Ancient DNA from Hungary-Christine Gamba et al

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Thanks to Dienekes for posting the study. Christine Gamba et al:

Genome flux and stasis in a five millennium transect of European prehistory:

This is the link to the study:
http://www.nature.com/ncomms/2014/141021/ncomms6257/full/ncomms6257.html

This is the direct link to the Dienekes thread:
http://dienekes.blogspot.com/2014/10/ancient-dna-from-ancient-inhabitants-of.html

Abstract:

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.

Y DNA: ( A total surprise for me...)
Individual KO1, E. Neol Körös (5,650–5,780 BC) = Y-Haplogroup I2a
Individual NE5, M. Neol. Late ALP (4,990–5,210 BC) = Y-Haplogroup C6
Individual NE6, M. Neol. LBK Culture (4,950–5,300 BC) = Y-Haplogroup C6
Individual NE7, L. Neol. Lengyel Culture (4,360–4,490 BC) = Y-Haplogroup I2a
Individual BR2, L. Bronze, Kyjatice Culture (1,110–1,270 BC) = Y-Haplogroup J2a1
Individual IR1, Iron Age, Pre-Scythian Mezőcsát Culture (830–980 BC) = Y-Haplogroup N

Still no R1b anywhere.

J2a has finally made an appearance, and it's in a Bronze Age context.

First comment on Dienekes:
The oldest neolithic sample KO1 is a dark haired blue eyed man with I2a and "Armenian" mDNA R3.

I'm not going to say another word until I read the entire paper twice! However, that "Armenian" comment is interesting in light of the tweets from Razib Khan (thanks to him) about the new Lazaridis paper saying that Yamnaya can be modeled as 50% Karelian / 50% "Armenian".


 
Last edited by a moderator:
The first ancient sample to have fair hair and fair eyes is Neolithic 7:
Individual NE7, L. Neol. Lengyel Culture (4,360–4,490 BC) = Y-Haplogroup I2a

Following is the PCA plot. The Neolithic samples and Sardinia form a sort of Venn Diagram. Neolithic 7 is right in the intersection autosomally if I'm reading it correctly...not too far from Otzi, actually, who is just to the southwest of Neolithic 7, and just outside the Sardinia group.
http://www.nature.com/ncomms/2014/141021/ncomms6257/fig_tab/ncomms6257_F2.html

Lactase persistence doesn't show up until the Bronze and Iron Age samples. Amazing.

KO1 plots all the way north with La Brana. Then KO2 plots all the way south. The two groups certainly mingled pretty quick in this part of the world, yes?

Could a moderator please post the diagram itself? I have no more room.

I have to check all of this again.
 
ncomms6257-f2.jpg

http://www.nature.com/ncomms/2014/141021/ncomms6257/fig_tab/ncomms6257_F2.html
 
KO1 plots all the way north with La Brana. Then KO2 plots all the way south. The two groups certainly mingled pretty quick in this part of the world, yes?
I suggest KO2 was replacement. New population. The next samples are north of it, which might be caused by bigger incoming KO2-ish population assimilating really small proportion of KO1-ish type hunters in their ranks. Because of "9 to 1"-ish or similar proportions NE circles went just slightly up.
 
The first ancient sample to have fair hair and fair eyes is Neolithic 7:
Individual NE7, L. Neol. Lengyel Culture (4,360–4,490 BC) = Y-Haplogroup I2a

Following is the PCA plot. The Neolithic samples and Sardinia form a sort of Venn Diagram. Neolithic 7 is right in the intersection autosomally if I'm reading it correctly...not too far from Otzi, actually, who is just to the southwest of Neolithic 7, and just outside the Sardinia group.
http://www.nature.com/ncomms/2014/141021/ncomms6257/fig_tab/ncomms6257_F2.html

Lactase persistence doesn't show up until the Bronze and Iron Age samples. Amazing.

KO1 plots all the way north with La Brana. Then KO2 plots all the way south. The two groups certainly mingled pretty quick in this part of the world, yes?

Could a moderator please post the diagram itself? I have no more room.

I have to check all of this again.

Ed.Since the ancient samples are "projected" onto the modern ones their placement isn't exact. (although it can give us a general idea) So, I don't think we should get too excited by the fact that the Bronze Age samples seem to plot with the French. Interestingly, though, isn't that about where the one decent "Thracian" sample plotted as well?
 
OK I need to ask a question here. I know I have said before I feel two steps behind in this area, but I thought I might have been playing myself a little short, now I`m not so sure. Bronze Age in this area, should be R1.. something...no?
 
