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.

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.

Ancient genomes of SE Asia

Just a quick mention because I have such a long queue of stuff from Europe that I really have no time to look but very shallowly onto this study, which looks extremely interesting. Credit for the reference to Kristiina.

Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter et al., Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia, BioRXiv (pre-pub) 2018. doi:10.1101/278374

Abstract

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

Obsidian exchange in Neolithic Sicily and Sardinia (video)

Thanks to Theasparagus for noticing this quite interesting video-lesson on quite obviously seagoing peoples of the Central Mediterranean and their journeys to distant volcanic islands to obtain the valuable obsidian (sharper than a scalpel) and also to the mainland to trade it for whatever goods.

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.

Happy 12,017

Yeah, 12,017. Why not? And I do mean the year that begins today per the Gregorian Calendar.

This is a surprisingly well thought idea that some prehistorianists (i.e. those who like Prehistory, regardless of wage-earning profession) have proposed: to get rid of the clearly uncomfortable Christian Era, alias Roman Era, alias Common or Conventional Era (CE) by adding 10,000 years to it and roughly starting counting at Göbekli Tepe (approx. date, because it's impossible to pinpoint an exact date, but the same happens with the alleged birth of baby Jesus anyhow), without doubt the first "civilizational" type of monument ever built, incidentally getting rid of negative counting for at least the whole Holocene (a most convenient feature indeed). 

They propose to call it the "Human Era" (HE), although I'd rather think that the Human Era begins with humans and that would be c. 200,000 years ago for Homo sapiens and two million years ago for the overall Homo genus, Humankind generally speaking. So maybe it's better to call it the Monumental Era, the Megalithic (big stone) Era or just the Mega-Era, for short. It'd be ME in any case.

The proposal, as far as I can tell, was made by Kurzgesagt, one of the YouTube channels that provide a good mix of entertainment and information for people interested in history and prehistory, young and elderly alike:

And I like it quite a bit, of course. So maybe worth spreading around, don't you think? 

In any case, I wish you all a happy and productive new year, one in which things may hopefully change for the better and not for the worse, for a change. 

And, like in every New Year Day, the holiday where most work is made, because of that floating notion that you are supposed to made up for all the laziness and procrastination of the past year, I will now proceed to assault my quite fatty "to do" list, and tell you about things that you may or not know already but that I think are worth taking note of.

Mitochondrial DNA from post-Neolithic Santimamiñe (Basque Country)

Four human remains dated to the Bronze Age were sequenced for mitochondrial DNA in Santimamiñe cave (Kortezubi, Biscay, Basque Country), along with single instances from the Neolithic, Chalcolithic and Roman period.

J.C. López Quintana et al., NUEVOS DATOS SOBRE LA SECUENCIA DE USO SEPULCRAL DE LA CUEVA DE SANTIMAMIÑE (KORTEZUBI, BIZKAIA). Arqueología y Prehistoria del Interior Peninsular (ARPI), 2016. Freely accessible (PDF) → LINK [no DOI]

The mtDNA study is not "brand new" but a synthesis of a previous doctoral thesis and advance publications:

Un primer avance de este estudio fue publicado en la monografía de las campañas de 2004 a 2006 de Santimamiñe (Cardoso et al. 2011), incluyendo el conjunto completo en la Tesis Doctoral de L. Palencia Madrid (Palencia 2015).

So we are talking of relatively old data, that has partly remained within the (sometimes absurdly greedy and anti-social) academic circles until now. The relative antiquity of the DNA study is important when assessing it, because genetic analysis is evolving very fast and, in most cases in the rather closed and under-budgeted Spanish universitary circles, they tend to do things "the old way", so we are almost certainly dealing here with HVS-I sequencing, something that is not explicit in the paper (I'm searching for Leire Palencia's thesis to make sure but no luck until now). 

If I am correct in this (and I should be), then we must understand that it is impossible in many cases to determine the exact haplogroup in the crucial R0 upper tier haplogroup, which includes HV and the extremely common H. Lacking the original HVS-I sequences by the moment, I can't but take the authors labels at face value but I must warn here that where it reads "R0" it is almost certainly H (HV0 or V are easy to recognize with this method, as is R0a) and where it reads "H1" it is probably H1 but not 100% certain. 

