North African Neolithic was influenced by Europe... and European Chalcolithic by Iberian Neolithic

Or so it seems considering the data of Fregel et al., a study I have in my to-do list for some time and that I don't see cited often or ever at all.

Rosa Fregel et al., Neolithization of North Africa involved the migration of people from both the Levant and Europe. BioRxiv 2017 (pre-pub). DOI:10.1101/191569

The critical piece is probably this selection from Admixture results but which repeats over and over through the study with many more analyzed populations from all West Eurasia and North Africa:

We see how KEB (Morocco Neolithic) is a mix of European Neolithic intermediate between Iberia (purple) and Sardinian (blue) on one side and, on the other, something like Mozabites (not shown in this detail, cream). TOR is a new Neolithic sample from Andalusia.

Another ancient Moroccan sample IAM (pre-Neolithic, not shown here either) is fully cream-colored like mostly are modern Mozabites. 

Interestingly we see for the first time the emergency of a purple-colored component that differentiates Iberian Early Neolithic from the rest (although this does not happen at lower K-values, so they are still related), a component that, in the MNChL (Middle Neolithic and Chalcolithic) period, somehow appears as dominant in Italy (no data for earlier times) and becomes quite dominant in Central Europe. 

This is intriguing to say the least. It must be said that modern Sardinians and Basques (these probably, not labeled) are low in the purple component, although less than other populations, and that somehow the Early Neolithic (blue) component made a comeback:

I do not want to over-interpret all this (autosomal genetics are not an exact science) but, judging on KEB, the purple component is not just a generic southern branch (Cardium Pottery) distinction but something specifically Iberian or Italo-Iberian. The matter needs more research but it is in any case very intriguing that the purple component seems to expand from Iberia or somewhere nearby (France?, Italy?) in the period leading to the Chalcolithic, a most critical one in the formation of the genetics of Europe.

There is a also a little hoard of DNAmt and Y-DNA, with G2a-M201 (in Europe), E1b-L19* (in pre-Neolithic North Africa) and T-M184 (in Neolithic North Africa) in the patrilineal side and quite a bit of varied K1a in the matrilineal one, as well as JT (also in both shores) and U6 and M1 in North Africa.

Worth reading and keeping in mind, no doubt.

Iberian genetic clusters

I've been the last two weeks or so chewing on this pre-pub and there's a point when no more chewing seems to be useful. So let's get to discuss it as well as possible.

Clare Bycroft et al. Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula. BioRxiv 2018 (pre-pub. DOI:10.1101/250191

The key finding is clustering of the populations of the Iberian Peninsula as in this map (locations for the Spanish state are precise, for Portugal unknown and located at random, also shadowing for Portugal is uniform for all the country):

Supp. Figure 1a

The weirdest thing for me is that the Catalan-Alacant and Seville-León-Asturias cluster are strongly related in the cladogram. I'll discuss this below.

Another very weird feature is the presence of a group in Pontevedra province (Galicia) that is the most different of all, even more distinct than Basques. It is composed of many small highly endogamous subgroups. I do not have at the moment any explanation for this, honestly.

External influences: mostly "French"

When factored as made up external populations, Iberians are mostly French (or something that approaches that label), although "mostly" varies from c. 60% in the West to c. 90% in Gipuzkoa. This pattern of "Frenchness" reminds that of the distribution R1b-S116. Correlation is not causation but it is still correlation and when R1b-S116 seems to stem from somewhere France and arrive to the Peninsula at least as early as the Bronze Age (or maybe before but still undetected, terminus ante quem at Los Lagos, as discussed recently). 

Supp. Fig 5a

The most affected population by this French influence are Basque1, which show no significant contribution from any other source (only very small from Italy1 and very tiny from North Morocco, see supp. fig. 7) but the authors say that (supp. info.):

Notably, the Basque-centred cluster has a markedly different profile from the rest. Firstly, it has much lower, or zero contributions from donor groups that contribute to all other clusters: Italy, NorthMorocco, and WesternSahara, and a very large contributionof 91% (88-93) from France. Additionally, the model fit for this cluster is strikingly less good than that for the other clusters (Supplementary Figure 4d), suggesting that Basque-like DNA is less well captured by the mixture of donor groups in this data set. Specifically the Basque share even more DNA with the French group than predicted by their mixture representation, which might reflect, for example, that the DNA the Basque share with present-day French is only a subset of modern French ancestry. This pattern is seen for other Spanish groups also, but to a much lesser extent.

Area that demands urgent genetic research

So it seems we may be dealing with some sort of "paleo-French" rather than modern Indoeuropeanized French. 

