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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Iberian prehistoric migrations in Genomics from Neolithic, Chalcolithic, and Bronze Age

iberia-neolithic-bronze-age

New open access paper Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia, by Valdiosera, Günther, Vera-Rodríguez, et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine)

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

iberia-admixture
(A) f4 statistics testing affinities of prehistoric European farmers to either early Neolithic Iberians or central Europeans, restricting these reference populations to SNP-captured individuals to avoid technical artifacts driving the affinities. The boxplots in A show the distributions of all individual f4 statistics belonging to the respective groups. The signal is not sensitive to the choice of reference populations and is not driven by hunter-gatherer–related admixture (Datasets S4 and S5). (B) Estimates of ancestry proportions in different prehistoric Europeans as well as modern southwestern Europeans. Individuals from regions of Iberia were grouped together for the analysis in A and B to increase sample sizes per group and reduce noise

Conclusion:

We present a comprehensive biomolecular dataset spanning four millennia of prehistory across the whole Iberian Peninsula. Our results highlight the power of archaeogenomic studies focusing on specific regions and covering a temporal transect. The 4,000 y of prehistory in Iberia were shaped by major chronological changes but with little geographic substructure within the Peninsula. The subtle but clear genetic differences between early Neolithic Iberian farmers and early Neolithic central European farmers point toward two independent migrations, potentially originating from two slightly different source populations. These populations followed different routes, one along the Mediterranean coast, giving rise to early Neolithic Iberian farmers, and one via mainland Europe forming early Neolithic central European farmers. This directly links all Neolithic Iberians with the first migrants that arrived with the initial Mediterranean Neolithic wave of expansion. These Iberians mixed with local hunter-gatherers (but maintained farming/pastoral subsistence strategies, i.e., diet), leading to a recovery from the loss of genetic diversity emerging from the initial migration founder bottleneck. Only after the spread of Bell Beaker pottery did steppe-related ancestry arrive in Iberia, where it had smaller contributions to the population compared with the impact that it had in central Europe. This implies that the two prehistoric migrations causing major population turnovers in central Europe had differential effects at the southwestern edge of their distribution: The Neolithic migrations caused substantial changes in the Iberian gene pool (the introduction of agriculture by farmers) (6, 9, 11, 13, 24), whereas the impact of Bronze Age migrations (Yamnaya) was significantly smaller in Iberia than in north-central Europe (24). The post-Neolithic prehistory of Iberia is generally characterized by interactions between residents rather than by migrations from other parts of Europe, resulting in relative genetic continuity, while most other regions were subject to major genetic turnovers after the Neolithic (4, 6, 7, 9, 25, 48). Although Iberian populations represent the furthest wave of Neolithic expansion in the westernmost Mediterranean, the subsequent populations maintain a surprisingly high genetic legacy of the original pioneer farming migrants from the east compared with their central European counterparts. This counterintuitive result emphasizes the importance of in-depth diachronic studies in all parts of the continent.

Related:

Population substructure in Iberia, highest in the north-west territory (to appear in Nature)

A manuscript co-authored by Angel Carracedo, from the University of Santiago de Compostela, and (always according to him) pre-accepted in Nature, will offer more insight into the population substructure of Spain, based on autosomal DNA.

Carracedo’s lecture about DNA (in Galician), including his summary of the paper (from december 2017):

Some of the points made in the video:

  • The study shows a situation parallelling – as expected – the expansion of Spanish Medieval kingdoms during the Reconquista (and subsequent repopulation).
  • In it, the biggest surprise seems to be the greater substructure found in Galicia, the north-western Spanish territory – greater even than expected by the authors.
  • As a side note, Galicia shows a great influence from Moorish” ancestral components, due mainly to the influx from Portugal, which shows more.

It is difficult to judge only from the image and his words, but one could say that there are:

  • Certain quite old ancestral Galician groups;
    • then two – also quite old – ancestral Basque groups;
      • then more recent Galician groups;
        • and then a common, central Spanish group – including
          • a wider Asturian-Catalan group, with a western Asturian-Leonese, and an eastern Catalan subgroup;
          • and a central Castillian-Aragonese group, also with a western Castillian, and an eastern Aragonese subgroup.
spain-autosomal
Spain’s population substructure, from the video.

