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.

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.

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.

The destiny of a cave lion: to serve as decoration

Quickies

Spanish researchers have concluded that a carpet or other comparable fur ornament (a tapestry?, a cape?) is why a late cave lion remains, the latest ones known in Iberia, were found in an otherwise human (Magdalenian) context in the cave of La Garma (Asturias, Spain): it was a fur, claws included, used as decoration of some sort.

Marian Cueto et al., Under the Skin of a Lion: Unique Evidence of Upper Paleolithic Exploitation and Use of Cave Lion (Panthera spelaea) from the Lower Gallery of La Garma (Spain). PLoS ONE, 2016. Open access → LINK [doi:10.1371/journal.pone.0163591]

Abstract

Pleistocene skinning and exploitation of carnivore furs have been previously inferred from archaeological evidence. Nevertheless, the evidence of skinning and fur processing tends to be weak and the interpretations are not strongly sustained by the archaeological record. In the present paper, we analyze unique evidence of patterned anthropic modification and skeletal representation of fossil remains of cave lion (Panthera spelaea) from the Lower Gallery of La Garma (Cantabria, Spain). This site is one of the few that provides Pleistocene examples of lion exploitation by humans. Our archaeozoological study suggests that lion-specialized pelt exploitation and use might have been related to ritual activities during the Middle Magdalenian period (ca. 14800 cal BC). Moreover, the specimens also represent the southernmost European and the latest evidence of cave lion exploitation in Iberia. Therefore, the study seeks to provide alternative explanations for lion extinction in Eurasia and argues for a role of hunting as a factor to take into account.

Fig 4. Cave lion distal phalanxes from the Lower Gallery of La Garma.

Note that only eight of nine specimens are depicted in the figure.

Above: the claws that are the only remnants found of said lion, whose cut marks are fully coincident with skinning techniques used in more recent times with similar decorative purpose. They are believed to be all anterior claws and that one is missing therefore. That is why they imagine the fur to have been cut with an aesthetic interest, because the hind claws would not be visible if the fur was, for example, hang on the wall, so they were probably cut off.

Whether hunting of lions by humans was a decisive, contributing or negligible factor in cave lion extinction remains unclear.

MtDNA U6 in Aurignacian Europe

The U6 haplogroup of Pestera Muierii is officially confirmed. 

Extra-officially, it also seems confirmed mtDNA H in Magdalenian El Mirón, another of the haplogroup challenged (without any reasoning) by Fu et al. In this last case, my sources suggest that Fu surely tested a bone belonging to a different individual, because the heap of bones could well include several people and the bones tested by Hervella (a tooth) and Fu (a femur) were different.

Anyhow, to the matter at hand:

Montserrat Hervella et al. The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Nature 2016. Open access → LINK [doi:10.1038/srep25501]

Abstract

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

The interesting part is that today U6 is pretty much constrained to Northwest Africa and parts of Iberia and it has usually been considered until now as a North African haplogroup, even if of Eurasian derivation. 

Fig. 2 - (A) Phylogenetic analysis and temporal estimates for lineages including the Peştera Muierii-1 (PM1) from the mitochondrial tree. (B) Location of the Peştera Muierii cave and surface map based on current frequencies of U6 lineages³⁰; the European borders map was generated in ArcMap 10.1 (ESRI, http://www.esri.com) by modifying the World Borders Dataset (http://www.thematicmapping.org/downloads/world_borders.php), which is licensed under the Attribution-ShareAlike 3.0 Unported license. The license terms can be found on the following link: http://creativecommons.org/licenses/by-sa/3.0/ (This map was created by A.A.).

Another interesting bit is that U6(xU6a'b'd,U6c), U6* for short, is not known to exist today anymore. So it is reasonable to speculate about the "ancestral" position of Muierii in the lineage, regardless of whether Muierii-2 was a true ancestor or just a more or less distant relative of the real ancestor of modern day U6 carriers. 

Complementary information is to be found Secher et al. (2014), which refined the knowledge of the U6 mitochondrial haplogroup, unveiling that the key basal (and rare) U6c sublineage is not only found in Morocco (as known earlier) but also in Europe. Specifically U6c, which hangs directly from the U6 root node, is found in: Hispanic America (5.7% of all U6 carriers), Spain (2.2%), Canada (12.5%), NW Europe (16.7%), Morocco (4.5%), Algeria (10%) and Tunisia (5.9%). It is missing in Brazil, Western, Central and East Africa, Romani ("Gypsies"), Jews, Azores, Madeira, Canary and Cape Verde Islands, Portugal, Central and Eastern Mediterranean, West Sahara, Mauritania and USA (African-Americans,  European-Americans and Hispanics).