All genetic roads lead to France, at least in Western Europe: it also happens in Great Britain and Ireland, and it is very apparent in the geographically sorted phylogeny of R1b-S116. And is also this area where we see the earliest signs of mitochondrial DNA "modernity": in Paternabidea (Navarre) and Gurgy (Burgundy), an area that demands much greater attention from genetic and archaeogenetic research than has received to this day. 

The other major contributors are: Italy (mostly Italy1), with peaks of c. 20% and influencing mostly the South and Center, North Morocco, with peak of c. 10% in Portugal and a West and South distribution, and Ireland, with peak of c. 6% in Eastern Asturias and a broadly Western distribution. 

Italian contribution (Italy1)

North Morocco contribution

Ireland contribution

What do exactly these contributor components mean? Hard to say, although part of the Italian and North Moroccan elements could well be related to historical episodes such as Roman and Muslim conquests. But only partly so,because the North African in Galicia just cannot be that high only from a Muslim conquest that was very limited in time, nor should we expect to be that much "Muslim" nor "Roman" in the remote and largely ignored area of modern Portugal: there must be more ancient origins, probably dating to the Neolithic, Chalcolithic or Bronze Age. 

minor West Sahara contribution

And in the case of the North African component we may have a guide in a minor West Saharan contribution (at right), which may well reflect an older and "purer" form of North Africanness and which is againcon centrated in Portugal and Galicia, with extension to parts of the Central Plateau but does not affect the South, the area where we should expect most of the Muslim period's genetic influence. 

We cannot trace a line in Portugal because of the uncertainty of the geographic origins of the samples but we can do it within the boundaries of Spain and that line suggests that the Muslim genetic influence could be intense by the Southern third and maybe all the way to Zamora by the Western part but should not be relevant in Galicia nor Asturias nor (inferred, uncertain) much of Portugal. That in these areas, the North African element is peculiar and looks older than the Emirate/Caliphate of Cordoba. 

Speculating on the possible origins of the Iberian clusters

This part has given me a true headache. It is very hard to understand how these clusters formed and I will not pretend here that I have all the answers. The most strange of all is the affiliation of the Central-West and Eastern clusters. 

The problem is not only the highly implausible relation between Asturias-León and West Andalusia, which the authors seem to believe product of historical colonization at the time of the Reconquista (13th century) but which makes no sense whatsoever because the Kingdom of Seville was never part of the barely autonomous Kindgom of León but an administrative division of Castile (of which León was by then just a dependency) and we should thus see at least some important influence of the Central (yellow triangles) cluster, which is dominant in Valladolid, Madrid and even the city (but not the countryside) of Burgos, and we do not see anything like that. 

One possibility is of course that the components or some of them are not that real but I do not see any indication of that in the study, so, in wait of independent replication, I'll take them at face value. 

So why then? I've been scratching my head until I could not think any further, I swear. 

And this is my hypothesis, risky as it may be:

1. The essence of the split between the related Spanish components (excluding Galicians and Basques) and the Portuguese-Galician component could be at the Early Neolithic. When I mask the areas not or weakly affected by the Earliest Neolithic in the components map I get this:

... what seems to correspond odly too well to the first major split in the cladogram between the Portuguese-Galician (purple) component and the rest.

2. The expansion inwards may correlate with Chalcolithic and Bronze Age processes, which seem to be way too important everywhere and also in Iberia. So I used the Bell Beaker map I copied from Harrison (see here) as cutoff for another mask (radius are relative to Bell Beaker density circles in the reference map):

If so the split between the Central (yellow) and East (orange) groups (to which the brown and red and other groups are closely affiliated) could be related to this Bell Beaker period and derived Bronze Age cultures. The yellow or Central component could originate in Los Millares (Almería province) and spread northwards to Ciempozuelos (Madrid province) and from there to other areas with the Cogotas I culture of the Bronze Age. 

The Purple (Western) component should be somehow related to Zambujal or Vila Nova de Sao Pedro (VNSP) culture of Portuguese Estremadura and spread northwards to tin-rich Galicia with the group of Montelavar already in the Bronze Age maybe.

The mysterious Red (Central-West) component could be related to some colonization of that area from the Bell Beaker dense area of Catalonia or the Denia district, or maybe even an older colonization, hard to say. What I know of that area in the late Prehistory is that it is ill-defined, partly for lack of research in the heavily farmed alluvial plain, and that it correlates with Southern Portugal but not fully, always showing a distinct personality, until it grows a clearly distinct personality in the Tartessian period, already in the Iron Age. It is also clear that the so-called Silver Road runs straight through that cluster and that it was important, and growingly so, in the Late Prehistory, having both commercial and religious significance and being clearly the main path of penetration of Phoenician influences inland, already in the proto-historical period. 

