Population structure in Argentina shows most European sources of South European origin

argentina-population

Open access Population structure in Argentina, by Muzzio et al., PLOS One (2018).

Abstract (emphasis mine):

We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A). We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola.

argentina-pca
Principal component analysis.
On the x axis is PC 1 while PC2 is the y axis. Plus symbols represent Argentinian samples and circles are for reference panels. Fig 2a (left) Argentinians with YRI and LWK for African references (“African”), IBS and TSI for European references (“European”) and the PEL, MXL, PUR and CLM as a Latin American references. Fig 2b (right) samples from Argentina with IBS, MXL, CLM and PEL.

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Ancient Patagonian genomes suggest origin and diversification of late maritime hunter-gatherers

ancient-patagonia-admixture

Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia, by de la Fuente et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine):

Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

pca-ancient-south-american
PCA of ancient and present-day South American populations. All of the ancient individuals were projected onto the first two PCs by using the lsq option from smartpca.

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Ancient DNA reveals temporal population structure of pre-Incan and Incan periods in South‐Central Andes area

Ancient DNA reveals temporal population structure within the South‐Central Andes area, by Russo et al. Am. J. Phys. Anthropol. (2018).

Abstract (emphasis mine):

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.

andes-populations
Location of the archaeological sites analyzed in this study (stars) and the South-central Andean populations used for comparisons (triangles). The punctuated line indicates the north-south subdivision of Quebrada de Humahuaca.1: Pe~nas Blancas, 2: San José, 3: Huacalera, 4: Banda de Perchel, 5: Juella, 6: Sarahuaico, 7: Tilcara, 8: Muyuna, 9: Los Amarillos, 10: Las Pirguas, 11: Tompullo 2, 12: Puca, 13: Acchaymarca, 14: Lauricocha. Map constructed from the obtained with the R package ggmap (Kahle & Wickham, 2013)

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.

pcoa-andes
Principal coordinates analysis (PCoA) based on individual genetic distances obtained with autosomal STRs data. Percentage of variance explained by each coordinate is shown in parenthesis. Colors were assigned according to the two clusters discovered with structure

See also:

Paternal lineages mainly from migrants, maternal lineages mainly from local populations in Argentina

New paper (behind paywall) Genetic variation in populations from central Argentina based on mitochondrial and Y chromosome DNA evidence, by García, Pauro, Bailliet, Bravi & Demarchi, J. Hum. Genet (2018) 63: 493–507.

Abstract (emphasis mine):

We present new data and analysis on the genetic variation of contemporary inhabitants of central Argentina, including a total of 812 unrelated individuals from 20 populations. Our goal was to bring new elements for understanding micro-evolutionary and historical processes that generated the genetic diversity of the region, using molecular markers of uniparental inheritance (mitochondrial DNA and Y chromosome). Almost 76% of the individuals show mitochondrial lineages of American origin. The Native American haplogroups predominate in all surveyed localities, except in one. The larger presence of Eurasian maternal lineages were observed in the plains (Pampas) of the southeast, whereas the African lineages are more frequent in northern Córdoba. On the other hand, the analysis of 258 male samples reveals that 92% of them present Eurasian paternal lineages, 7% carry Native American haplogroups, and only 1% of the males show African lineages. The maternal lineages have high genetic diversity homogeneously distributed throughout central Argentina, probably as result of a recent common origin and sustained gene flow. Migratory events that occurred in colonial and recent times should have contributed to hiding any traces of differentiation that might have existed in the past. The analysis of paternal lineages showed also homogeneous distribution of the variation together with a drastic reduction of the native male population.

argentina-mtdna-haplogroups
Maps showing continental mtDNA haplogroups frequencies in 20 population samples from central Argentina. References for populations abbreviated names are from the tables.

Interesting excerpts:

The immigration waves had less impact in the north–central and northwestern regions, the most populated areas of the country in pre-Hispanic times. The spatial structure of genetic diversity has its origins in historical factors. It is possible to distinguish different stages in migratory processes from abroad, with a heterogeneous regional impact. The genetic composition of central Argentina gives account of these processes. On one hand, the political boundaries between provinces influenced the configuration of the genetic structure of the populations that were formed. In this sense, Córdoba—an important economic and commercial center since colonial times—has a greater component of foreign lineages than the populations of San Luis and Santiago del Estero. On the other hand, the genetic structure of central Argentina also accounts for other processes related to different migration phases and occupations of space over the last 500 years.

argentina-maternal-native-american
Maternal continental contribution (in percentages), and Native American haplogroup frequencies, by population

Similarly, negative values observed in the neutrality tests (Tajima’s D and Fu’s FS), indicate relatively recent population growth, probably associated with technological and organizational changes leading to new lifestyles and important demographic and territorial expansion [75]. In conclusion, the molecular markers of maternal inheritance shows large genetic diversity homogeneously distributed throughout central Argentina, probably as result of a recent common origin and sustained gene flow between sub-populations. In addition, migratory events that occurred in colonial and recent times should have contributed to hiding any traces of differentiation that might have existed in the past. The analysis of paternal lineages showed also homogeneous distribution of the variation across the region but also a drastic reduction of the native male population, with a large prevalence of haplogroups of European origin.

argentina-y-dna
Y chromosome haplogroups frequencies in three provinces from central Argentina and other 19 samples from Argentina, Chile, and Paraguay

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