Figure 1

Surface maps, based on HVI frequencies (in o/oo), for total U6 (U6), total U6a (Tot U6a), U6a without 16189 (U6a), U6a with 16189 (U6a-189), U6b'd, U6c, U6b and U6d.

While the exact pattern of U6 expansion is not clear except for Africa (with a Moroccan origin surely), Sacher et al. believe that at least this part is related to the Iberomaurusian (aka Oranian) culture, which seems primarily an offshoot of Iberian Solutrean, also with origin in North Morocco (Taforalt) and European-like human looks (Cromagnoid).

Another complementary reference is Carmela L. Hernández et al. (2015):

An inspection of the U6 phylogenetic tree (S1 Dataset) showed that it is not easy to infer whether Iberia or North Africa bear more basal lineages. (...) The U6c (9.9 ky [5.0–15.0]) and U6d (12.0 ky [6.9–17.3]) are present in Iberia, Europe and North Africa at low frequencies.

While she seems to support a North African origin, the data is in fact somewhat contradictory:

Fig 5. Founder analysis for mtDNA U6 haplogroup. The plots show probabilistic distributions of U6 founder clusters for HVS-I sequences (A) and complete genomes (B) across migration times scanned at 200-year intervals from 0 to 60 ky.

Fig 7. Bayesian Skyline Plot (BSP) analysis of entire mtDNA U6 sequences.

Temporal changes of the effective population size, Ne in sub-Saharan Africa (brown color), North Africa (green color), and Iberian Peninsula (red color) are depicted. Solid lines represent the median values for the log10 of Ne on the Y-axis within each analyzed geographic region. The 95% HPD (highest posterior density) interval is shown for the three distributions (dashed lines).
Notice that the "LGM" label is very wrong: it should be around 21.000 years ago!

Usually U6 genetic history is envisioned as a migration from southwest Asia through North Africa [50]. This hypothesis is based on the general origin of haplogroup U sub-clades in Southwest Asia, which is also the center of the geographical distribution of U sub-clades: Europe, India, Central Asia, East Africa and North Africa. Two possible scenarios for the first U6 haplotype (bearing mutations 3348 and 16172) can be advanced: i) these mutations aroused in the founder region but did not leave any genetic legacy in current human populations there; ii) they originated probably somewhere in North Africa, after the arrival of the U6 founder haplotype. Within North Africa U6 is only significantly frequent at its western edge (as well as in South-western Europe). More importantly, all the most basal branches are virtually restricted to that region (U6b, U6c and U6d), what could indicate its western origin. Nevertheless, it cannot be excluded the major sub-clade U6a, which shows a richness of sub-clades in Northwest Africa [29] although a few of derivative branches also include sequences from East African and the Middle Eastern populations (e.g. U6a2).

Her conclusions (insisting on an African origin and first arrival via Egypt) are not something I can share at this stage of the research but her data is clearly very interesting and, combined with the rest, useful in discerning the possible route of primeval U6 to the Gibraltar Strait area, where it found no doubt its niche for consolidated expansion. 

After the Muierii finding the question is open: did primeval U6 arrive to North Africa via Iberia, being pruned in Europe afterwards just because of genetic drift and the sizable impact of Paleolithic migrations in low density areas? I cannot be 100% sure but I would say it is a very likely conclusion based not just on Muierii but also on the rather high basal diversity of U6 in Iberia (and surprisingly NW Europe!) and also on the archaeological data that makes almost necessary to root the first Upper Paleolithic of NW Africa (the Iberomaurusian) in the Iberian Solutrean.


(Special thanks to Jean Lohizun again).


Update (Jun 17):

The Hernández 2015 paper also mentions that  U6a1 appears to be of European and specifically Portuguese origin:

Our U6 tree built from mitogenomes shows that U6a1 is predominantly European because it contains a significant number of sequences of Mediterranean individuals mainly from the northwestern shore with a leading Iberian contribution (21 of the 29 European samples) and has an ancestral node in Portugal (accession number HQ651694).

Thanks to Geog M. for highlighting this important detail.

H. heidelbergensis is Neanderthal ancestor and not 'Denisovan' cousin

Quickies

The unprecedented sequencing of a small fraction of the autosomal DNA of Homo heidelbergensis from the Sima de los Huesos of Atapuerca proves that they are in direct ancestral line to H. neanderthalensis and not particularly related to Denisovans.

Matthias Meyer et al., Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 2015. Pay per view → LINK [doi:10.1038/nature17405]

Abstract

A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago¹. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals². However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.