While still caught with feeble pins, this Silver Road speculative explanation seems to make much better sense than the Reconquista hypothesis the paper appears to spouse and which I see nonsensical because the patterns observed are not as we could expect. 

But of course it is always up to you to make up your own mind, I'm just offering some variant considerations that for me make some sense but that are by no means a well finished theory either, just better than the simplistic historical interpretation, which does not fit the facts too well.

A bit of satire

Disclaimer: this is a fictional work, any coincidence with reality is, well, coincidence... or something...

I told you years ago it would be like this. Having a nervous breakdown are we? Mwahahaha!

Plenty of us in the Nordic Horde Party have also looked at this. It is settled.

Iberia, the French samples we have, plus the British Neolithic samples tell us what the rest of France was like...

So now France is part of Britain? I see, I see who's "losing it".

Game over!
 
The megalithism stuff too. Forget it. Admit you didn't interpret stuff right.

It is about you because...

... because I'm stating the inconvenient truth, the obvious contradictions and limitations of the Pan-Indoeuropeanist ideology?

Do you only see the pictures or read the papers?
   
 

(Laughing) I read cartoons only. Preferably manga with no text, all cries and extremely slow action designed to dumb down the newer generations.

But by all means, please keep the comedy rolling on.

  

Uh, alright. You want comedy, don't you? 

Just be at peace with the fact your predictions based on modern DNA were wrong. And we the Nordic Horde Party has THE TRUTH. You can't fight against The Nordic Horde, just as Elcano could never even dream to circumnavigate the World on a rotten carrack.
   

J.S. Elcano, first person to sail around Earth

(Elcano shows up from the Netherworld)

I did though!

Thanks buddy for clarifying that. 

(Elcano vanishes in a puff of smoke)





 

Just, deal with the facts: with our alternative facts!

Everyone in Europe has Steppe ancestry. Basques too, Sardinians too, everyone belongs to the Nordic Horde, hierarchically organized by greater purity of Nordic Horde ancestry!

... conveniently deformed by forced pseudoanalyses so the Brits and Germans retain top-dog position in your Nordicist revised hierarchy rather than being semi-Basque? I see...

...  they also influenced the Basque despite the fact Basque speak a non-Indo European language. 20-30% contribution.

Uh, here it says zero contribution. And here too, and here, and here, and here...

Nein, nein, nein, Impossible!

Is R1b Z2103 in Yamnaya not good enough for you?

No. It's a very high distinct branch within M269 and has no direct relation with either S116 nor U106, nor their direct precursors, M412, etc.

Deny, deny, deny. Eventually you'll accept the truth.

You're completely insane, but at the very least try and get the facts right. Our facts, our alternative facts!

Ancient DNA will never prove you right. You will have to deal with this sooner or later. And if it does: we'll claim it is 'dubious', 'contaminated', whatever we need to impose our doctrine, because remember that a lie repeated one thousand times becomes truth, mwahahaha!

Truth defends itself.

There's a new paper coming... I have connections, I know the future, mwahahaha! I'll enjoy seeing you try and squirm your way out of what you just said after you see the results.
  

I heard that before and most of the time it was nothing like you imagined.

There's no getting away from it.

OK, abracadabra, whatever, agur.

Quickie: the pre-Indoeuropean evolution of ancient Iberians: from 'Sardinian' to 'Basque'

This may be needed as transition between the ancient Iberian genetic data of Valdiosera and Günther that I discussed two days ago and the modern Iberian genetic data that I'm planning to discuss very soon (just chewing on the data, because it is a bit perplexing in some aspects, but ref. Bycroft 2018 if you want to peek on it on your own). 

Fig. 1B from Valdiosera, Günther et al. 2018, annotated by me.

Just that: we see very clearly how ancient Iberians were at the beginning of Neolithic like modern Sardinians and by the time of Chalcolithic in some cases and at the Bronze Age everywhere, they had turned into something like modern Basques, i.e. more Paleoeuropean but not yet more Indoeuropean at all. 

Modern Spaniards/Iberians seem to be mostly that Basque-like Bronze Age base plus some Indoeuropean admixture from either the continent (Celts surely) or Italy (Romans no doubt). 

Maybe it is like stating the obvious but the obvious is not always obvious for everyone and understanding this will be handy when dealing with modern Iberian DNA and its structure.

Oldest known Iberian R1b-S116 (and DF27) is NOT at all Indoeuropean

This study is very interesting but it is very wrongly argued, maybe in an attempt to fit their findings with what has sadly become the mainstream current of "explanation" about the origins Y-DNA haplogroup R1b-S116 (also P312, etc.)

