I extracted the following number of SNPs from the different individuals, that were in common with my main HGDP reference:
- 15,734 SNPs: Gok4 (TRB / farmer)
- 15,385 SNPs: Ajv52 (PWC / hunter-gatherer)
- 25,108 SNPs: Ajv70 (PWC / hunter-gatherer)
K7b and K12b are based on a set of 166,770 SNPs, so I intersected the SNPs of the ancient individuals with them, resulting in:
- 4,054 SNPs: Gok4
- 4,077 SNPs: Ajv52
- 6,631 SNPs: Ajv70
A problem with comparing against extant populations, rather than ancestral components is that relationships are averaged: for example, Turks in Skoglund et al. appear quite distant to both Neolithic groups, but we cannot know to what extent this is due to their small levels of central/east Eurasian ancestry and to what extent this is due to their native Anatolian ancestry.
We now have two ancient autosomal DNA sampling locations, and both turned up unexpected results. The Iceman, a Copper Age inhabitant of the Alps resembled modern Sardinians. A Megalithic Swedish farmer resembled Southern Europeans, while his hunter-gatherer contemporaries were outside the range of modern variation. These results should give us caution about the identity of past populations elsewhere.
As I have argued elsewhere, the past seems to have been much more dynamic than many had suspected, and the people that walked and rowed to the ends of the Earth during the Upper Paleolithic did not suddenly grow fetters or decided to stay put during the Neolithic as many "Paleolithic continuity" adepts had proposed.
A couple more caveats:
- Irrespective of their actual origin, these individuals would still be inferred to be some admixture of the ancestral components adding up to 100%. This hints at their affiliations, but does not -in itself- supply evidence of their absolute proximity to the ancestral components.
- As more and more ancient individuals are sampled, we will be able to generate genuine ancient populations that are ancestral to modern ones. When that happens, we can directly test modern individuals against panels of ancient ones. For the time being, we have to make do with the reverse, i.e., test ancient individuals against panels of modern ones.
RESULTS
In all comparisons with other K7b results, you should take into account the much smaller number of SNPs used on the Neolithic remains from Sweden.
The K7b results are below. Consult the spreadsheet for comparative values in modern populations.
The K12b results are below. Consult the spreadsheet for comparative values in modern populations.
The raw percentages can be seen below; I have also added the results previously calculated for Oetzi, the Tyrolean Iceman:
DISCUSSION
The results for the two hunter-gatherer samples are as expected predominantly "Atlantic_Baltic" at K=7 and "North_European" at K=12. Since these two samples are outside modern variation, it is expected that their mapping may have added noise; see this post about the dangers lurking at the edges of variation.
Nonetheless, the results can be interpreted as reflecting the fact that the "Atlantic_Baltic" and "North_European" components partially reflect the pre-farming population of Europe. At K=12 it is noteworthy that there is a minor "Atlantic_Mediterranean" admixture in the two hunter-gatherer samples. In my opinion, this may reflect either some level of admixture with the incoming farmers and/or the pre-farming component (but of Western European rather than Baltic type) that may also exist in these foragers. On balance, however, the "North_European" component far outweighs the "Atlantic_Mediterranean" one, which is also consistent with their location (Gotland) which ties them to the Baltic rather than Atlantic Europe.
The farmer sample is remarkable in that, like the Tyrolean Iceman, she seems to be made up entirely of "Atlantic_Baltic" and "Southern" at K=7. There is a hint that the order of the two components are reversed in Gok4 relative to Oetzi, which probably makes sense. The third major West Eurasian component at this level of resolution, the "West Asian" one is conspicuously absent. This component -bimodal in the Caucasus and Balochistan, and strongly represented in the highlands of West Asia in between the two- does occur at ~10% in modern Northern Europeans, so its absence in all Neolithic samples so far hints at its later introduction into at least parts of Europe.
The result at K=12 is fascinating, since Gok4 turns out to be 81% "Atlantic_Mediterranean", and, like Oetzi, with a noticeable "Southwest_Asian" strain. The "Atlantic_Mediterranean" component is bimodal in modern Sardinians and Basques, while the "Southwest_Asian" radiates from southern parts of the Near East into Mediterranean Europe.
