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As in other Latin American populations, Argentinians are the result of the admixture amongst different continental groups, mainly from America and Europe, and to a lesser extent from Sub-Saharan Africa. However, it is known that the admixture processes did not occur homogeneously throughout the country. Therefore, considering the importance for anthropological, medical and forensic researches, this study aimed to investigate the population genetic structure of the Argentinian Patagonia, through the analysis of 46 ancestry informative markers, in 433 individuals from five different localities. Overall, in the Patagonian sample, the average individual ancestry was estimated as 35.8% Native American (95% CI: 32.2-39.4%), 62.1% European (58.5-65.7%) and 2.1% African (1.7-2.4%). Comparing the five localities studied, statistically significant differences were observed for the Native American and European contributions, but not for the African ancestry. The admixture results combined with the genealogical information revealed intra-regional variations that are consistent with the different geographic origin of the participants and their ancestors. As expected, a high European ancestry was observed for donors with four grandparents born in Europe (96.8%) or in the Central region of Argentina (85%). In contrast, the Native American ancestry increased when the four grandparents were born in the North (71%) or in the South (61.9%) regions of the country, or even in Chile (60.5%). In summary, our results showed that differences on continental ancestry contribution have different origins in each region in Patagonia, and even in each locality, highlighting the importance of knowing the origin of the participants and their ancestors for the correct interpretation and contextualization of the genetic information.

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.

Y‐chromosomal haplogroups and the Y‐SNPs defining them are relevant for the exploration of male lineages, inference of paternal ancestry, and reconstruction of migration pathways, to name a few. Currently, over 300,000 Y‐SNPs have been reported, defining 20 main haplogroups. However, ascertainment bias in the investigations has led to some haplogroups being overlooked, which hinders a representative depiction of certain populations and their migration events. For migration pattern analyses of the first settlers of the Americas, the Native American main founding lineage Q‐M3 needs to be further investigated to allow clear genetic differentiation of individuals of different ethnogeographic origins. To increase the resolution within this haplogroup, a total of 7.45 Mb of the Y chromosome of 59 admixed South Americans of haplogroup Q was targeted for sequencing using hybridization capture enrichment. Data were combined with 218 publicly available sequences of Central and South Americans of haplogroup Q. After rigorous data processing, variants not meeting the quality criteria were excluded and 4128 reliable Y‐SNPs were reported. A total of 2224 Y‐SNPs had previously unknown positions in the phylogenetic tree, and 1291 of these are novel. The phylogenetic relationships between the Y‐SNPs were established using the software SNPtotree in order to report a redesigned phylogenetic tree containing 300 branches, defined by 3400 Y‐SNPs. The new tree introduces 117 previously undescribed branches and is the most comprehensive phylogenetic tree of the Native American haplogroup Q lineages to date. The 214 sequences were assigned to 135 different low‐ to high‐resolution branches, while in the previous phylogenetic tree, only 195 sequences could be sorted into 14 low‐resolution branches with the same quality criteria. The improved genetic differentiation of subhaplogroup Q‐M3 has a great potential to resolve migration patterns of Native Americans.

The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63-68%), 31% Indigenous American (28-33%) and 4% African (3-4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73-79%; Northeast (NEA) 54%, 95%CI: 49-58%; Northwest (NWA) 33%, 95%CI: 21-41%; South 54%, 95%CI: 49-59%; p<0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75-86%) versus 68% (95%CI: 58-77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88-94%) compared to 54% (95%CI: 51-57%) among those with no European grandparents (p<0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.

Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. To expand current information on genetic characterization of the first agricultural communities of the southern Calchaquí Valleys, we present and discuss the first mitochondrial ancient DNA information obtained on samples dated to ca. 3,600–1,900 years before present from the Cajón Valley, Catamarca Province. Reproducible mtDNA hypervariable region 1 (HVR-1) sequences were obtained in seven individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups, D1 (57.1%), C1 (28.5%), and B2 (14.2%), with absence of A2. Our results show that the Cajón Valley sample, with predominance of D1 and C1, differs from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup B2. The fact that the Cajón Valley and Pampa Grande (Salta Province, Argentina) share a prevalence of haplogroup D1 could provide additional evidence to support possible genetic affinities between the valleys and the eastern sub-Andean region during the Formative Period in Northwest Argentina, expanding the archaeological evidence of contact between both populations. Future complete mitogenomic analysis will provide substantial information to formulate new hypotheses about the origins and phylogenetic relationships between the individuals of the Cajón Valley and other groups from the Andes, Gran Chaco, and the Amazon.

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.

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample. Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

Allele frequencies for the 15 short tandem repeats (STRs) loci included in the AmpFlSTR® Identifiler kit were estimated in a sample of unrelated individuals from Mar del Plata (MDQ; N  = 180) and Bahia Blanca (BB; N  = 85) (Buenos Aires, Argentina). Biological samples were obtained from voluntary donors and forensic cases. Both populations were in Hardy–Weinberg equilibrium after Bonferroni correction, except for locus vWA in MDQ and D2S1338 in BB. FGA was the most informative locus, and the least discriminating locus was TPOX in both samples. The combined power of discrimination (PDc) and the combined probability of exclusion (PEc) were similar in MDQ and BB samples (0.999999998 < PDc < 0.999999999 and 0.999999979 < PEc < 0.999999989). The multidimentional scaling plot from Rst genetic distance matrix and the interethnic admixture estimation supported a higher European contribution in populations of the central region compared with populations from other regions of Argentina with higher Amerindian composition. These results enlarge the Argentine databases of autosomal STR loci, revealed as an excellent tool for human identification tests and population genetic analysis.

Similar to other South American regions, Tierra del Fuego has an admixed population characterized by distinct ancestors: Native Americans who first occupied the continent, European settlers who arrived from the late 15th century onwards, and Sub-Saharan Africans who were brought to the Americas for slave labor. To disclose the paternal lineages in the current population from Tierra del Fuego, 196 unrelated males were genotyped for 23 Y-STRs and 52 Y-SNPs. Haplotype and haplogroup diversities were high, indicating the absence of strong founder or drift events. A high frequency of Eurasian haplogroups was detected (94.4%), followed by Native American (5.1%) and African (0.5%) ones. The haplogroup R was the most abundant (48.5%), with the sub-haplogroup R-S116* taking up a quarter of the total dataset. Comparative analyses with other Latin American populations showed similarities with other admixed populations from Argentina. Regarding Eurasian populations, Tierra del Fuego presented similarities with Italian and Iberian populations. In an in-depth analysis of the haplogroup R-M269 and its subtypes, Tierra del Fuego displayed a close proximity to the Iberian Peninsula. The results from this study are in line with the historical records and reflect the severe demographic change led mainly by male newcomers with paternal European origin.