Cristina Valdiosera, Thorsten Günther et al. Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia. PNAS 2018. DOI:10.1073/pnas.1717762115

The issue is that they found the very first known carrier of R1b-S116 (and R1b-DF27, the main Iberian haplogroup) in an individual of the Bronze Age of Lower Rioja (Cueva de Los Lagos, Alhama de Cervera), belonging very clearly to the Central Iberian culture of Cogotas I, even if it is at its very northeast margin.

What is wrong? Well, the very title is wrong. It is nothing but an artifact produced by forced (supervised) results of Admixture within the simplistic 3-population model. Even then their result is in fact so weak that it immediately cried to me as "artifact" (noise or whatever you want to call it) and it is effectively nothing but that. 

And to demonstrate it is as simple as digging into the supplementary materials and look at the unsupervised Admixture run (dataset S03), whose optimal columns (lowest CV scores) are K=16-19 (all four are optimal, what is fine with me but makes explanation and understanding a bit more dense). 

As that unsupervised admixture is massive, with lots of global populations ancient and modern, I made a selection using only the four optimal K-values (K=16 to K=19, from left to right):

Click to expand (labels at bottom are mine)

And it is absolutely clear from K=16 to K=18 that there is not a speck of the Caucasus component which is absolutely universal in all the true Indoeuropean samples. There is a tiny speck of it in the K=19 column but there even Sardinians and some Anatolian Neolithic individuals have it at much greater values and thus cannot anymore be automatically interpreted as Indoeuropean marker, but just as extra Caucasus affinity present in some Neolithic-derived populations or individuals more than others since the very beginning of mainline (Vasconic) European Neolithic at the Aegean.

And this is it. Quod erat demonstrandum (Q.E.D): R1b-S116, at least in Iberia, has nothing to do with Indoeuropean expansion, nothing at all: it is absolutely clear that it is a pre-Indoeuropean thing. And it has been present in Lower Rioja since at least the Bronze Age.

Furthermore, when we look at the Central European Bell Beaker (Central BB) samples and compare them with their immediate chronological precursors of (definitely Indoeuropean) Corded Ware culture, we must admit that there is a decrease of the Caucasus component and an increase of the Vasconic Neolithic (light blue) element. This also speaks against the Indoeuropean "explanation" for the expansion of R1b-S116 into Central Europe, because the first known such ancient carriers are from the Bell Beaker period and not a moment earlier, and these clearly express an anti-Indoeuropean tendency in their autosomal genomes.

There is however a sizable Indoeuropean component in modern non-Basque Iberians, smaller than in most other European populations but very clear nevertheless. This must have arrived at later times: (1) with the Celts, who arrived to Catalonia at the end of the Bronze Age, later expanding into Central and Western Iberia, (2) with the Romans, (3) maybe also to some extent with the Germanic invaders of the late Roman period. None of these expansions seem particularly associated with R1b-S116, however the c. 1% R1a and the c. 8% J2 (with plausible Italo-Roman origin) should be related to it, along with an assortment of other haplogroups. 

For those willing to dig in the details, there is also a small treasure trove of other ancient Y-DNA, mostly I (which underlines the Paleoeuropean influence in Neolithic Iberia, regardless of whether this is local or was carried on from further East by the Neolithic settlers), as well as one instance of unspecific R1b, another of G and another of H.

Someone may ask, which is then the origin and means of expansion of R1b-S116, if not Indoeuropean? Good question to which I don't have yet a well defined answer. But my tentative explanation is that it should be related to two ultimately related processes within Western European "Neolithic" (Late Neolithic and Chalcolithic): 

1. The well documented phenomenon of increase, in most areas at least, of the Paleoeuropean component time passes, this may be to some extent because of simple absorption of local subneolithic "hunter-gatherers" but it probably also produced different subpopulations within the Western Neolithic and in some cases we do see these peripheral "Second Neolithic" groups expanding at the expense of the "First Neolithic" peoples. This is most clear in Central Europe with the expansion of Funnelbeaker cultures from, probably, Denmark and nearby areas of Low Germany. In fact Michelsberg culture and its close relative in France Seine-Oise-Marne basically wipe out the first farmers of LBK (Linear Pottery) at what I usually describe as the Chalcolithic but is often described as Middle or Late Neolithic in other sources.
2. Clearly Bell Beaker had something to do: we see their impact in Germany, Britain and Ireland and one could argue that Cogotas I is somehow derived from the Bell Beaker of Ciempozuelos, although in this I'm going to remain neutral and a bit skeptic until more evidence shows up. 