For more details see the relevant PhyloTree page, where the HVS-I markers are the last bloc in blue, beginning always with the sequence "16" (the other markers in blue of lower numerical value are HVS-II, more rarely used, and the ones in black are the coding region markers, which are in this case fundamental for proper assignment).

The mtDNA haplogroups (as reported) are:

• Neolithic:
• U5a2a (S2011-M2, c. 5100 BCE)
• Chalcolithic:
•  T2b (S-1, c. 2000 BCE)
• Bronze Age:
• U5b (S2011-M1 c. 1700 BCE) 
• H1 (S2011-M4, c. 1700 BCE)
• R0 (S2011-M6, c. 1500 BCE)
• U3a (S2011-M3 c. 1300 BCE)
• Roman period: 
• R0 (S2011-M5, c. 300 CE)

Interpretation attempts

It's difficult to extract conclusions from them but they should be compared with other sequences from the area, for which I recommend my 2013 synthesis. In general, treat "R0" as meaning "H", even if I chose to use a different color (magenta instead of red) for exactitude. 

In order to aid that analysis, I reproduce here my 2013 graphic:

We cannot compare the single Neolithic and Roman Era individuals but we can compare the Satimamiñe Chalcolithic+Bronze group of five sequences with the peripheral Chalcolithic large dataset of De La Rúa:

1. R*+H (very similar):
1. Peripheral "Basque" Chalcolithic: ~40%
2. Santimamiñe Chalcolithic+Bronze: 40% 
3. Santimamiñe Bronze only: 50%
2. U(xK) (very different):
1. Peripheral "Basque" Chalcolithic: ~15%
2. Santimamiñe Chalcolithic+Bronze: 40%
3. Santimamiñe Bronze only: 50%
3. Other lineages (all them of certain Neolithic immigrant origin, very different too):
1. Peripheral "Basque" Chalcolithic: ~45%
2. Santimamiñe Chalcolithic+Bronze: 20%
3. Santimamiñe Bronze only: 0%

However one of the U(xK) lineages in Santimamiñe is U3, which is also quite certain to be of Neolithic immigrant origin, and one is an important figure when n=5 so we can also see it this way:

1. Paleolithic lineages:
1. Peripheral "Basque" Chalcolithic: ~55%
2. Santimamiñe Chalcolithic+Bronze: 60%
3. Santimamiñe Bronze only: 75%
2. Neolithic lineages:
1. Peripheral "Basque" Chalcolithic:  ~45%
2. Santimamiñe Chalcolithic+Bronze: 40%
3. Santimamiñe Bronze only: 25%

The comparison of #1 with #2 is much more similar. This could be important, because Santimamiñe is not anymore a "peripheral" site, as are those from De La Rúa's dataset, but a rather central one with a extremely long and uninterrupted Paleolithic sequence, dating to Neanderthal-made Chatelperronian culture. It is still a single site with a small number of samples but it does provide a counterpoint that, in one approach could produce similar results. 

But, surprisingly, when we consider a distinct Bronze Age category, comparing not anymore with #2 but with #3 everything changes, suggesting a totally different interpretation of the available dataset, in which, the "Chalcolithic interlude" (if real at all, more data is needed) would be reversed quickly with the onset of the Bronze Age. 

I am sorry but I cannot lean for either interpretation: the data is just not extensive enough to allow for conclusions. I am tempted to support the continuity hypothesis, allowing only for lesser changes to happen, and keep the Chalcolithic dataset under a big question mark, but the question mark is admittedly a bit smaller now: something in terms demographic may have happened in the Chalcolithic period and may have been reversed in the Bronze Age. But "may" is not "for sure", we need more data points.

Feel free to discuss in good mood, as always.

Thanks for the heads up to Jean Lohizun (again).

Gobero (Green Sahara key site) documentary

This site of Gobero (Niger) was news in the archaeology and anthropology circles a few years ago and today I stumbled on this quite nice video documentary on it that I believe will be of interest for many readers:

All the Neolithic and Chalcolithic of Ireland in a single paper

This entry should be a "quickie" because I wouldn't even know where to begin in order to analyze this comprehensive synthesis and not at all because it is a lesser study, all the oposite. Just to say that the average reader of this blog will want to read it, much more if they are Irish.