Gok4 appears to be "even more Atlantic_Mediterranean" than any modern population. As I mention in the original post, the inhabitants of megalithic monuments of North-Western Europe were believed by Coon to belong to a "Long Barrow type" which he considered ancestral to the modern "Atlanto-Mediterranean" type. Here is his description:
Toward the end of the Neolithic period, the western Mediterranean countries were invaded by seafarers of a tall, exceptionally long-headed Mediterranean variety; some of these invaders passed through the Straits of Gibraltar, whence they also invaded the British Isles and Scandinavia.I would say that the evidence is not incompatible with this scenario. We must probably wait to see whether Gok4 was descended from seafarers from the eastern Mediterranean (where the "Southern" component is modal), following the Mediterranean and then Atlantic coasts up to Scandinavia, or whether they are descended from a different group of people who followed the plains and river valleys of the Balkans and Central Europe and arrived to the north via the inland route. The strong Atlantic_Mediterranean result, coupled with high levels of allele sharing in Cyprus, Greece, France, and the Netherlands, but not particularly in the northern Balkans leads me to prefer the maritime colonization scenario, at least for now. Ancient DNA from more European regions will hopefully help us better understand "what really happened in prehistory."
42 comments:
Dienekes,do you know to what Y-DNA the 2 hunter gatherers and the farmer are belonging to ?
The Sub-Saharan admixture in Avj52 is remarkable. And even more remarkable is its absence in Gok4.
Dienekes,do you know to what Y-DNA the 2 hunter gatherers and the farmer are belonging to ?
Ajv70 is the only one listed as male, and no Y chromosome data were reported in the paper.
The Sub-Saharan admixture in Avj52 is remarkable. And even more remarkable is its absence in Gok4.
I doubt that's real, probably an artefact.
From the data, it appears that we are looking at the synthesis of the 2 primary components in modern Europe - Mediterranean and North Euro, at the expense of SW Asian, which seemed to be absent in the north European mates, which is why it is so rare here today. It also explains why populations of Scandinavia have retained low levels of the SW Asian component as through lower immigration and some bottlenecking
Looks like some of the theories surrounding the spread of megalithic culture are probably true.
Some east Med exchanges and a west Med trip around the Atlantic seaboard.
http://i-m26.blogspot.com/
@ AWood
How do you explain Basques who are high in mediterranen but have 0% Southwest- Asian.
Dienekes do you think then that the ''North European'' ancestral component is made up of mostly old Mesolithic North European alleles?
Nice analysis. We really need some HG DNA from the Mediterranean region (preferably west) to better understand how much of that is possibly absorbed in the Atlantic_Med component (vs. early SE agriculturalists).
Thinking a bit more how little admixture with northerners she has, I now also tend to believe she is a recent newcomer, perhaps coming (rather late, though) with the people who brought Megalithism to TRB. Human nature tells me that people in close proximity mix more over 1,000 or more years than indicated, here (let alone the millennia before, during LBK).
Unfortunately, just a single data point.
Hm.
Are those H/G more like Fins before they admixed with Sibirians or like Balts before the advent of the Caucasus element?
One of them even has enough AntMed to be Polish minus Caucasus.
"How do you explain Basques who are high in Mediterranean but have 0% Southwest- Asian."
The Mediterranean and Southwest Asian clusters are very closely related. The main difference between them is that Southwest Asian has some sort of East African influence.
So what ADMIXTURE seems to be doing with Basques, is lumping all the Southwest Asian alleles into the Mediterranean cluster.
Maybe Southwest Asian is Mediterranean modified by more recent East African admixture, and Basques + Neolithic Mediterranean farmers come from a population that left the Middle East before this happened?
In any case, it's really important to note that having 0% of a component, need not mean no admixture from the part of the world where that component peaks.
Are those H/G more like Fins before they admixed with Sibirians or like Balts before the advent of the Caucasus element?
Fanty,
I think they are a bit remote from original Scandinavian HGs (who, in my opinion, are still partially represented today in central Swedes and Norwegians). Yes, they are closer probably to Finns (one even has a bit of Asian admixture), but probably closest to HGs from the mid-to-semi-northern region of Belorussia and Russia all the way close to the Urals - before much Uralic and much Asian admixture, nor West Asian/ Caucasian admixture.