But what seems very apparent tome is that R1b-S116 should have expanded from somewhere in France, probably towards the South. And we do need better genetic studies, including archaeogenetic ones, on the Hexagon before we can jump to conclusions. France is not the most affected area by Bell Beaker, so I am cautious about attributing too much weight to only Bell Beaker and I would rather think on a complex succession of expansions associated to various cultures. 

Of great interest here should be the ill-known but fascinating Artenacian culture, which expanded in all West France and Belgium from a core at Dordogne before the BB period and coincident with the Corded Ware expansion in Central Europe. Like Bell Beaker folk, they were adept at bowmanship but their area is not densely affected by Bell Beaker later on (although there is indeed a scatter of findings). I do wonder if somehow Bell Beaker is derived from Artenac, even if it is clearly not the same thing. Food for thought.


Update (March 18): small steppe-like noise appears in diverse Iberian samples since the Late Neolithic/Chalcolithic.

This has arisen in the discussion below (h/t to MZ): when the supervised (forced assignment to rigid three populations) is used, the appearance of "steppe" ancestry is found here and there also before the Bronze Age. As we see above, this is not real: it does not happen in the unsupervised model at all but mere "noise" or "artifact" produced by the excessive simplicity of the three populations model.

This does not make the three populations model "wrong": it is still approximately right but "evidence" produced  ONLY from rigidly applying this model is not evidence of anything, just a hint to be confirmed or rejected via wider analysis at best.

Ancient DNA from the Balkans

This study has been for several months around but I have not discussed until now and is well worth a mention.

Ian Mathieson et al., The Genomic History Of Southeastern Europe. BioRXiv (pre-pub) 2017. doi:10.1101/135616

There is a lot of ancient autosomal DNA from the region but it basically says one thing: everything was almost exactly as expected from archaeology. The Karanovo-Gumelnita people, famed for inventing the Bronze Age a whole millenium earlier than anyone else, and nearby related cultures, were within the mainstream (Vasconic) Neolithic genetic grouping. This changed however with the kurgan invasion expressed primarily in the Ezero culture, which I've been told should be considered direct precursors of Thracians. But the change is not something radical: more genetic affinity with the steppe is visible than before and more generalized through all samples. 

Fig. 1-D - Supervised ADMIXTURE plot, modeling each ancient individual (one per row), as a mixture of
populations represented by clusters containing Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green).  (click to expand)

Well, it is not exactly everything what is as expected, if we consider Polish Globular Amphorae culture, which I would have expected to be at least somewhat steppary, Indoeuropean, already but were not. Thus it seems I have to concede on this culture and its precursors being still part of the Vasconic Neolithic. This makes Indoeuropean penetration into Central-North Europe a much more sudden episode and one directly tied to Corded Ware culture and nothing else. It must have been perceived by its victims like a massive catastrophe, because it was a huge area which they conquered and to a large extent colonized in a very short span of time.

Lots of R1b in Epipaleolithic Balkans

Most interesting anyhow is the huge hoard of ancient Y-DNA R1b in the Iron Gates region (Lepenski Vir) before the Neolithic. This not only demonstrates, again, that this haplogroup is Paleoeuropean, at least in part, but, quite intriguingly makes earlier findings on modern data suggesting a possible origin or R1b-M269 in or near modern Serbia (Morelli 2010 and Myres 2010) at least somewhat plausible. However none of the Iron Gates R1b is described as R1b-M269 and in some cases it is excluded that it could be this sublineage. 

Thus the issue of the ultimate origins of this key lineage remains open, but let me underline that these Iron Gate individuals belonged to the WHG grouping, as did Villabruna (so far the oldest R1b carrier kown) and that they breach this way the assumed haplogroup homogeneity I2 conceived on merely Central and Northern European samples. Just as happened with mtDNA U haplogroup homogeneity when mtDNA H was detected by several independent studies of Iberian ancient DNA. It is normal to expect more diversity towards the south for several reasons but maybe the most critical of them is just average temperature, which makes the southern lands naturally more fertile (notably so for crops domesticated in the Middle East) and easier to inhabit. 

This trend was only broken in the Middle Ages when the heavy plough allowed the improved exploitation of deep Oceanic soils, being useless in the Mediterranean region of shallow soils however. It was only then when the center of European development moved from south to north, to Belgium specifically, where it remains till present day. So let's take Southern Europe a bit seriously, please.

Two big issues with Olalde 2018 (Indoeuropean Bell Beaker speculation)

"Just for being published in Nature it does not mean it is necessarily wrong" (popular saying).