We thought that certain parts of the British Isles could show ancestral components related to the old population, although this has not proven exactly right, due to more recent population expansions.

However, this paper might shed light to the controversy surrounding Lusitanian (possibly Gallaico-Lusitanian) as a Pre-Celtic Indo-European group of Iberia, either slightly older as an Italo-Celtic dialect, or potentially from the Bell Beaker expansion, whose genetic imprint might have survived the Roman conquest, which apparently didn’t replace its ancestral population.

Given the presence of a central Spanish group opposed to the other minor groups – and knowing that (at least part of) the Medieval kingdoms should be related to the Occitan region – due to the Celtic expansion, and also potentially later during the Visigothic Kingdom, and the Carolingian Empire – , we can only guess that the other (north-western and Basque) groups are potentially quite old, and reflect prehistoric population structures.

Just speculating here, of course. Another interesting genetic paper to await…

Seen first in the Facebook group Iberia ADN.

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Iberian Peninsula: Discontinuity in mtDNA between hunter-gatherers and farmers, not so much during the Chalcolithic and EBA

iberia-mtdna

A new preprint paper at BioRxiv, The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age, by Szécsényi-Nagy et al. (2017).

Abstract:

Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic makeup of the Neolithic (~ 5500-3000 BCE), Chalcolithic (~ 3000-2200 BCE) and Early Bronze Age (~ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.

iberian-mtdna-samples
Iberian mtDNA samples

Detailed conclusions of their work,

The present study, based on 213 new and 125 published mtDNA data of prehistoric Iberian individuals suggests a more complex mode of interaction between local hunter-gatherers and incoming early farmers during the Early and Middle Neolithic of the Iberian Peninsula, as compared to Central Europe. A characteristic of Iberian population dynamics is the proportion of autochthonous hunter-gatherer haplogroups, which increased in relation to the distance to the Mediterranean coast. In contrast, the early farmers in Central Europe showed comparatively little admixture of contemporaneous hunter-gatherer groups. Already during the first centuries of Neolithic transition in Iberia, we observe a mix of female DNA lineages of different origins. Earlier hunter-gatherer haplogroups were found together with a variety of new lineages, which ultimately derive from Near Eastern farming groups. On the other hand, some early Neolithic sites in northeast Iberia, especially the early group from the cave site of Els Trocs in the central Pyrenees, seem to exhibit affinities to Central European LBK communities. The diversity of female lineages in the Iberian communities continued even during the Chalcolithic, when populations became more homogeneous, indicating higher mobility and admixture across different geographic regions. Even though the sample size available for Early Bronze Age populations is still limited, especially with regards to El Argar groups, we observe no significant changes to the mitochondrial DNA pool until the end of our time transect (1500 BCE). The expansion of groups from the eastern steppe, which profoundly impacted Late Neolithic and EBA groups of Central and North Europe, cannot (yet) be seen in the contemporaneous population substrate of the Iberian Peninsula at the present level of genetic resolution. This highlights the distinct character of the Neolithic transition both in the Iberian Peninsula and elsewhere and emphasizes the need for further in depth archaeogenetic studies for reconstructing the close reciprocal relationship of genetic and cultural processes on the population level.

So it seems more and more likely that the North-West Indo-European invasion during the Copper Age (signaled by changes in Y-DNA lineages) was not, as in central Europe, accompanied by much mtDNA turnover. What that means – either a male-dominated invasion, or a longer internal evolution of invasive Y-DNA subclades – remains to bee seen, but I am still more inclined to see the former as the most likely interpretation, in spite of admixture results.

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Featured images: from the article, licensed BY-NC-ND.

Analysis of R1b-DF27 haplogroups in modern populations adds new information that contrasts with ‘steppe admixture’ results

R1b-DF27-iberia

New open access article published in Scientific Reports, Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ, by Solé-Morata et al. (2017).

Abstract

Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.

Some people like to say that Y-DNA haplogroup analysis, or phylogeography in general, is of no use anymore (especially modern phylogeography), and they are content to see how ‘steppe admixture’ was (or even is) distributed in Europe to draw conclusions about ancient languages and their expansion. With each new paper, we are seeing the advantages of analysing ancient and modern haplogroups in ascertaining population movements.