A few questions:
How much do you think this affects your "womb of nations" theory, having seen these samples and how they fit into your cluster analysis?
Also, does this change your opinions on the divergence time analysis between clusters which you've found?
Do you think a treemix analysis including these samples would be viable or useful?
Not pushing you for answers at all, maybe the samples not even rich enough in SNPs to begin considering any of these.
How much do you think this affects your "womb of nations" theory, having seen these samples and how they fit into your cluster analysis?
I'd say they are compatible with it, since the "womb of nations" theory suggests that Europeans did not adopt farming but received population influxes from the Near East.
Also, does this change your opinions on the divergence time analysis between clusters which you've found?
Not particularly, the divergence times in the paper appear to be quite low overall, which is consistent with recent shared ancestry.
Do you think a treemix analysis including these samples would be viable or useful?
It wouldn't be too useful because the data is so limited and most of it is haploid, i.e., only one allele was called per locus. So, it makes very little sense to speak about allele frequencies.
This story has already been published on the web site of one of Greece's most infuential newspapers:
http://www.tovima.gr/science/technology-planet/article/?aid=455152&h1=true
I am really dying to see a forensic facial reconstruction of the Farmer individual. Let's hope that some sort of a miracle will happen, and we will get to see how she looked like.
"I think they are a bit remote from original Scandinavian HGs (who, in my opinion, are still partially represented today in central Swedes and Norwegians). Yes, they are closer probably to Finns (one even has a bit of Asian admixture), but probably closest to HGs from the mid-to-semi-northern region of Belorussia and Russia all the way close to the Urals - before much Uralic and much Asian admixture, nor West Asian/ Caucasian admixture."
The best sampled hunter-gatherer, Ajv70, is closest to Poles, Swedes, and other continental North-Central-Eastern Europeans.
The only reason these hunter-gatherers came out closest to Finns in some comparisons, is because other key samples weren't included. Also, the HGs lack what current North-Central Europeans have at around 10%, which is admixture from the southeast somewhere, probably Anatolia or Caucasus.
So they're most similar to Finns in a broad sense, but most alike to other North-Central Europeans in a more meaningful sense, which shows up in the PCAs in the original study, as well as in the allele sharing table.
There's no evidence anywhere to suggest these hunter-gatherers were especially close to who was living in modern Belorussia or Russia at the time. I won't even mention the Urals.
We don't know who was living there. But ancient mtDNA suggests they might have been significantly Siberian/East Asian.
On the other hand, other ancient mtDNA data suggest that these hunter-gatherers might have been very similar to HGs in Western Europe, including even Iberia.
Hey Dienekes, is there any way you can run a PCA of Ajv70 against samples from across Northern Europe, and not just cherry picked ones like Skoglund did, using all available 25,000 SNPs?
And then one with the Finns removed, and only the North Euros included with at least a few percent of West Asian admix.
How about also using STRUCTURE instead of ADMIXTURE? He might make his own cluster, if he's so out of range of modern variation?
I found that ADMIXTURE is hopeless with less than 40,000 markers, but STRUCTURE works quite well even with 10,000.
@Davidski
There are plenty of runs from you or Dodecad in which the Fst tables shows the Mediterranean closer to Balto-Slavic or North-Euro than to Southwest-Asian. Also how do you explain the Mediterranean position here :
http://2.bp.blogspot.com/-7x7WY7OHUSk/TqAHTw3UP0I/AAAAAAAAAnI/gDCnw1IVyEk/s1600/plink.png
^ What does that have to do with anything?
The Mediterranean Neolithic groups most likely came from Cyprus, and probably the Levant before that.
Their cluster comes off the same phylogenetic tree as the Southwest Asian.
But the Mediterranean cluster now includes European alleles, while the Southwest Asian cluster includes East African alleles.
That won't change. It'll only become clearer.
And I bet you that when Iberian hunter-gatherers are genotyped, they'll be closer overall to modern Balts and Finns than to Iberians.
"Maybe Southwest Asian is Mediterranean modified by more recent East African admixture, and Basques + Neolithic Mediterranean farmers come from a population that left the Middle East before this happened?"
Thats what this tree building software suggested.