However I think that the paper raises some interesting questions regarding the chronology of "modern genetic Irishness" and the arrival of the Y-DNA lineage R1b to the island, which I cast below for your insights.

T. Rowan McLaughling et al., The Changing Face of Neolithic and Bronze Age Ireland: A Big Data Approach to the Settlement and Burial Records. Journal of World Prehistory 2016. Open access → LINK [doi:10.1007/s10963-016-9093-0]

Abstract

This paper synthesizes and discusses the spatial and temporal patterns of archaeological sites in Ireland, spanning the Neolithic period and the Bronze Age transition (4300–1900 cal BC), in order to explore the timing and implications of the main changes that occurred in the archaeological record of that period. Large amounts of new data are sourced from unpublished developer-led excavations and combined with national archives, published excavations and online databases. Bayesian radiocarbon models and context- and sample-sensitive summed radiocarbon probabilities are used to examine the dataset. The study captures the scale and timing of the initial expansion of Early Neolithic settlement and the ensuing attenuation of all such activity—an apparent boom-and-bust cycle. The Late Neolithic and Chalcolithic periods are characterised by a resurgence and diversification of activity. Contextualisation and spatial analysis of radiocarbon data reveals finer-scale patterning than is usually possible with summed-probability approaches: the boom-and-bust models of prehistoric populations may, in fact, be a misinterpretation of more subtle demographic changes occurring at the same time as cultural change and attendant differences in the archaeological record.

The study should be very useful to anyone trying to understand the prehistory of Ireland, not the least because of its many maps and this extremely cool sequential maps video from pre-Neolithic times (5th millennium BCE) to the gates of the Bronze Age (early 2nd millennium BCE). Notice that in the Isles they tend to call "Bronze Age" to the Chalcolithic (Copper and Stone Age) and hence the title, which is a bit misleading.

An example of the very cool and highly informative maps and data you'll find in this study:

Fig. 3 - Map of Ireland showing Early Neolithic sites

 

Depopulation and resettlement? When?

An intriguing issue is the boom and bust cycles, particularly the almost total absence of signs of human activity around the end of the 4th millennium (3300-3000), suggesting maybe a depopulation after the first farmer colonization (?). There are clear booms around 4000, 3700, 3500, 2900, 2500 and since 2200 (Bell Beaker era). All this is something to chew about.

Particularly I'd raise the following question here: we know that a woman from c. 3400-3100 BCE (just at the depopulation gap?) was a typical Neolithic European, most similar to SE Spaniards and Sardinians, and that a man from c. 2200-1500 (Bell Beaker boom) was virtually identical to modern Irish and "British Celts" like Scots, Welsh and Cornish, carrying the common and controversial R1b patrilineage. 

The initial reading many of us made was that these new genetics may have arrived with Bell Beaker and that maybe Bell Beaker was more influential in terms demographic than we used to think, at least in Ireland. However, with this archaeological sequence on hand it seems at least reasonable to think that the major resettlement of an almost deserted Ireland happened after 3000 BCE but significantly earlier than the Bell Beaker phenomenon, which only reaches Northern Europe (Ireland included) c. 1500 BCE. What's your opinion?

Genetic prehistory of European bovine cattle

Quickies

Another study on European cattle, suggesting little to no admixture with aboriginal aurochs. However, as far as I can see, they did not directly compare with European aurochsen, so I'm rather skeptic, as their conclusions seem to derive only from modeling out of an incomplete dataset.

Amelie Scheu et al., The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genetics 2016. Open access → LINK [doi:10.1186/s12863-015-0203-2]

Abstract

Background

Cattle domestication started in the 9th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication.

Results

Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE.

Conclusions

The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers.

Figure 1

MDS Plot of d-loop sequences from 13 spatiotemporal groups of ancient domesticated cattle. The MDS plot is based on Reynolds’ F_ST. Numbers represent the age of samples in BCE per group; brackets contain the number of sequences per group.

Neolithic DNA from Southern Anatolia

I know, I know: I'm decaying into a total procrastinator. I don't have any excuse other than I don't feel like blogging as of late: neither on anthropology nor on politics. I rather feel like learning new stuff and playing, rather than writing and I lack of the structured environment to force myself to do otherwise than what I feel like most of the time. Being of compulsive temperament only worsens things.