Quite recently there was a suggestion based on steppe admixture that Basque-speaking Iberians resisted the invasion from the steppe. Observing the results of this article (dates of expansion and demographic data) we see a clear expansion of Y-DNA haplogroups precisely by the time of Bell Beaker expansion from the east. Y-DNA haplogroups of ancient samples from Portugal point exactly to the same conclusion.

The situation of R1b-DF27 in Basques, as I have pointed out elsewhere, is probably then similar to the genetic drift of Finns, mainly of N1c lineages, speaking today a Uralic language that expaned with Corded Ware and R1a subclades.

The recent article on Mycenaean and Minoan genetics also showed that, when it comes to Europe, most of the demographic patterns we see in admixture are reminiscent of the previous situation, only rarely can we see a clear change in admixture (which would mean an important, sudden replacement of the previous population).

Equating the so-called steppe admixture with Indo-European languages is wrong. Period.

The following are excerpts from the article (emphasis is mine):

Dates and expansions

The average STR variance of DF27 and each subhaplogroup is presented in Suppl. Table 2. As expected, internal diversity was higher in the deeper, older branches of the phylogeny. If the same diversity was divided by population, the most salient finding is that native Basques (Table 2) have a lower diversity than other populations, which contrasts with the fact that DF27 is notably more frequent in Basques than elsewhere in Iberia (Suppl. Table 1). Diversity can also be measured as pairwise differences distributions (Fig. 5). The distribution of mean pairwise differences within Z195 sits practically on top of that of DF27; L176.2 and Z220 have similar distributions, as M167 and Z278 have as well; finally, M153 shows the lowest pairwise distribution values. This pattern is likely to reflect the respective ages of the haplogroups, which we have estimated by a modified, weighted version of the ρ statistic (see Methods).

Z195 seems to have appeared almost simultaneously within DF27, since its estimated age is actually older (4570 ± 140 ya). Of the two branches stemming from Z195, L176.2 seems to be slightly younger than Z220 (2960 ± 230 ya vs. 3320 ± 200 ya), although the confidence intervals slightly overlap. M167 is clearly younger, at 2600 ± 250 ya, a similar age to that of Z278 (2740 ± 270 ya). Finally, M153 is estimated to have appeared just 1930 ± 470 ya.

Haplogroup ages can also be estimated within each population, although they should be interpreted with caution (see Discussion). For the whole of DF27, (Table 3), the highest estimate was in Aragon (4530 ± 700 ya), and the lowest in France (3430 ± 520 ya); it was 3930 ± 310 ya in Basques. Z195 was apparently oldest in Catalonia (4580 ± 240 ya), and with France (3450 ± 269 ya) and the Basques (3260 ± 198 ya) having lower estimates. On the contrary, in the Z220 branch, the oldest estimates appear in North-Central Spain (3720 ± 313 ya for Z220, 3420 ± 349 ya for Z278). The Basques always produce lower estimates, even for M153, which is almost absent elsewhere.

R1b-DF27-tree
Simplified phylogenetic tree of the R1b-M269 haplogroup. SNPs in italics were not analyzed in this manuscript.

Demography

The median value for Tstart has been estimated at 103 generations (Table 4), with a 95% highest probability density (HPD) range of 50–287 generations; effective population size increased from 131 (95% HPD: 100–370) to 72,811 (95% HPD: 52,522–95,334). Considering patrilineal generation times of 30–35 years, our results indicate that R1b-DF27 started its expansion ~3,000–3,500 ya, shortly after its TMRCA.

As a reference, we applied the same analysis to the whole of R1b-S116, as well as to other common haplogroups such as G2a, I2, and J2a. Interestingly, all four haplogroups showed clear evidence of an expansion (p > 0.99 in all cases), all of them starting at the same time, ~50 generations ago (Table 4), and with similar estimated initial and final populations. Thus, these four haplogroups point to a common population expansion, even though I2 (TMRCA, weighted ρ, 7,800 ya) and J2a (TMRCA, 5,500 ya) are older than R1b-DF27. It is worth noting that the expansion of these haplogroups happened after the TMRCA of R1b-DF27.

R1b-DF27-PCA
Principal component analysis of STR haplotypes. (a) Colored by subhaplogroup, (b) colored by population. Larger squares represent subhaplogroup or population centroids.