Iñigo Olalde et al., The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe. doi:10.1101/135962 (pre-pub version, no way I'm spending 1/3 of my monthly income on this, in case you're willing to waste your money, it's been recently published in Nature)

Issue 1: All comparisons are made between Anatolia Neolithic or other Early Neolithic in some cases and Yamna or Corded Ware.  Late Neolithic is not used nor, critically, is Hunter-Gatherer populations or anything related. 

This means that everything will be much more Yamna-like than it should, just because Yamna are 50% HG, while Early Neolithic are very low in this component. 

This is very apparent in the PCA:

It's junk-in: junk-out.

Issue 2: there is a huge sampling gap precisely where ancient mtDNA (and modern Y-DNA) tells us that the origin of the modern West-Central European genetics should be: in France and nearby areas like the Basque Country, West Germany. Sure: they sample some Eastern French sites but see "issue 1" above.

Nuff said.

Dystruct versus Admixture

Not really able yet to discern if this is an alternative way ahead for autosomal archaeogenetics or just another dead end. But it does seem interesting enough to mention here in any case.

It may be very important in the deciphering of the so-called "ANE" ghostly genetic influence.

Tyler A. Joseph & Itsik Pe'er. Inference of population structure from ancient DNA. bioRXiv 2018 (pre-pub). DOI:10.1101/261131

Methods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.

Still digesting this one but I do find very intriguing that they claim that Dystruct has much less time-entropy than ADMIXTURE (i.e. the relation between ancient and modern populations seems to be better identified) and that, using this method they get that the Samara (proto-Indoeuropean) population becomes much more clearly related to Kostenki-14 (a Gravettian hunter-gatherer from the Don area) and that the Paleo-Siberian "ANE" individuals form then their own distinct cluster with very limited impact in Europe (but much larger in parts of Asia (not labeled: South Asia?). This Kostenki-Samara "orange" component keeps influencing Western Indoeuropeans (Corded Ware, Unetice) but at markedly decreasing frequencies of "purity". 

However the first admixture of Corded Ware is not with earlier farmers (mostly "green") but with some sort of late "hunter-gatherer" population ("brown" or "maroon" component. Only after the backlash of Bell Beaker, which in Central Europe appears as a mix of Neolithic peoples, Indoeuropeans and maybe even more of that mysterious extra HG element, we see some "return of the farmers", which clearly persists in Unetice.

In general, modern Europeans are (fig.5a, not shown here) quite "greener" than Unetice and some populations (I'm guessing Sardinians and Basques, no labels provided) have zero "orange" (IE) component, which ranges (my visual estimate) between 9% and  27% otherwise.

Fig.5-b (click to expand): Ancestry estimates for 92 ancient samples. The three leftmost samples are the Pleistocene hunter-gatherers. In Dystruct, late Neolithic samples and beyond present as a mixture of hunter-gatherers, Yamnaya steppe herders,and early Neolithic samples, matching supported historical migrations of steppe herders into Eastern and Western Europe.

The patrilineage R1b-DF27 in North Iberia

Just weeks ago a new study on Northern Iberian Y-DNA, focused specifically on R1b-DF27, was published. It covers Asturias, Cantabria, Basque Country and Aragon, finding greater diversity in the Basque Country and Cantabria and lower in Aragon and Asturias.

Patricia Villaescusa et al., Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. FSI-Genetics 2017. Pay per view → LINK [doi:10.1016/j.fsigen.2016.12.013]

Abstract

The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27. Our results reveal frequencies over 35% of DF27 haplogroup in the four North Iberian populations analyzed and high frequencies for its subhaplogroups. Considering the low frequency of DF27 and its sublineages in most populations outside of the Iberian Peninsula, this haplogroup seems to have geographical significance; thus, indicating a possible Iberian patrilineal origin of vestiges bearing this haplogroup. The dataset presented here contributes with new data to better understand the complex genetic variability of the Y chromosome in the Iberian Peninsula, that can be applied in Forensic Genetics.

The study, quite conveniently, differentiates between "native Basques" (those whose patrilineal ancestors lived in the Basque Country for at least the last three generations) and "resident Basques" (those whose recent patrilineal ancestors immigrated, mostly from NW Iberia).

R1b-DF27 is one of four major R1b sublineages in Western Europe and one of the three "brothers" that can be tracked to an origin somewhere in what is now Southern France, most likely, i.e. together they form part of R1b-S116. The fourth lineage would be, naturally, R1b-U106, "brother" of S116 and found typically around the North Sea. It is the one with the southernmost distribution, being very dominant in Iberia and among Basques. Probably it is also important in all the south of modern France but clear data is missing as of now.