I also know that this is not the proper way to start an article. Yes, I know. Do I even care?

So getting to mention now some of the stuff that I have not discussed in these last months and is definitely worth posting about. First of all this key study on more easterly Anatolian early farmers than those seen so far.

Intriguingly they are notoriously similar to those sequenced farther West (see here), what seems to support the model of Anatolian origin of European Neolithic peoples, largely ancestral to modern Europeans. However even Western Anatolian early farmers show already some extra admixture with the Paleoeuropean "WHG" component relative to their Southern Anatolian precursors. So, as the authors suggest, admixture between immigrant farmers and native foragers was a gradual and continuous process beginning in Asia Minor itself.

Gülşah Merve Kılınç, Ayça Omrak, Füsun Özer et al., The Demographic Development of the First Farmers in Anatolia. Current Biology 2016. Open access → LINK [doi:10.1016/j.cub.2016.07.057]

Summary

The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [ 1–3 ]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [ 4 ]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

Autosomal DNA

Maybe the most informative graph is this one (fig. 2):

Genetic Structure and Diversity of Central Anatolian Neolithic Populations
(A) PCA on contemporary west Eurasian populations onto which a total of 85 ancient individuals are projected from this study and previous studies. See Table S1 for number of SNPs per individual. Neighboring modern populations and ancient Anatolian populations are shown encircled. Modern population names are in italics.
Etc. (not so interested here in B, C and D, legend too long, check in the original paper)
Click to expand

It is interesting that, in spite of the Anatolian origin of this ancient ancestral population, they do not tend so much to modern Anatolian Turks but rather to Levant populations like Cypriots (closest ones), Lebanese, Palestinians, etc.

This is probably because, even if early Neolithic peoples of the Levant were not quite like them (see here again) they had become almost like them before the Bronze Age because of regional admixture, which I understand was mostly (but not only) north-to-south flow.

Notice that the Boncuklu (Bon) people had very low genetic diversity and they seem to be a dead end rather than directly ancestral. Instead, the Tepecik-Çiftilik (Tep) population seems a good proxy for the ancestors of Neolithic peoples of Western Anatolia and Europe. 

When we think about South Anatolia Neolithic, we usually think first and foremost about the famous Çatalhöyük site. Well, this ancient settlement is in the area of Boncuklu (to the West, both are near Konya) rather than that of Tepecik-Çiftilik (to the East, near Niğde), so it is quite possible that it is another demographic dead end, related but not directly ancestral to mainline European Neolithic. 

Personally I still think they could well have migrated at least partly by boat, along the southern Turkish coast but, until new data comes, I may need to alter my hypothesis of the ultimate origin being in the Northern Levant (Syria, Lebanon, Cyprus even) rather than Anatolia. These people of Tepecik-Çiftilik were, if not direct ancestors at least very closely related to the actual source population, which may well have lived closer to the coast in any case.

Mitochondrial DNA

The newly sequenced South Anatolian farmers had some of the lineages that were later present in Hungary's and Germany's "Danubian Neolithic", notably the now rare N1a1a1, found in 4/9 samples in this study. Also present were K1a (3/9, incl. one K1a12a), U3 (1/9) and N1a1b (1/9).

So it is time to dismiss the hypothesis that claimed N1a1a1 as a European aboriginal lineage: it came with the immigrant farmers and now there can be no doubt about it.

Ancient genomes from Neolithic West Asia

This week we got to know a lot more about the genetics of ancient West Asians, from the Mesolithic, Neolithic and later times. All in a single major study:

Iosif Lazaridis et al., The genetic structure of the world's first farmers. BioRxiv 2016. Freely accessible (pre-pub) → LINK [doi: http://dx.doi.org/10.1101/059311]

Abstract

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Highlights:

• There were (at least) two clearly distinct populations in West Asia in the Mesolithic and Early Neolithic times.
• Both populations contributed to the West Anatolian farmers that are precursors of the settlers of Neolithic Europe.
• The so-called "Basal Eurasian" component is not yet clarified if it is something local or admixture with Africans or both. However it is clear that it is associated with reduced Neanderthal admixture.
• West Eurasian genetic composition can be now understood quite well as the mixture from four sources: two West Asian ones, favored by the Neolithic revolution, and two Paleo-European ones.