Technically it (that tree thingy) said:
1. Northern European leaved Caucasian womb. All other recieve East African.
2. Indians leave the womb. All others recieve more East African.
3. Caucasus leaves the womb, all others recieve once again more East African.
4. Finaly, Atlanto Mediteranean leaves the womb and the remaining (SW Asian) again recieves more East African.
So, it seemed to simply tie it to various degrees of East African admixture.
"There are plenty of runs from you or Dodecad in which the Fst tables shows the Mediterranean closer to Balto-Slavic or North-Euro than to Southwest-Asian."
Thats explained with the tree software aswell. It claimed, in the last thing was, that Northeuro absorbed AtlantoMed. This would make these 2 components closer again.
"I am really dying to see a forensic facial reconstruction of the Farmer individual. Let's hope that some sort of a miracle will happen, and we will get to see how she looked like."
I am kind of disapointed with facial reconstruction.
It only works kind of well, if the reconstructor assumes the right ethnicy.
I recall US-American forensics once reconstructed a face of a child as a "White boy" and no one missed this child. But someone missed a native American girl. One Forensic gave the skull a second try and reconstructed it in a way, how it must be done for such and bingo, it resembled her.
I am sure, 2 years ago she would have been reconstructed looking like a Swede. Now, she will come out, looking like a Spaniard or something. ;-)
Just look at various reconstructions of Oetzi. All forensic artists used the same skull for basic material, but in some he looks northern European and in some southern.
Dienekes
I studied your K12 spreadsheet and there is one thing I find difficult to explain, namely the distribution of the Gedrosia component in Europe.
I know that these are not ancestral populations, but somewhat virtual reference points of the model that should be interpreted carefully. Still the Gedrosian component must have eastern origin in Europe.
However what I can see here that the peak of the Gedorosian component is in northwest Europe, particularly in Irish/British population, after that Dutch, French, Basque, but even the Norwegian and Swedish show a consistent higher Gedrosian affinity that the whole Mediterranean region (included Cypriots). In central Europe and north Balkan the Gedrosian affinity even seems to spread from west to east.
What is the possible explanation for that?
Now Gok4 does not show any Gedrosian affinity unlike the modern local population and that is interesting too, since I do not know any migration later that could bring this component there. The IE migration is surely not.
And just a small footnote to Sardinians and Basques: because both populations are a bit off of the current European groups, there are people who contact them. However K12 shows them drastically different, components that are strong in one completely missing from another. OK, this type of analysis should be carefully handled for kinship determination as you told earlier, but these differences are big.
Now Gok4 does not show any Gedrosian affinity unlike the modern local population and that is interesting too, since I do not know any migration later that could bring this component there. The IE migration is surely not.
I think archaeologists need to play catch up with the new lines of genetic evidence. For example, the main Y-chromosome lineage in modern Europe as a whole is R1 and this is lacking in three of the earliest sampling sites (Treilles, Oetzi, LBK) that form a triangle encompassing a quite big chunk of Europe.
I would say that current archaeological models cannot really know what to do with this finding. Most archaeologists would never have anticipated that as recently as 5,000 years ago the main lineage in modern Europeans was absent from Western/Central Europe.
So, there must have been events that have been under-appreciated by existing models.
Also, I'm not sure why you don't think the Indo-Europeanization of Europe could have been involved in the differentiation of modern Atlantic Europeans vis a vis these Neolithic people; after all, IE languages arrived late to Atlantic Europe (only Celtic is really "native" there, and that is an Iron or at most Bronze Age phenomenon)
However K12 shows them drastically different, components that are strong in one completely missing from another.
Yes, they are quite different from each other. The possession of a common ancestral component to a high degree is not incompatible with a large degree of differentiation, because differentiation is caused by the elements that are _not_ shared in common.
For example, in Skoglund et al. (2012), Sardinians are much more Gok4-related than Basques (95.3% vs. 65%), and the remainder in Basques. This 30% difference is surely related to the "Southern"/"Atlantic_Baltic" difference between these two populations, which is about 20% and which becomes ~34% if one uses the relationship between Gok4-related ancestry and K7b (http://dodecad.blogspot.com/2012/04/estimating-your-gok4-related-ancestry.html).