Reconstructed spread of R1b to Western Europe and within it (dates objectively unknown so far, own work)

This is the key data table of the study, showing the frequency of the various sublineages of R1b-DF27 ("*" means "others", so "DF27", without asterisk, means "all DF27" and "DF27*" means instead "remaining DF27 after exclusion of the other mentioned subclades"):

Click to expand (frequencies are absolute, relative to whole sample)

It is also worth sticking this other graph, which shows (top right) the (SNP-based) true phylogeny of the haplogroup R1b-DF27 and, complementarily, the (somewhat messy) haplotype structure based on a limited number of short tandem repeats (STR), in which only Z220 appears clearly defined:

Click to expand

The study is very limited in its scope but it does show that there is a very high diversity for this lineage among Basques. This however does not necessarily indicate that Basques are the direct origin: much more data from the rest of Iberia and very especially from France is required before we can jump to any conclusion. Based on the limited data we have, I am of the opinion that the lineage did not originate in Iberia most likely but rather in what is now Southern France, migrating southwards via the two natural corridors: the Basque Country and Catalonia. 

Sadly enough we just do not have enough modern data, much less ancient one, in order to issue a definitive judgment on the matter. However the overall pattern of distribution of R1b-S116 strongly suggest a "Southern French" origin, not just for "Iberian" DF27 but also for the other two "brother" lineages: "Alpine" U152 and "North Atlantic" M529. 

The big question is how and when did this expansion took place. A "South French" origin was much easier to explain when the Paleolithic continuity model seemed reasonable, however recent ancient DNA findings strongly suggest that the Neolithic and Chalcolithic saw major population changes in much of Europe until stabilization was achieved -- exact patterns vary on specific regions: in some cases this does not happen until the Bronze Age, in others, like the Basque Country and quite possibly the Atlantic parts of France, it may have happened much earlier, even as soon as the early Neolithic. 

So my best recipe for an explanation is that we have to look very carefully at what happened in Western Europe, particularly towards the Atlantic Ocean in that "transitional" period, when not just large cultural phenomena like Dolmenic Megalithism or later also Bell Beaker manifested in quite expansive and dynamic manner but also a dearth of smaller cultures were the actual social or ethnic pieces making them possible. For example it is plausible that Michelsberg culture (originating in Lower Rhineland apparently and swiftly replacing the early Neolithic LBK culture in Germany, North France and nearby areas) could be involved in the expansion southwards of R1b-U106 and other traits of the modern genetic pools we observe. Another culture well worth taking a look at is the Artenac culture, which expanded from Dordogne towards the North up to Belgium soon after the Michelsberg/SOM era. Rather than one single and sudden expansion of a well defined population, it seems to me that we are before a jigsaw puzzle of several cultures and several chronologies, related maybe but not exactly the same.

See also:

• Some improved knowledge of major R1b sublineage S116
• Basque R1b-DF27
• Basque and Gascon Y-DNA survey (DF27 was not yet described but the imprecise data is still quite suggestive of its strong presence among Gascons, sublineage Z196 was reported anyhow)

Thanks once again to Jean Lohizun.

Extensive ancient Iberian mtDNA analysis

A very interesting thesis on Iberian ancient mitochondrial DNA is available (found via Bell Beaker Blogger):

Christina Roth, Once upon a time in the West : paleogenetic analyses on Mesolithic to Early Bronze Age individuals from the Iberian Peninsula. University of Mainz (thesis), 2016. Freely available → LINK

As all theses, it is very extensive, and I can only make some comments here (space and time are always too limited, you know), hoping to grasp the most interesting aspects of it.

First of all Roth finds that Iberian hunter-gatherers (HGW in the paper) were not quite like Central European ones (HGC), at least not in the mtDNA. Instead, in this aspect the Central European hunter-gatherers were closer to Eastern European ones (HGE), as well as to the Pitted Ware late subneolithic population of Gotland.

Iberia-only mtDNA analysis

This will be a recurrent issue along the analysis she makes. But let's focus on Iberia by the moment. Notice that she does not just use her own data but also from many other sources, including some unpublished materials, this makes a bit difficult to follow all the details, so I feel I can only focus on the statistical analysis she makes and which is the core of the thesis.

Annotated by me, because I found the abbreviations quite hard to follow

The general overview is confirmed, with minor variations, in the cluster analysis (which I also took the liberty of annotating, but take my notes for what they are: mere scribbling on the margin in an attempt to better understand the data, nothing else):

Particular care not to take the arrows of my notes too seriously: they are just conceptual, a very loose sequencing of the available data for a very tentative visualization of it. If it helps you, cool, else ignore please.