This graphic shows pretty well how the ancient populations of West Eurasia are expressed as a mixture of those four founder populations:

That is if you can get through the nomenclature, which is inherited in many cases from a long array of recent studies. I'm not even sure myself in many cases what samples exactly and where from are thrown in each category. But the most important part is that Iran_N and Levant_N are the two Neolithic-specific founder populations of the Fertile Crescent (yeah, N stands for "Neolithic", not "North") and that the other two founder populations from pre-Neolithic Europe are WHG (Epi-Magdalenian peoples from Western and Central Europe) and EHG (Eastern European hunter-gatherers, of Epigravettian culture and maybe even proto-Uralic in one case).

Then we see in the case of Europe how:

1. Anatolia_N (precursors of mainline European Neolithic) are a mix of both West Asian farmer groups, plus a sizable fraction of Western Paleo-european ancestry already.

2. This fraction of Western Paleoeuropeanness increases as the farmers expanded into Europe (EN) and then as there was probably some backflow of Western origins in relation to Megalithism and Bell Beaker (MNChL). But in general remains the same basic genetic composition and in no known case incorporates any Eastern Paleoeuropean component at all, not yet.

3. It is only with the Indoeuropean ("Kurgan") invasions reflected in the category LNBA, when the EHG component begins feeling very important in Europe. If I'm correct, all those samples are from Germany other areas of Central and North Europe, with the Iberian and Italian ones of similar chronology placed in the MNChL tag instead. The LNBA/MNChL contrast is not a strictly chronological analysis but an analysis by categories of ancestry that do overlap in time.

4. In Armenia instead, we see a decrease of the minor EHG component but then an increase in the MLBA ("middle and late Bronze Age") when Armenians arrive from the Balcans and Phrygia, conquering the pre-existing Hurro-Urartean peoples (whose language was probably related to Chechen and other NE Caucasian languages), which should correspond to the formation of Urartu and more specifically to the Hayasa-Azzi and Shupria stages, both considered Urartean (Hurrian). The WHG and Levant-N components we see since the Chalcolithic is similar to what we see in West Anatolia and probably reflect interactions corresponding to Central-Eastern Anatolia, Kurdistan and Syria, for which we have no direct ancient data yet.

Ancient samples (colored and labeled) projected on a PCA of modern West Eurasian populations (in gray):

For a reference on which are the modern populations in gray, a good reference is this older but fully labeled PCA by Olalde.

Briefly: Natufians fall on top of modern Palestinians, their slightly admixed Neolithic descendants fall between Palestinians and Jews, Middle Neolithic European Farmers fall on top of Sardinians, the so-called Europe-Steppe continuum (early Western Indoeuropeans) fall between Central Europe, France and the Balcans, most Western Europeans do not overlap with ancient samples but appear to have even greater Paleoeuropean admixture instead, etc.

Y-DNA Haplogroups

Iranian Mesolithic and Neolithic samples carried the following patrilineages:

• Mesolithic: J(xJ2a1b3,J2b2a1a1)
• Ganj Dareh Neolithic: P1(xQ,R1b1a2,R1a1a1b1a1b,R1a1a1b1a3a,R1a1a1b2a2a) and an undefined CT
• Late Neolithic: G2a1(xG2a1a)

Meanwhile Palestinian Mesolithic and Neolithic samples carried: 

• Natufian (Mesolithic): E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), E1b1(xE1b1a1,E1b1b1b1), E1b1b1b2(xE1b1b1b2a,E1b1b1b2b), plus two undefined CT.
• Pre-Pottery Neolithic B/C: H2, E(xE2,E1a,E1b1a1a1c2c3b1,E1b1b1b1a1,E1b1b1b2b), E1b1b1, T(xT1a1,T1a2a), E1b1b1(xE1b1b1b1a1,E1b1b1a1b1,E1b1b1a1b2,E1b1b1b2a1c), plus three ill-defined CT.

CT is the main pan-Eurasian macro-haplogroup and is not informative, except in Palestine because it implies exclusion of E.