The Y-DNA is unfortunately missing deep subclade testing. It would be helpful for all of the samples, and maybe would clarify why all of the Neolithic samples look Mesolithic on the Y line. The Iron Age N would also be interesting to know more about.

I'm guessing that the Mesolithic-looking I2a and C6 are just coincidences and that if we had more local samples we'd be seeing more G2a and the like. Well, for every sample but KO1, which seems to be a genuine assimilated hunter-gatherer.

As a minor nitpick, the statement by Dienekes that "two other ones were I2a which is what Loschbour and Swedish hunter-gatherers had" and the statement in the paper that KO1's "Y-chromosome lineage, I2a, matches the only haplogroup reported to date in Mesolithic Central and Northern Europeans" aren't quite correct. Motala 2 was I2 but not I2a, and probably was I2c. Several others may have been something other than I2a, because their calls weren't clear. Also, if we count Pitted Ware as Mesolithic (since they were hunter-gatherers), then we can also add Ajvide 70, which wasn't Haplogroup I at all. I went into more details here.
 
OK I need to ask a question here. I know I have said before I feel two steps behind in this area, but I thought I might have been playing myself a little short, now I`m not so sure. Bronze Age in this area, should be R1.. something...no?

I'm surprised too, but these are such small sample sizes.

The Neolithic period results are surprising too. Maybe, as has been suggested, it's just because it's a small sample, and at this period Hungary was pretty mixed in terms of yDna.

We aren't getting much resolution either, so who knows what particular flavor of I2a we have at each time period.

We do know that come clades of I2a were incorporated into Neolithic communities and then expanded. Maybe that's what happened here? They're certainly "Neolithic" in autosomal terms.

I'm still plowing through the paper. Life is getting in the way. :)

I see Dienekes has made some comments. He's certainly right about the pigmentation. Pigmentation changes were taking place before the Indo-Europeans ever showed up, I think, and it was happening among people very much like the Sardinians and Otzi.

Why does lactase persistence appear so late in history? Does anyone have any ideas? It must have something to do with pastoralism, yes?( i.e. milk consumption instead of just processed milk products like cheese?) Could that also have speeded up the pigmentation changes? If Bronze Age pastoralists got the light pigmentation alleles from the Neolithic farmers, and their diet was very dairy based, the selection for both would occur, perhaps, given that you need Vitamin D to absorb calcium?
http://www.health.harvard.edu/newsweek/vitamin-d-and-your-health.htm

Just thinking out loud, folks...
 
It is fascinating, thanks for posting Angela, and kudos to Hungarian archeologist. Some of these samples are rather surprising. Lot of farmers with hg C and lack of hg G or E!

Individual KO1, E. Neol Körös (5,650–5,780 BC) = Y-Haplogroup I2a
Individual KO2, E. Neol Körös (5,640 BC) = Y-Haplogroup ?

This is very interesting. Times when Hunter Gatherers met first farmers in Hungary. KO1 plots as extreme HG and KO2 as extreme farmer. These two might reset definitions of EEF and WHG. KO1 bones were found in primitive and short lived agricultural village of very early Neolithic in Hungary. I wonder if he was trying his luck in farming or was he a slave or sacrifice to gods done by farmers? Has dark hair and blue eyes. Typical HG look of this period.
KO2 has brown hair and brown eyes.

Mid Neolithic samples:
Individual NE5, M. Neol. Late ALP (4,990–5,210 BC) = Y-Haplogroup C6
Individual NE6, M. Neol. LBK Culture (4,950–5,300 BC) = Y-Haplogroup C6
Individual NE7, L. Neol. Lengyel Culture (4,360–4,490 BC) = Y-Haplogroup I2a

Wow. Where are the Gs and Es? C6 is still alive and I2a is farming!
The biggest surprise is to find only and very Hunter-Gatherer Y hg I2a and C6 in Neolithic farmers from Hungary! Did HG in Hungary suddenly turned farmers mid Neolithic?
Not really, PCA plot tells very different story. They plot exactly with today's Sardinian pop., the most EEF of all europeans. If not HG haplogroups we wouldn't even know that they had some HG heritage looking at autosomal DNA.
They plot North from older KO2, this might indicate some HG admixture happening with time, but not more than in modern Sardinians. Haplogroups are surprising but autosomally they are typical EEF farmers from Neolithic. NE7 looks very blond though. More blond than the rest of samples from bronze and iron age. Interesting.