So, I'd say the Skoglund et al. model is concordant with the Dodecad one.
Dienekes
First, thank you for your answers.
I must explain my words about the IE influence.
"Also, I'm not sure why you don't think the Indo-Europeanization of Europe could have been involved in the differentiation of modern Atlantic Europeans vis a vis these Neolithic people; after all, IE languages arrived late to Atlantic Europe (only Celtic is really "native" there, and that is an Iron or at most Bronze Age phenomenon)"
I do think that Indo-Europeanization had a big role. What I do not think that specifically the Gedrosian compoent in Skandinavia can be explaied by this. And I do not think that, because this component is completely absent from some close regions influenced by IE (Polish, Ukrainan, Russian, Baltic).
Unless we assume that IE people where already (or from the beginning) diverged to genetically different subgroups, which is not impossible, but I do not think so.
Unless we assume that IE people where already (or from the beginning) diverged to genetically different subgroups, which is not impossible, but I do not think so.
They almost certainly were. Opinions differ as to the time depth of Indo-European, but most people would agree that by 5,000, PIE had already broken down. By the Bronze Age we can very reasonably hypothesize that Indo-European related languages were spoken by people of very different genetic background. So, I don't think it's a stretch to exclude that the "Gedrosia" component was IE-related because it is present mostly in W Europe and not E Europe.
Actually, no modern population is actually descended only from the Proto-Indo-Europeans. But, they were IMO a population that is related to the K7b "West_Asian" and K12b "Caucasus"/"Gedrosia" components and this legacy was progressively watered down as the IE "package" was passed on, just as it was in historical times (e.g., so many non-Romans adopting the Roman "package" or non-Slavs adopting the Slavic one).
Actually, no modern population is actually descended only from the Proto-Indo-Europeans. But, they were IMO a population that is related to the K7b "West_Asian" and K12b "Caucasus"/"Gedrosia" components and this legacy was progressively watered down as the IE "package" was passed on, just as it was in historical times (e.g., so many non-Romans adopting the Roman "package" or non-Slavs adopting the Slavic one).
My problem, that there is absolutely no correlation between the Gedrosia and the Caucasus components in NW Europe. This tell me that this two components where brought here by two different migrations. Also the Gedrosian component is the strongest in the aeras that were reached by IE migration last, which is not really consistent with the gradual dilution (watering down) of the IE legacy.
The Caucasian component in NW Europe very likely from IE (consistent with "watering down", because Irish and Norwegian have the lowest level), but the Gedrosian compoent must have a different suorce.
> I'd say they are compatible with it, since the "womb of nations" theory suggests that Europeans did not adopt farming but received population influxes from the Near East.
But they didn't leave munch of a genetic impact in the north. The north Europeans (maybe more so for k = 12 "north European") seem to mostly be pre neolithic European. Wasn't your theory that they would largely be neolithic, or later, West Asian?
But they didn't leave munch of a genetic impact in the north. The north Europeans (maybe more so for k = 12 "north European") seem to mostly be pre neolithic European. Wasn't your theory that they would largely be neolithic, or later, West Asian?
Incorrect, they do not seem to be "mostly pre neolithic European". As I've said countless times, the K=12 "North European" component is not equivalent to a pre Neolithic European component.
The 8.6% Southwest Asian component at K12b for Gok4 and the 7.6% Southwest Asian component for Oetzi are interesting because in modern central and northern European populations this component is small or absent. If Gok4 is typical of Mediterranean-derived farmers responsible for the highly significant Atlantic_Med component amongst northern and southern West Europeans through the Megalithic cultural complex then what happened to the Southwest Asian component in the populations?
If the people were closest to Greeks and Cypriots why can we not safely say the Aegean sphere, and have to keep reaching into the East? I saw a NOVA not long ago about uncovering (maybe in submerged coast?) a large city in Greece way before it was thought there was mainland development beyond villages. Like Eurologist said in another post:
"if these people originated in Anatolia, wouldn't it be strange that they managed to conquer most of Europe, but are no longer present in Anatolia?"