Otherwise we see an important presence of E (mostly E1b1b) a lineage we know was carried by early farmers into Europe and that has ultimately African origins. It probably indicates migration of NE Africans into Palestine in the Mesolithic, something also supported by Archaeology. However these NE Africans were surely already mixed with Eurasian ancestry, which probably arrived to the Nile Basin in the early LSA, some 50-40 Ka ago. So it's a complex story of multiple admixture events in the continental crossroads that is Egypt and also Palestine and other nearby areas.

We also see G2a1 in Late Neolithic Iran, and this one is the main lineage brought to Europe by the early farmers if we are to judge on known ancient sequences (today it is not more important that E1b but it is maybe more evenly distributed). However we only see it in the Late Neolithic, so it may have originated further west.

We see too little J, only J(xJ1a,J2a1,J2b) in Chalcolithic Iran and in Bronze Age Jordan: J(xJ1,J2a,J2b2a) again and J1(xJ1a). I guess that a lot remains to be researched on this issue because J is by far nowadays the most common haplogroup of West Asia, and also impacted Europe and South Asia (J2) and North and NE Africa (J1).

On the issue of "Basal Eurasian": African or West Asian?

The question remains unanswered, as I said before but there are two clues: on one side the presence of E1b in Mesolithic and Neolithic Palestine clearly supports a direct NE African influence, also backed by archaeological evidence. But there is some nuance in the issue of FST distances that I want to highlight.

The distances are available in a very extensive supplementary table, so I took just a few to get a better understanding, not only of this issue but in general of the genetic distances of the four founder populations:

Quite ironically it is not the Natufians who are the closest to the African reference population (Yoruba) but the CHG, Iran-N and Levant-N groups. In fact the Natufians are the most distant ones after the WHG population. However this is tricky because the affinity to Yoruba may also be caused by the "ghost" Basal Eurasian population, claimed first of all by Lazaridis 2014, which would be a remnant of the Out of Africa Migration (not strictly African but close enough and impossible to discern from true African admixture in most analyses).

So we may imagine that the "Highlander" (CHG and Iran-N) populations were somehow influenced by that Basal Eurasian ghostly population, which might have survived in the Persian Gulf oasis, for example. Or whatever else.

The presence of the same or similar element in Levant-N reflects possibly admixture with Iran-N or a similar population, something that is implicit in the table above but I'll address below more explicitly.

If there is (and there must be, because of Y-DNA E1b) some African admixture in the Natufian population, it was very diluted already in the autosomal (general DNA) aspect before farming began.

Update (Jul 2): all the four paragraphs above are possibly misleading to some extent because, as several commenters have rightfully pointed out, generic drift alone just causes the effect of increased distance to general reference populations like Yoruba and Han, this genetic drift is caused by relative isolation, so it seems that Magdalenian Europeans (WHG) and Natufian Palestinians (Natufian) were both more isolated populations in general terms than the Iran-Caucasus-Eastern Europe ones, whose sheer numbers apparently kept them more similar to the generic root of Humankind, less endogamous. 

However, per archaeology, such "sheer numbers" are not to be expected in that area, rather the opposite (Western Europe and Palestine are much more richer areas in terms archaeological, suggesting denser populations). So the question remains open as far as I can tell but it should be discerner with more precise tools than mere FST.

A visual of smallest genetic distances between (each "-" represents 0.01 in the table above):

a) Ancient West Asians:

CHG-----IrN-------LeN----Nat

Neolithic peoples of West Asia, even if different, are closer among them than their pre-Neolithic precursors.

b) Pre-Neolithic West Eurasians:

WHG--------EHG----------CHG--------------Nat

The distances between Natufians and everyone else are comparable to those with Han Chinese, however only in the case of the populations that appear to have extra affinity to East Asia (Iran, Caucasus and Eastern Europe), otherwise it is smaller.

All four populations were distant enough from each other to be considered clearly distinctive. Even EHG and WHG were quite dissimilar.

c) The four West Eurasian founders considered above:

WHG--------EHG----------IrN-------LeN

There is much greater similitude between Iran and Levant Neolithic peoples than between their Mesolithic precursors. This implies some sort of intense admixture as agriculture and herding developed. Not enough to erase the differences but enough to blur them significantly.

Genetic influence from East Asia or a related population is also apparent in all Northeastern populations but even more so in Iran Neolithic. Why?

There is much more in the study and supp. materials but I can only review so much.

