I've seen quite a few comments on this blog suggesting that most of the Ancient North Eurasian (ANE) admixture found in Northern Europe today might come from Scandinavian hunter-gatherers like Motala12 and Ajvide58. It's probably obvious to most that this is not realistic, because the Scandinavian forager genomes sequenced to date show very high ratios of Western European Hunter-Gatherer (WHG) ancestry (>80%), so basically the math doesn't add up.
Nevertheless, I thought it might be useful to drive the point home using this Principal Component Analysis (PCA) based on my new West Eurasia K8 test. The datasheet is available here. You can view a spreadsheet of the results with extra samples here.
Please note that neither Motala12 nor Gokhem2, a late Neolithic farmer from south Sweden belonging to the Funnelbeaker culture, can pass for present-day Swedes. Moreover, mixing Gokhem2 with Motala12, in any proportions, will not produce a result even vaguely similar to present-day Swedes (ie. the outcome will fall somewhere along the dotted line).
I'd say one of the most obvious ways to get the right result would be to blend the Scandinavian forager and farmer with at least one other sample from somewhere below (ie. geographically speaking, east or southeast) of the Swedish cluster.
It might be possible to come up with a more precise plot location, and thus perhaps geographic origin, for this putative third source of Swedish ancestry by running some complex tests with the PCA datasheet. If anyone wants to have a go at that, and you actually manage to come up with a coherent outcome, then feel free to post your findings in the comments below.
I've decided not to bother, because as far as I can see, the options are infinite. What we really need are more genomes from the Swedish late Neolithic/early Bronze Age (LN/EBA), preferably belonging to one of the local spin-offs of the Corded Ware culture, which is thought to have originated in Eastern Europe, to provide more datapoints and help narrow down the options.
On a related note, I'm catching up on some reading this holiday season, and currently going through this book chapter which discusses the upheavals during the LN/EBA in south Scandinavia as seen through its archeology.
Rune Iversen, Beyond the Neolithic transition - the "de-Neolithisation" of south Scandinavia
See also...
Bell Beaker, Corded Ware, EHG and Yamnaya genomes in the fateful triangle
210 comments:
«Oldest ‹Older 201 – 210 of 210Matt, based on that triangle you've got, where would you put a Yamnaya dot that is 50/50 Armenian/EHG, and a Corded Ware dot that is 73% Yamnaya?
@Krefter
"The selection for the lactose persistent mutation is more surprising. People who barely admixed all suddenly were able to take in lactose after just a few hundred years before only a small minority couldn't."
on positive selection/amplification for light skin and lactase persistance in europe:
two factors:
1) milk retains higher lactose levels in cold placeswhere as it is cultured easily in warm climates.
2) preliminary studies correlate between light colored eyes and perceived pain during childbirth. pain tolerance is correlated with melatonin levels as well.
SLC24A5 is shared btw south asia and europe probably form a common middle east ancestor. It does not undergo the same positive selection in south asia.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912.
@ Chad
Why do you think there is Basal in Ust-Ishim? Aren't all indications otherwise?
@ David, not too sure where I'd place those populations in the triangle, sorry.
I was taking a look at the paper by Lazaridis et al. here:
http://arxiv.org/abs/1312.6639v2
And I noticed something quite new to me. I was looking at the table S14.9 (page 111 on the PDF) and then I looked above at figure S14.12 (page 110). This figure is a successful 3-way fit for French population, basically explaining that a population of pHunters (some kind of a nickname for PIE?? In any case, the population that spread ANE ancestry into Europe) that were made of 70% WHG ancestry and 30% ANE entered France, and they represented about 45% of the population (the other 55% being EEF, which in turn were 62% WHG and 38% Basal Eurasian/Near Easterners).
That's why on table S14.9 on the next page French are 55.4/31.1/13.5 EEF/WHG/ANE.
All good with France.
But then I checked the values for the successful 3 way fit of other populations and found the interesting thing: For Greece, these pHunters were 27.8% WHG and 72.2% ANE.