The amount of similarity to Turkey they did find seems enough to explain some seeding first to islands, then eventually a rugged mainland, that were already populated and would only have so much extra room for new people - who would have likely been previous trading partners anyhow, so it wouldn't be like trekking around "leap frogging" turning a blind eye to strangers. I can believe gradually spreading the march of farming gradually over contiguous land but to cross ocean to wage war to kick people out to farm seems far fetched at that time period.
So they're most similar to Finns in a broad sense, but most alike to other North-Central Europeans in a more meaningful sense, which shows up in the PCAs in the original study, as well as in the allele sharing table.
There's no evidence anywhere to suggest these hunter-gatherers were especially close to who was living in modern Belorussia or Russia at the time. I won't even mention the Urals.
Davidski,
You cannot compare to a small set of extant populations and conclude an origin from that. However, what we do know is that Scandinavia (and mostly the SE of it) was at the absolute margin of PWC, which had its center and origin somewhere in Belarus or Russia, and was intrusive in the West. In other words, following the archaeological record, that's where these people came from. There is no local HG continuity.
If Gok4 is typical of Mediterranean-derived farmers responsible for the highly significant Atlantic_Med component amongst northern and southern West Europeans through the Megalithic cultural complex then what happened to the Southwest Asian component in the populations?
Amanda S,
I think that's another reason to believe she was not typical of the local (ultimately LBK-derived) farmers, but a recent immigrant from Atlantic Megalithism.
Well we will see, once more people are tested.
Since 2 years they only test "untypical" ancient peoples DNA. At least if it comes to the comments on it.
Such bad luck. They never seem to pick anyone typical. ;-D
truth: My hypothesis would be that Basque are in fact a young population. We knew this already though because they are not ripe from the stone age due to their indigenous words for metals and local equestrian skills. That said, northern Europe had 0% SW Asian, and it looks like the Mediterraneans bred heavily with the northern people. This could ultimately reduce their scores to next to nil of all other components in the long run - let's say a few thousand years. Basque are about 60% Mediterranean, 40% North.
"I bet you that when Iberian hunter-gatherers are genotyped, they'll be closer overall to modern Balts and Finns than to Iberians."
Maybe the Franco-Cantabrians will, but I'm not so sure about the Mesolithic shell-middens of the Tagus valley in Portugal, the Muge men. They are described as being Sub-Saharan looking, short like African pygmies, resembling a proto-Etiopic Homo aurignacensis type.
Surely there are more Mesolithic genetic substructures to enveil...
"The Sub-Saharan admixture in Avj52 is remarkable. And even more remarkable is its absence in Gok4.
I doubt that's real, probably an artefact."
You should've included American Indians for comparison. At K12 you have a Siberian component in Ajv70.
"I saw a NOVA not long ago about uncovering (maybe in submerged coast?) a large city in Greece way before it was thought there was mainland development beyond villages."
There are quite a few of these underwater archaeological remains across the world. For example, the Yonaguni formations in Japan, reports of submerged cities off the coast of India, plus reports of a submerged city off the coast of Cuba near Pinar del Rio, and of course, the well-known formation called Bimini Road in the Bahamas. Some of the dating for these items place their construction closer to the end of the latest Ice Age, which of course would clash with the current scientific consensus about the lower cultural and technological levels fo "stone age" humans.
Yonaguni is a geological formation. The Pavlopetri site is a real Bronze Age submerged city.
http://dienekes.blogspot.com/2011/10/pavlopetri-4000-year-old-underwater.html
Pavlopetri yes!
> Incorrect, they do not seem to be "mostly pre neolithic European". As I've said countless times, the K=12 "North European" component is not equivalent to a pre Neolithic European component.
In map A the Russians and the Finnish are closer to the neo h/g's then they are to the Adygei, the neo farmer, or any combination of the latter two. (Actually that farmer is admixed herself...)
So basically, their closer to the h/g's than the farmers and non European areas of today, which strongly indicates more than half their heritage is from h/g Europe.
Additionally, in map B the Northern Europeans are far closer to the neo h/g's than the farmer, the Greeks, and the Turkish.
"Yonaguni is a geological formation." My background is not in the physical sciences, but I find it vey hard to believe that nature alone could have produced the quantity of straight lines and right angles in the rock formations at that site.
Modern gotlanders deviate from other Swedes in a Baltic direction too. Apparently ever since the stone age.
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