant but much smaller (52.9%) and considerably larger Native American and African contributions (39.6% and 7.5%, respectively). Genetic analysis revealed continental genetic contributions whose associated phenotypic traits have been mostly lost. The observed differences between the estimated continental genetic contribution proportions based on autosomal DIPs and X-DIPs reflect the effects of autosome and X-chromosome transmission behaviour and their different recombination patterns. This work shows the ability of the tested DIP panels to infer ancestry and confirm mating bias. To the best of our knowledge, this is the first study focusing on ancestry-informative autosomal DIP and X-DIP comparisons performed in a sample representing the entire Argentinean population.

A Mitochondrial DNA Variant Elevates the Risk of Gallstone Disease by Altering Mitochondrial Function

BACKGROUND AND AIMS

Gallstone disease (cholelithiasis) is a cholesterol-related metabolic disorders with strong familial predisposition. Mitochondrial DNA (mtDNA) variants accumulated during human evolution are associated with some metabolic disorders related to modified mitochondrial function. The mechanistic links between mtDNA variants and gallstone formation need further exploration.

METHODS

In this study, we explored the possible associations of mtDNA variants with gallstone disease by comparing 104 probands and 300 controls in a Chinese population. We constructed corresponding cybrids using trans-mitochondrial technology to investigate the underlying mechanisms of these associations. Mitochondrial respiratory chain complex activity and function and cholesterol metabolism were assessed in the trans-mitochondrial cell models.

RESULTS

Here, we found a significant association of mtDNA 827A>G with an increased risk of familial gallstone disease in a Chinese population (odds ratio [OR]: 4.5, 95% confidence interval [CI]: 2.1-9.4, P=1.2×10-4). Compared with 827A cybrids (haplogroups B4a and B4c), 827G cybrids (haplogroups B4b and B4d) had impaired mitochondrial respiratory chain complex activity and function and activated JNK and AMPK signaling pathways. Additionally, the 827G cybrids showed disturbances in cholesterol transport and accelerated development of gallstones. Specifically, cholesterol transport through the transporter ABCG5/8 was increased via activation of the AMPK signaling pathway in 827G cybrids.

CONCLUSIONS

Our findings reveal that mtDNA 827A>G induces aberrant mitochondrial function and abnormal cholesterol transport, resulting in increased occurrence of gallstones. The results provide an important biological basis for the clinical diagnosis and prevention of gallstone disease in the future.

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.

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.

Genetic structure of Mataco-Guaycurú speakers from Argentina and the extent of their genetic admixture with neighbouring urban populations

Argentina hosts more than 30 Native American groups, who are widely distributed throughout the country. Mataco-Guaycurú speakers settled in the ecoregion of Gran Chaco and represent 26.7% of the extant aboriginal population of the country. To further investigate the genetic attributes of these speakers, we focused our attention on four aboriginal groups, namely, Wichí, Toba, Pilagá and Mocoví, belonging to the Mataco-Guaycurú linguistic group. Our main goal was to evaluate the interrelationships among the groups and the relationships of these groups with admixed urban populations and to assess correspondences between molecular analysis and historical information. A total of 890 samples (282 Native Americans and 608 inhabitants of admixed urban areas) were analysed. Genetic information was gathered from 15 autosomal STRs, 17 Y-STRs, entire mtDNA control region sequences, 24 AIM-SNPs and 46 AIM-DIPs. Native American signatures were detected in 97.9% of mtDNA lineages, 89.1% of Y-haplotypes and 90.3% to 96.9% of autosomal markers. Wichí exhibited the genetic composition with the largest Native American contribution among the groups and a weak signal of gene flow. This work provides extended genetic information of potential interest in the fields of molecular anthropology and forensic genetics.

Historical records under the genetic evidence: "Chiriguano" tribe genesis as a test case

Historical records suggest that Chiriguano tribe is the result of a genetic admixture event. The process involved the arrival of Guaraní tribesmen descending from Amazonian region of Brazil along with groups of Arawak origin that inhabited the foothill plains of Bolivia. Later they arrived in Argentina at the beginning of the twentieth century. Aiming to test the historical records, we analysed a set of 46 samples collected at San Ramon de la Nueva Orán, Province of Salta, Argentina. A wide set of uni- and biparentally transmitted genetic markers were analysed, including 23 autosomal STRs; 46 AIM-DIPs and 24 AIM-SNPs all located at diverse autosomal chromosome locations; 23 Y-STRs and the entire mtDNA D-Loop sequence. Ancestry informative markers allowed for the detection of a strong Native American component in the genomes (> 94%), while all mtDNA haplotypes showed Native American characteristic motives, and 93% of Y-haplotypes belonged to the Q1a3a Y-haplogroup. The analysis of mitochondrial haplotypes and Y chromosome, although they did not match other populations, revealed a relationship between the Chiriguano and other groups of Guaraní and Arawak origin inhabiting Brazil and Bolivia, confirming, at least in part, the historical records describing the origins of Chiriguano tribal settlements in northwestern Argentina.