In any case, it seems clear cluster 2 is more influenced by hunter-gatherer genetics and that, with the data available in this study, we reach the end of the timeline within it in the following regions: Upper Ebro and Basque Country (data up to Late Neolithic but see my own 2013 compilation for a longer period), Southern Iberia (up to Chalcolithic) Southeast and Northeast, this one after originally being in the "more Neolithic" cluster 1 (in fact the author does argue for Catalonia as main "gate" for Neolithic genetics into Iberia on light of the available data, which does not include another important "gate", the SE one, for lack of data for the early period).

Inversely, cluster 1 is more influenced by "farmer" genetics, first detected in the Northeast (Catalonia and nearby areas of Aragon) but then also affecting the Northern Plateau and the West (Central Portugal). This last is very important because it is here where a key civilizational hub, the oldest known civilization of the Atlantic shores, emerged in the Chalcolithic, playing a key role in the wider Megalithic and Bell Beaker phenomena. I have at times speculated that it might be the origin of "modernity" in Western European genetic pools but on light of this data I have to recant, the origin should be elsewhere, probably in/around what is now France (and therefore it's not likely to be directly related to Bell Beaker, except maybe in the islands, but rather to Michelsberg/SOM, Artenacian and such -- always in wait of more data, just a cautious hypothesis). 

Finally the farmer-leaning cluster reaches the Southern Plateau, near Madrid, what suggests a N→S move of the then-forming Cogotas I herder culture, rather than the opposite. 

What we do see is not inconsistent with modern Iberian genetics anyhow: while Central Europe seem to have seen an increase of "hunter-gatherer" genetics along time, in Iberia the main tendency is the opposite: an increase of "farmer" genetics and further dilution of the aboriginal genetic pool. There is however at least one clear exception in the Northeast and that is also consistent with modern Iberian genetics. Some regions (south, southeast and the totally unknown northwest) have only fragmentary sequences here, so unclear, although the final tendency, up to the Bronze Age, is to cluster 2b (i.e. mixed but rather tending to "hunter-gatherer" genetics).

To finish with the Iberia-only bloc, notice that these are the lineages found among early Iberian farmers by region (in color those haplogroups associated to the arrival of Neolithic per the available data):

Notice how the pool in the Northern region is quite modern-like, not yet exactly as it is locally today but it would pass quite unnoticed in a map of Europe.

Iberia and the rest of Europe

What about the pan-European context (with the usual huge blanks in France, Britain, etc.)? Quite interesting as well:

Annotated by Maju on fig. 23 (click to enlarge)

As mentioned before, the Iberian hunter gatherers (HGW) appear clearly distinct from their Central and Eastern cousins in the mtDNA analysis. And with all this Iberian dataset it becomes apparent that there seem to be two "zones of admixture": one for Iberians and another for Central Europeans, the difference being on which aborigines they mix with. 

Notice that it is not possible to differentiate here between local Central European and intrusive Eastern European admixture, as both aboriginal hunter-gatherer populations appear closely related in all analyses (maybe an artifact of the sampling strategy or maybe actually relevant, can't say). 

It also caught my eye that a German site (Blätterhöhle, Westfalia, famed because farmer and hunter-gatherers living side by side were located there some years ago), clusters intensely with Iberian hunter-gatherers and related populations. I have to research more on this matter (which I had ignored so far) but I suspect it may be very relevant, because we could get an even longer chain of early "modern" mtDNA pools, adding this site to Paternabidea (Navarre) and Gurgy (Burgundy), spanning a long stretch of Western Europe, an area quite neglected by archaeogenetics so far, it must be said.

It is also worth mentioning that UC (which I believe stands for Unetice Culture) pulls the "Central European zone of admixture" in the PCA downwards, with a polarity of its own, a polarity that should probably be considered as specifically Indoeuropean. 

The cluster analysis confirms much of what I just said above, not annotated for a change:

We see very clearly here a larger cluster more influenced by "farmer" genetics and a smaller one that includes all pre-Neolithic aborigines, plus two populations already post-Neolithic but clearly identifiable as at least largely aboriginal (PWC and BLA), plus a subcluster of Neolithic Iberians, from the North (NSE and EVN) and the West (CPE). 

The author notices that: Bernburg (BEC) and Funnel Beaker (FBC) samples (...) show almost no significant differences to any Iberian group, except to the Early Neolithic of Northern Spain (NSE) and Chalcolithic of East Spain (ESC). Hard to interpret but worth noticing, no doubt.

And there is a lot more in the thesis but I can only review so much, so take a look and tell me and the World if I'm missing something of relevance or you feel I'm misinterpreting something or whatever.