Sum up and discussion

We have characterized the geographical distribution and phylogenetic structure of haplogroup R1b-DF27 in W. Europe, particularly in Iberia, where it reaches its highest frequencies (40–70%). The age of this haplogroup appears clear: with independent samples (our samples vs. the 1000 genome project dataset) and independent methods (variation in 15 STRs vs. whole Y-chromosome sequences), the age of R1b-DF27 is firmly grounded around 4000–4500 ya, which coincides with the population upheaval in W. Europe at the transition between the Neolithic and the Bronze Age. Before this period, R1b-M269 was rare in the ancient DNA record, and during it the current frequencies were rapidly reached. It is also one of the haplogroups (along with its daughter clades, R1b-U106 and R1b-S116) with a sequence structure that shows signs of a population explosion or burst. STR diversity in our dataset is much more compatible with population growth than with stationarity, as shown by the ABC results, but, contrary to other haplogroups such as the whole of R1b-S116, G2a, I2 or J2a, the start of this growth is closer to the TMRCA of the haplogroup. Although the median time for the start of the expansion is older in R1b-DF27 than in other haplogroups, and could suggest the action of a different demographic process, all HPD intervals broadly overlap, and thus, a common demographic history may have affected the whole of the Y chromosome diversity in Iberia. The HPD intervals encompass a broad timeframe, and could reflect the post-Neolithic population expansions from the Bronze Age to the Roman Empire.

While when R1b-DF27 appeared seems clear, where it originated may be more difficult to pinpoint. If we extrapolated directly from haplogroup frequencies, then R1b-DF27 would have originated in the Basque Country; however, for R1b-DF27 and most of its subhaplogroups, internal diversity measures and age estimates are lower in Basques than in any other population. Then, the high frequencies of R1b-DF27 among Basques could be better explained by drift rather than by a local origin (except for the case of M153; see below), which could also have decreased the internal diversity of R1b-DF27 among Basques. An origin of R1b-DF27 outside the Iberian Peninsula could also be contemplated, and could mirror the external origin of R1b-M269, even if it reaches there its highest frequencies. However, the search for an external origin would be limited to France and Great Britain; R1b-DF27 seems to be rare or absent elsewhere: Y-STR data are available only for France, and point to a lower diversity and more recent ages than in Iberia (Table 3). Unlike in Basques, drift in a traditionally closed population seems an unlikely explanation for this pattern, and therefore, it does not seem probable that R1b-DF27 originated in France. Then, a local origin in Iberia seems the most plausible hypothesis. Within Iberia, Aragon shows the highest diversity and age estimates for R1b-DF27, Z195, and the L176.2 branch, although, given the small sample size, any conclusion should be taken cautiously. On the contrary, Z220 and Z278 are estimated to be older in North Central Spain (N Castile, Cantabria and Asturias). Finally, M153 is almost restricted to the Basque Country: it is rarely present at frequencies >1% elsewhere in Spain (although see the cases of Alacant, Andalusia and Madrid, Suppl. Table 1), and it was found at higher frequencies (10–17%) in several Basque regions; a local origin seems plausible, but, given the scarcity of M153 chromosomes outside of the Basque Country, the diversity and age values cannot be compared.

Within its range, R1b-DF27 shows same geographical differentiation: Western Iberia (particularly, Asturias and Portugal), with low frequencies of R1b-Z195 derived chromosomes and relatively high values of R1b-DF27* (xZ195); North Central Spain is characterized by relatively high frequencies of the Z220 branch compared to the L176.2 branch; the latter is more abundant in Eastern Iberia. Taken together, these observations seem to match the East-West patterning that has occurred at least twice in the history of Iberia: i) in pre-Roman times, with Celtic-speaking peoples occupying the center and west of the Iberian Peninsula, while the non-Indoeuropean eponymous Iberians settled the Mediterranean coast and hinterland; and ii) in the Middle Ages, when Christian kingdoms in the North expanded gradually southwards and occupied territories held by Muslim fiefs.

DF27-iberia-france
Contour maps of the derived allele frequencies of the SNPs analyzed in this manuscript. Population abbreviations as in Table 1. Maps were drawn with SURFER v. 12 (Golden Software, Golden CO, USA).

I wouldn’t trust the absence of R1b-DF27 outside France as a proof that its origin must be in Western Europe – especially since we have ancient DNA, and that assertion might prove quite wrong – but aside from that the article seems solid in its analysis of modern populations.

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Text and figures from the article, licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.