Ok, these probably means that when they entered Europe from the east they were much higher in ANE ancestry, but as they moved west they picked up more WHG admixture. Right?
Wrong. I checked Ukraine, expecting they would be 80%+ ANE (since from there they went to Greece), but found this: 72% WHG and 28% ANE. Then I checked Spain (where they should have arrived after France) and got this: 35.6% WHG, 64.4% ANE.
So the pattern (of picking up WHG ancestry and losing ANE one) didn't seem to go east to west, but clearly south to north. Confirmed by the values of Sicily and Malta, where those pHunters were 100% ANE and 0% WHG.
So using some storytelling abilities it looks like these pHunters (again, PIE??) first came by boat to the Mediterranean islands (Malta, Sicily) being 100% ANE, then moved to the southern parts of Europe (Greece, Spain, Italy) where they picked up some 20%-40% WHG. In Bulgaria they were already 50% WHG. In Hungary 60% WHG. By the time they arrived to Scotland, Norway or Lithuania they already reached 70%+ WHG and had less than 30% ANE left.
Ah, the exception as usual is Sardinia, an island that they first ignored but after arriving to the north of Europe they decided to go back and invade the island, though by then they were already 95.6% WHG and just had 4.4% ANE left.
Interesting tale, isn't it? The meaning of it I have no idea. Those are just the numbers extracted from that table in the paper (that somehow they managed to not put explicitly except for the French they used as an example). Note that those numbers are irrelevant of the EEF population and just refer to the "other" (3rd) population that came later and spread ANE throughout Europe.
Davidski, how did you make the graphs in that Ancient DNA youtube video you created?
http://bga101.blogspot.com/2014/11/short-clip-making-of-modern-europe.html
Alberto,
pHunter is something like proto-Hunter. There's also pFrench and pStuttgart on that Admixturegraph.
What they're trying to say, in a very simplified way, is that the data show that most Europeans descend from basically the same farmer and hunter populations via two main ancestral groups.
However, there's no guarantee that these ancestral groups were pure farmers and hunters. In fact, it looks quite certain now that one was EEF/WHG and the other EEF/WHG/ANE, and they started mixing during the Copper Age. The latter was probably PIE.
Krefter,
I'd have to write up a tutorial, and I can't be bothered right now. You'll probably need something like Adobe movie pro, or whatever that's called.
David, I guess they are TRYING to say that, but the numbers they got to fit their model are just... well, they make no sense.
Forcing those protoHunters to have anything between 100% ANE and 4% ANE to fit each population, and that cline going south to north is totally unrealistic, in my opinion.
Anyway, I think you're doing a great job trying to determine and isolate accurately the main 3 components in European populations, and I think it will be fruitful. It's not an easy task with the data available, but trying and trying you can get closer and closer.
The most difficult one at this point I think is the "3rd component" (that you are calling ANE). I still think it can be further refined. For example, some things that catch my eye:
- In the f3 statistics you made with ancient genomes to fit modern day populations (https://docs.google.com/spreadsheets/d/10gaCNMpadAjueogTKEthjYxfHXiTb5ILwYNXDjXr_hQ/edit?usp=sharing) I think that one clear conclusion is that the "3rd component" is lower in the South West than in the rest of Europe, which I think we all agree. However, in the similar stats from Laz et al. paper, one conclusion seems to be that the "3rd component" is higher in the South East of Europe (since populations from the Balkans and South Italy prefer MA-1/Stuttgart over Loschbour/Caucasus or Loschbourh/Iraqi_jew). If this is correct, it would leave a map with the "3rd component" being higher in the SE, lower in the SW and middle level in the North of Europe. Coincidentally, this profile matches the "West Asian" one (which is also related to this "3rd component"), while the ANE profile is higher in the North, lower in the South East and even lower in the South West.