Some articles that describe the findings:

→ at Nature News

→ at Público (in Spanish)

Matthieson also found that the Sima de los Huesos hominids were closer to Denisovans and Neanderthals in mtDNA two years ago. But this sequencing of their nuclear DNA puts them much closer to Neanderthals instead.

Prüffer et al. found in 2013 that Neanderthals form a cline with "Denisovans" in nuclear DNA but not in mtDNA, in which they are closer to us. This one is a very interesting read for background, as it explores in great detail the various possible scenarios.

That "Denisovans" could be closely related to H. erectus (a catch-all term for most archaic populations, particularly in Asia) has been considered as very possible before (Waddell et al. 2012) but there is no genetic confirmation so far, neither strong rejection. Getting DNA from such ancient specimens is considered a breakthrough and this partial sequencing of 400,000 years ago is believed to be within the very limits of absolute possibility.

[Conclusions edited on Mar 19th because I got it all wrong and don't wish to keep confusing anybody else. Instead I listed several relevant background studies, judge yourself].

A Magdalenian campsite map from Catalonia

Quickies

A neat curiosity from the Ice Age:

Marcos García Díez & Manuel Vaquero, Looking at the Camp: Paleolithic Depiction of a Hunter-Gatherer Campsite. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0143002]

Abstract

Landscapes and features of the everyday world were scarcely represented in Paleolithic art, especially those features associated with the human landscape (huts and campsites). On the contrary, other figurative motifs (especially animals) and signs, traditionally linked to the magic or religious conceptions of these hunter-gatherer societies, are the predominant themes of Upper Paleolithic art. This paper seeks to present an engraved schist slab recently found in the Molí del Salt site (North-eastern Iberia) and dated at the end of the Upper Paleolithic, ca. 13,800 years ago. This slab displays seven semicircular motifs that may be interpreted as the representation of dome-shaped huts. The analysis of individual motifs and the composition, as well as the ethnographic and archeological contextualization, suggests that this engraving is a naturalistic depiction of a hunter-gatherer campsite. Campsites can be considered the first human landscape, the first area of land whose visible features were entirely constructed by humans. Given the social meaning of campsites in hunter-gatherer life-styles, this engraving may be considered one of the first representations of the domestic and social space of a human group.

Ancient mtDNA from a Megalithic tomb near Atapuerca

A new study has produced 22 mitochondrial sequences from a Megalithic tomb (dolmen) in Alto del Reinoso, some 7 Km NE of Atapuerca.

Kurt W. Alt, Stephanie Zech et al., A Community in Life and Death: The Late Neolithic Megalithic Tomb at Alto de Reinoso (Burgos, Spain). PLoS ONE 2016. Open access → LINK [doi:10.1371/journal.pone.0146176]

Abstract

The analysis of the human remains from the megalithic tomb at Alto de Reinoso represents the widest integrative study of a Neolithic collective burial in Spain. Combining archaeology, osteology, molecular genetics and stable isotope analysis (87Sr/86Sr, δ15N, δ13C) it provides a wealth of information on the minimum number of individuals, age, sex, body height, pathologies, mitochondrial DNA profiles, kinship relations, mobility, and diet. The grave was in use for approximately one hundred years around 3700 cal BC, thus dating from the Late Neolithic of the Iberian chronology. At the bottom of the collective tomb, six complete and six partial skeletons lay in anatomically correct positions. Above them, further bodies represented a subsequent and different use of the tomb, with almost all of the skeletons exhibiting signs of manipulation such as missing skeletal parts, especially skulls. The megalithic monument comprised at least 47 individuals, including males, females, and subadults, although children aged 0–6 years were underrepresented. The skeletal remains exhibited a moderate number of pathologies, such as degenerative joint diseases, healed fractures, cranial trauma, and a low intensity of caries. The mitochondrial DNA profiles revealed a pattern pointing to a closely related local community with matrilineal kinship patterns. In some cases adjacent individuals in the bottom layer showed familial relationships. According to their strontium isotope ratios, only a few individuals were likely to have spent their early childhood in a different geological environment, whilst the majority of individuals grew up locally. Carbon and nitrogen isotope analysis, which was undertaken to reconstruct the dietary habits, indicated that this was a homogeneous group with egalitarian access to food. Cereals and small ruminants were the principal sources of nutrition. These data fit in well with a lifestyle typical of sedentary farming populations in the Spanish Meseta during this period of the Neolithic.

While the nutritional part has some interest, it is ultimately not too conclusive (high protein diet, similar to that of Dordogne Neolithic, high incidence of caries, three individuals who may have been raised outside the "closely knit" community), so I will focus my attention on the mitochondrial lineages.