Mitochondrial DNA control region diversity in a population from Parana state-increasing the Brazilian forensic database

The entire mitochondrial DNA (mtDNA) control region (nucleotide position 16024-576) sequences were obtained through Sanger sequencing method for 122 individuals from Parana state, South of Brazil. We observed a total of 108 different haplotypes of which 97 were unique and 11 were shared by more than one individual. The haplogroups were classified according to the updated mtDNA phylogeny, by EMMA (estimating mitochondrial haplogroups using a maximum likelihood approach). Our results revealed the predominance of Amerindian haplogroups with a frequency of 49.2% of the population sample, followed by European lineages with 38.5% and 12.3% of African lineages. Parana population sample set presented a high haplotype diversity (0.9976) and the random match probability was 0.0106. The phylogenetical findings and the diversity indices confirm the high genetic heterogeneity of this population and suggest a high informativeness of mtDNA analyses in forensic cases. The population data will contribute to increase the Brazilian mtDNA database for forensic purposes and it is available through EMPOP (European DNA Profiling Group mitochondrial DNA population database) under the accession number EMP00714.

High interpopulation homogeneity in Central Argentina as assessed by Ancestry Informative Markers (AIMs)

The population of Argentina has already been studied with regard to several genetic markers, but much more data are needed for the appropriate definition of its genetic profile. This study aimed at investigating the admixture patterns and genetic structure in Central Argentina, using biparental markers and comparing the results with those previously obtained by us with mitochondrial DNA (mtDNA) in the same samples. A total of 521 healthy unrelated individuals living in 13 villages of the Córdoba and San Luis provinces were tested. The individuals were genotyped for ten autosomal ancestry informative markers (AIMs). Allele frequencies were compared with those of African, European and Native American populations, chosen to represent parental contributions. The AIM estimates indicated a greater influence of the Native American ancestry as compared to previous studies in the same or other Argentinean regions, but smaller than that observed with the mtDNA tests. These differences can be explained, respectively, by different genetic contributions between rural and urban areas, and asymmetric gene flow occurred in the past. But a most unexpected finding was the marked interpopulation genetic homogeneity found in villages located in diverse geographic environments across a wide territory, suggesting considerable gene flow.

Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA)

The assignment of haplogroups to mitochondrial DNA haplotypes contributes substantial value for quality control, not only in forensic genetics but also in population and medical genetics. The availability of Phylotree, a widely accepted phylogenetic tree of human mitochondrial DNA lineages, led to the development of several (semi-)automated software solutions for haplogrouping. However, currently existing haplogrouping tools only make use of haplogroup-defining mutations, whereas private mutations (beyond the haplogroup level) can be additionally informative allowing for enhanced haplogroup assignment. This is especially relevant in the case of (partial) control region sequences, which are mainly used in forensics. The present study makes three major contributions toward a more reliable, semi-automated estimation of mitochondrial haplogroups. First, a quality-controlled database consisting of 14,990 full mtGenomes downloaded from GenBank was compiled. Together with Phylotree, these mtGenomes serve as a reference database for haplogroup estimates. Second, the concept of fluctuation rates, i.e. a maximum likelihood estimation of the stability of mutations based on 19,171 full control region haplotypes for which raw lane data is available, is presented. Finally, an algorithm for estimating the haplogroup of an mtDNA sequence based on the combined database of full mtGenomes and Phylotree, which also incorporates the empirically determined fluctuation rates, is brought forward. On the basis of examples from the literature and EMPOP, the algorithm is not only validated, but both the strength of this approach and its utility for quality control of mitochondrial haplotypes is also demonstrated.

The genetic legacy of the pre-colonial period in contemporary Bolivians

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1-2%) of a sub-Saharan component in Bolivians.

Mitochondrial DNA control region data reveal high prevalence of Native American lineages in Jujuy province, NW Argentina

Mitochondrial control region (16024-576) sequences were generated from 180 individuals of four population nuclei from the province of Jujuy (NW Argentina), located at different altitudes above sea level. The frequency at which a randomly selected mtDNA profile would be expected to occur in the general population (random match probability) was estimated at 0.011, indicating a relatively high diversity. Analysis of the haplogroup distribution revealed that Native American lineages A2 (13.9%), B (56.7%), C1 (17.8%), D1 (8.9%) and D4h3a (1.1%) accounted for more than 98% of the total mtDNA haplogroup diversity in the sample examined. We detected a certain degree of genetic heterogeneity between two subpopulations located at different points along the altitudinal gradient (Valles and Puna), suggesting that altitude above sea level cannot be ruled out as a factor promoting divergences in mtDNA haplogroup frequencies, since altitude is closely associated with human living conditions, and consequently, with low demographic sizes and the occurrence of genetic drift processes in human communities. In all, mitochondrial DNA database obtained for Jujuy province strongly points to the need for creating local mtDNA databases, to avoid bias in forensic estimations caused by genetic substructuring of the populations.

Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes

With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (MTDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11-13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.

An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups

After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ~15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.

Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes

It is now widely agreed that the Native American founders originated from a Beringian source population ∼15–18 thousand years ago (kya) and rapidly populated all of the New World, probably mainly following the Pacific coastal route. However, details about the migration into the Americas and the routes pursued on the continent still remain unresolved, despite numerous genetic, archaeological, and linguistic investigations. To examine the pioneering peopling phase of the South American continent, we screened literature and mtDNA databases and identified two novel mitochondrial DNA (mtDNA) clades, here named D1g and D1j, within the pan-American haplogroup D1. They both show overall rare occurrences but local high frequencies, and are essentially restricted to populations from the Southern Cone of South America (Chile and Argentina). We selected and completely sequenced 43 D1g and D1j mtDNA genomes applying highest quality standards. Molecular and phylogeographic analyses revealed extensive variation within each of the two clades and possibly distinct dispersal patterns. Their age estimates agree with the dating of the earliest archaeological sites in South America and indicate that the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr. This study confirms that major sampling and sequencing efforts are mandatory for uncovering all of the most basal variation in the Native American mtDNA haplogroups and for clarification of Paleo-Indian migrations, by targeting, if possible, both the general mixed population of national states and autochthonous Native American groups, especially in South America.

Mitochondrial diversity in Amerindian Kichwa and Mestizo populations from Ecuador

This study presents mitochondrial DNA (mtDNA) data from 107 unrelated individuals from two of the major ethnic groups in Ecuador: Amerindian Kichwas (n = 65) and Mestizos (n = 42). We characterized the diversity of the matrilineal lineages of these Ecuadorian groups by analyzing the entire mtDNA control region. Different patterns of diversity were observed in the two groups as result of the unique historical and demographic events which have occurred in each population. Higher genetic diversity values were obtained for the Mestizo group than for the Amerindian group. Interestingly, only Native American lineages were detected in the two population samples, but with differences in the haplogroup distribution: Kichwa (A, 49%; B, 3%; C, 8%; and D, 40%) and Mestizo (A, 33%; B, 33%; C, 10%; and D, 24%). Analysis of the complete mtDNA control region proved to be useful to increase the discrimination power between individuals who showed common haplotypes in HVSI and HVSII segments; and added valuable information to the phylogenetic interpretation of mtDNA haplotypes.

The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial DNA genome

BACKGROUND

The genetic background of Argentineans is a mosaic of different continental ancestries. From colonial to present times, the genetic contribution of Europeans and sub-Saharan Africans has superposed to or replaced the indigenous genetic 'stratum'. A sample of 384 individuals representing different Argentinean provinces was collected and genotyped for the first and the second mitochondrial DNA (mtDNA) hypervariable regions, and selectively genotyped for mtDNA SNPs. This data was analyzed together with additional 440 profiles from rural and urban populations plus 304 from Native American Argentineans, all available from the literature. A worldwide database was used for phylogeographic inferences, inter-population comparisons, and admixture analysis. Samples identified as belonging to hg (hg) H2a5 were sequenced for the entire mtDNA genome.

RESULTS

Phylogenetic and admixture analyses indicate that only half of the Native American component in urban Argentineans might be attributed to the legacy of extinct ancestral Argentineans and that the Spanish genetic contribution is slightly higher than the Italian one. Entire H2a5 genomes linked these Argentinean mtDNAs to the Basque Country and improved the phylogeny of this Basque autochthonous clade. The fingerprint of African slaves in urban Argentinean mtDNAs was low and it can be phylogeographically attributed predominantly to western African. The European component is significantly more prevalent in the Buenos Aires province, the main gate of entrance for Atlantic immigration to Argentina, while the Native American component is larger in North and South Argentina. AMOVA, Principal Component Analysis and hgs/haplotype patterns in Argentina revealed an important level of genetic sub-structure in the country.

CONCLUSIONS

Studies aimed to compare mtDNA frequency profiles from different Argentinean geographical regions (e.g., forensic and case-control studies) should take into account the important genetic heterogeneity of the country in order to prevent false positive claims of association in disease studies or inadequate evaluation of forensic evidence.

Mitochondrial DNA diversity in a population from Santa Catarina (Brazil): predominance of the European input

The state of Santa Catarina (Brazil) is known to have represented a cultural crossroads in South America due to several historic migrations mainly from Europe and Africa. We set out to scrutinize whether the genetic imprint of these migrations could be traced through analysis of the matrilineal gene pool of the Catarinenses. The entire control region of the mitochondrial DNA was studied in 80 healthy and maternally unrelated individuals. The analysis of haplogroup distribution revealed that this population is extremely heterogeneous, showing the coexistence of matrilineal lineages with three different phylogeographic origins. European lineages are the most frequent due mainly to the impact of relatively recent migratory waves from Europe. In spite of this, Native American lineages and African lineages incorporated with the slave trade are also present in noticeable proportions. The strikingly high variability generated by intense gene flow is mirrored in a high sequence diversity (0.9930) and power of discrimination (0.9806). Thus, analysis of the entire mitochondrial DNA control region emerges as a valuable tool for forensic genetic purposes in this highly admixed population, an attribute common to several present-day Latin American populations.