- Also in those stats you made I guess you noticed something strange: Most populations prefer Stuttgart/MA-1 over Stuttgart/Loschbour. This is understandable since the first combination provides the 3 components needed, while the second provides only 2 of them (the "3rd component" is missing in both Stuttgart and Loschbour). However, most populations also prefer Stuttgart/Loschbour over Stuttgart/Motala12. Isn't this very strange when Motala12 is similar to Loschbour but with some ANE? The only explanation I can think of is that Motala12 does not really provide that "3rd component" either, so the difference with Loschbour is pretty small and for some reason Loschbour seem to match modern Europeans a little bit better. But if this is the case, wouldn't it mean that ANE is not EXACTLY that "3rd component" we're looking for? And again in this case the West Asian admixture gives us a better answer, because Motala12 has 0% West Asian admixture.
- Then there is the Fst distances between components. The "3rd component" should be closer to the HG than to the Basal Eurasian, but in your stats ANE is closer to Basal Eurasian. I know you said that Fst distances can be easily skewed, but still, and since we're not talking about individuals but about a components, I think they should match at least to some point the expectations. And in this case again in K7b test, the West Asian component has an Fst distance to Atlantic_Baltic which is half the distance it has to the Southern component.
So... am I saying that West Asian is a better fit for that "3rd component"? NO, not really. West Asian has its shortcomings too. For example, it scores way too high in Near Easterners. Lebanese score maybe 45% West Asian, while in reality I think they should have some 15% of the "3rd component". Also West Asian doesn't show at all in Amerindians, and I think that the "3rd component" should show in Amerindians (though I really think not as high as ANE shows, but rather in the ~15% range too).
Sorry for the long post. Just some thoughts about why I still think that ANE (as currently defined) is not totally accurate and could be further refined (but don't ask me how!).
Alberto,
There are no indications in any of the analyses that an ANE-like component peaks in southeastern Europe. In West Eurasia ANE most definitely peaks in the northeast Caucasus, followed by Northeastern Europe.
Southeastern Europe is different from other parts of Europe because it experienced significant post-Neolithic gene flow from West Asia, which means that a lot of the ANE there comes not from the Copper Age steppe, like in most of Europe, but from West Asia. Maybe that's what you're seeing in some of the data? But in any case there really never was a pure West Asian ancestral population; it's just a modern composite produced by Near Eastern farmers mixing with ANE and heavy genetic drift in the Caucasus. You can see that in the K8 results and the PCA.
As for the f3-stats, they're not easy to interpret. But the results make sense when cross checked with other data. For instance, it seems like the English get Loschbour/Iranian_Jew as their top f3-stat because Iranian Jews have less SSA than most other Near Easterners and less ANE than Caucasians. On the other hand, Northeast and East-Central Europeans, who are known to carry more ANE/EHG/Yamnaya ancestry, usually get Loschbour/Georgian as their top stat.
Also, keep in mind that the ancient genomes vary in coverage and the amount of markers they offer. It's likely that Loschbour/Stuttgart is a better option than Motala12/Stuttgart in my f3-stats simply because Motala12 is low coverage and doesn't offer as many markers as Loschbour. However, despite the fact that MA-1 is also low coverage and doesn't offer as many markers as Loschbour, it usually does better than Loschbour, and that's because it's a pure ANE sample. If Motala12 carried more than 16-19% ANE it would also do much better in these f3-stats.
"We don't have any Neolithic DNA from Lithuania yet, so there's not much point focusing on Lithuanians."
There are new finds in Lithuania however, which would be an excellent target for DNA testing. A unique find for the Baltic states was discovered this summer - burials of Neolithic herders, it is a first time that a man is found buried, along with other offering, with a skinned a cow (man is laying on his side, in a crunched “foetus” position). Similar burials were found in Belorussian and Polish territories but never in the Baltic states before. The carbon dating says the burial is of circa 4000 years old (one of ANE arrivals to the East Baltic territory?) The burial was found accidentally, the archaeologist are looking for private and other funding to continue with the excavation during the next year.
There earlier Mesolithic (circa 9000-8000 years before now) burials of hunter-gatherers are of different type (red ochre).
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