These are:

• U5b - 2
• U5b2b3 - 4
• U5b3 - 1*
• U4 - 1*
• V - 2
• K - 4
• K1a - 1
• K1a1 - 3
• X - 3
• T2b - 3
• T2a1b - 1*
• H3 - 1
• J - 1

The three individuals marked with an asterisk (*) might have been raised in other villages, two of them are adult men and the third one a teen-ager of unknown gender. While the possible immigration of men could suggest matrilocality, the reality is that most individuals buried whose gender could be discerned are men anyhow, and all the rest seem to share the same kind of diet (i.e. probably raised in the Alto del Reinoso community), so most unclear.

Notice also that, because of the limitations in haplogroup identification in ancient DNA, apparent "upstream" lineages such as U5b or K can perfectly be the same as "downstream" ones like U5b2b3 or K1a1 respectively. We just do not know for sure.

My preliminary diagnostic was that it looks a quite typical "mixed Neolithic" pool, much like the one of El Portalón in nearby Atapuerca, with dominance of "Neolithic" lineages (K, X, T, J - maybe also V and H3, not yet detected in Western hunter-gatherers) but also a high frequency of "Paleolithic" ones of the U typology (U5 and U4). It is almost absolutely "pre-modern", lacking the high frequencies (40-60%) of mtDNA H found today (and also found in the Neolithic of Paternabidea and Gurgy, in Navarre and Burgundy respectively) and therefore having great excess of both "Neolithic" and U frequencies.

It must be said that Northern Burgos is even today quite low in mtDNA H, with only 33% of this widespread lineage (half of it H3), being also unusually high (30%) in haplogroup U frequencies (ref.), but in any case the mtDNA pool is at the very least not standard for the wider geography and must have experienced some changes in the meantime therefore.

For that reason I considered comparing with the other nearby sites within this small Atapuerca-La Brújula mountain gates area that divides the Duero from the Ebro basins. The result (in percentages) is as follows:

Site	date (BCE)	n	U5	U4	H*	H1	H3	V	J	T2	X	K	U3
Reinoso	~3700	22	27	5	-	-	5	9	5	18	14	18	-
Portalón	~3000	7	29	-	-	-	29	-	14	-	14	14	-
Mirador	~2500	20	-	-	5	20	-	-	10	20	20	20	5

[Ref. links for El Portalón and El Mirador (both in Atapuerca)].


The three sites provide jointly a most interesting sequence for the district. I would say that Reinoso and Portalón seem quite similar, especially considering that the latter sample is very small, allowing for some random fluctuations (decrease in V and T2, increase in H3 and J). However in El Mirador, some 500 years later, we just cannot ignore that there are notable changes.

While the main "Neolithic" lineages (J, T, X, K) remain pretty much the same, all the rest is completely different: U5 (and its faithful sidekick U4) has vanished, has happens with H3 and V, instead we see a sudden outburst of H1 (and H*) and also the less impressive appearance of U3.

What does this mean? Let's go back to the modern mtDNA pool in Northern Burgos Province (n=24) as per Behar 2012:

• H1: 2 (8%)
• H3: 4 (17%)
• U: 8 (33%)
• K: 2 (8%)
• T: 2 (8%)
• J: 2 (8%)
• Singletons: H*, H4, V, L2

It seems to me that those ancient genetic pools are still very present: although there are greater frequencies of H and U than the average produced by merely admixing Reinoso and Mirador, the underlying typology that we can discern (within H most clearly) seems to conform to what those ancient populations already had. Instead the "Neolithic" lineages are less common.

Why?

My guess is that these ancient sites lay all in a key passage of a most strategic route, Spain's National Road 1, St. James' Way, Roman road Ab Asturica Burdigalam and surely much older trade and cultural routes went through that series of mountain passes. This may have attracted more immigrants from the Neolithic settler populations from the Mediterranean, who may have been surrounded by others of more "aboriginal" roots (mostly Paleolithic ascendancy) and rather low visibility for archaeologists.

It remains to be confirmed if Bell Beaker (associated with El Mirador site) may be directly blamed for the introduction of mtDNA H1 in the district. It is indeed possible but in any case the long term impact was limited.

It must also be understood that all this has very little to no relationship with what may have happened in the Basque Country, in spite of being not far away: the genetics involved, both ancient and modern, are quite different. It may be surprising how much the genetic pool can vary in just 200 Km but the rugged geography and diverse ecology seem to favor this kind of sharp distinctions. And, regardless of the causes and the surprise, it may cause, the data is there and is very clear.