Neolithic DNA from Greece and NW Anatolia and their influence on Europe

This is a most interesting study that brings to us potentially key information on the expansion of European Neolithic and the formation of modern European peoples.

Zuzana Hofmanová, Susanne Kreutzer et al., Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 2016. Open access → LINK [doi:10.1073/pnas.1523951113]

Abstract

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Uniparental DNA

One of the most important findings is that the two Epipaleolithic samples from Theopetra yielded mtDNA K1c, being the first time in which haplogroup K has been detected in pre-Neolithic Europe. Sadly enough these two individuals could not be sequenced for full genome. 

The other five individuals are all Neolithic (three early, two late) and did provide much more information.

• Rev5 (c. 6300 BCE): mtDNA X2b
• Bar31 (c. 6300 BCE): mtDNA X2m, Y-DNA G2a2b
• Bar8 (c. 6100 BCE): mtDNA K1a2
• Pal7 (c. 4400 BCE): mtDNA J1c1
• Klei10 (c. 4100 BCE): mtDNA K1a2, Y-DNA G2a2a1b (same as Ötzi's)

I color coded their abbreviated names according to the usage in the study's many maps, for easier reference: green shades are for Greece (Western Macedonia), red shades for Turkey (Bursa district). It is also very convenient to get straight their real geography because many of the map-styled graphs are not precise at all about that:

Fig. 1.

North Aegean archaeological sites investigated in Turkey and Greece.

Autosomal DNA affinities

This is probably the most interesting part. There is a lot about it in the supplementary information appendix but I find that the really central issue is how they relate to each other (or not) and to other ancient and modern Europeans. I reorganized figs S21 and S22 to better visualize this:

Ancient samples compared to each other and other ancient samples ("inferred proportions of ancestry")

Ancient samples compared to modern Europeans ("inferred proportions of ancestry")

So what do we see here? First of all that the strongest contribution of known Aegean Neolithic peoples on mainline European Neolithic is from Bar31, which is from NW Anatolia, and not from Greece. Bar8 is a less important contributor but may have impacted particularly around the Alps (Stuttgart-LBK, modern North Italians).

This goes against most archaeology-based interpretations, which rather strongly suggest a Thessalian and West Macedonian origin of the Balcanic and, therefore, other European branches of the mainline Neolithic of Aegean roots, and do instead support some sort of cultural barrier near the European reaches of the Marmara Sea. Of course we lack exhaustive sampling of Greek Neolithic so far, so it might be still possible that other populations from Thessaly or Epirus could have been more important. However the lack of Anatolian-like influence on the Western Macedonian Neolithic until c. 4100 BCE, makes it quite unlikely.

So it seems that, once again, new archaeogenetic information forces us to rethink the interpretative theories based on other data.

However we do see a strong influence of Greek Neolithic and particularly the oldest sample, Rev5, in SW Europe, very especially among Basques, who seem to have only very minor Anatolian Neolithic ancestry, unlike everyone else relevant here. This impact is also apparent in Sardinia and to some extent North Italy (but overshadowed in these two cases by the one from Anatolia, particularly Bar31).

There are also similar analyses for other four ancient samples (Lochsbour, Stuttgart, Hungary Neolithic and Hungary Bronze) but they don't provide truly new information, so I'm skipping them here. As I said before, there's a hoard of analyses in the SI appendix, enjoy yourselves browsing through them and feel free to note in the comments anything you believe important.

A synthesis of the various "inferred proportions of ancestry" analyses is anyhow shown in fig. 3:

Fig. 3. (click to expand)

Inferred mixture coefficients when forming each modern (small pies) and ancient (large pies, enclosed by borders matching key at left) group as a mixture of the modern-day Yoruba from Africa and the ancient samples shown in the key at left.

The fractions may be misleading however, especially for the ancients. For example: Lochsbour (a total outlier among the ancients in this study) appears best correlated with Pal7 but in fig. S24 it is clear that does no correlate with any Neolithic sample at any significant level. But in general terms it can give a good idea of where does ancestry, particularly for modern samples, come from.

Note: elsewhere someone was being a crybaby about the Polish sample (may well be an error) or the Kalmyk sample (who are obviously most related to East Asians, not used here) but those are minor issues.

Of course there's a lot more to learn from the remains of the ancients. Let's keep up the good work.