Copper Age
Individual CO1, L. Neol. Lengyel Culture (2,810 BC) = Y-Haplogroup ?
Plots exactly like the rest of Neolithic farmers. Copper age doesn't seem to bring any population change, at least in Hungary.

Bronze Age
Individual BR1, (2,080 BC) = Y-Haplogroup ?
Individual BR2, L. Bronze, Kyjatice Culture (1,110–1,270 BC) = Y-Haplogroup J2a1

Too bad that we have 3 thousand year gap from last neolithic Yhg to BR2 individual. Well at least we can say that J2 existed in central Europe way before Romans could introduce it around their empire from Near East, as some stubbornly insisted. I think it will show up in copper age first (Varna and Cucuteni) but we can't learn this from this study. I still can be right, lol.

On the graph we can see a big shift in plotting. Not pure EEF anymore but with admixtures pulling them towards East Europeans and West Asians (ANE?). I would speculate that this is due to Indo-European invasions which started around 2,500 BC. They are also pulled up on a chart toward, I presume, WHG admixture.

Iron Age
Individual IR1, Iron Age, Pre-Scythian Mezőcsát Culture (830–980 BC) = Y-Haplogroup N
Weird, plots somewhere between Russians and Caucasus and has hg N. Perhaps he is the true source of Hungarian language? He has blond hair and brown eyes.
Does "Arm" indicate Armeniens?
 
I'm surprised too, but these are such small sample sizes.

The Neolithic period results are surprising too. Maybe, as has been suggested, it's just because it's a small sample, and at this period Hungary was pretty mixed in terms of yDna.
Right, got it now. Thanks Angela..:)
 
The first ancient sample to have fair hair and fair eyes is Neolithic 7:
Individual NE7, L. Neol. Lengyel Culture (4,360–4,490 BC) = Y-Haplogroup I2a

Blonde hair, Blue eyes, and Light skin! Preceding Indo-Europeans...

9TxOjdC.png
 
It is fascinating, thanks for posting Angela, and kudos to Hungarian archeologist. Some of these samples are rather surprising. Lot of farmers with hg C and lack of hg G or E!

Individual KO1, E. Neol Körös (5,650–5,780 BC) = Y-Haplogroup I2a
Individual KO2, E. Neol Körös (5,640 BC) = Y-Haplogroup ?

This is very interesting. Times when Hunter Gatherers met first farmers in Hungary. KO1 plots as extreme HG and KO2 as extreme farmer. These two might reset definitions of EEF and WHG. KO1 bones were found in primitive and short lived agricultural village of very early Neolithic in Hungary. I wonder if he was trying his luck in farming or was he a slave or sacrifice to gods done by farmers? Has dark hair and blue eyes. Typical HG look of this period.
KO2 has brown hair and brown eyes.
It will be impossible to infer what KO1 hunter gatherer was doing in agricultural village.
The earliest agricultural communities belong to the Körös culture (Criş in Romania),
which is part of the Balkan Early Neolithic complex, the “First Temperate
Neolithic”10–12. Early Neolithic burials across eastern Europe are characterized by a
lack of cemeteries, in contrast to those of later Neolithic periods. Furthermore, the
majority of burials are found inside what seem to be refuse pits. In most cases it is not
possible to discern whether the artifacts recovered from these pits were simply
deposited or discarded into the pit or were rather interred with the person as grave
goods 44,45. In the specific case of skeletons from Körös culture sites from Hungary
only 13 of the 184 burials were accompanied by objects or fragments of objects that
could be identified to belong to a grave assemblage 46
 
It will be impossible to infer what KO1 hunter gatherer was doing in agricultural village.

Whatever he was doing there, the Neolithic Farmer's daughters must have liked him because his DNA was still there 1000 years later. :LOL:
 
I'm not surprised by the shift from a Sardinian like population to one that includes some eastern mix by the Bronze Age, and the skin and eye colour results would suggest a dietary influence. And the Y haplotype I2 isn't surprising but the C certainly is - if C haplotype hunter gatherers made the transition to agriculture, why did C later become rare. And I'm surprised there's no R1a in the Bronze or Iron Age samples. I'd agree that maybe the Y haplotypes aren't going to prove to be typical examples.
 
Whatever he was doing there, the Neolithic Farmer's daughters must have liked him because his DNA was still there 1000 years later. :LOL:
That's why her father thrown him into the garbage, lol, or whatever was left after he was done with him.

Seriously, KO1 lived in primitive farming village, which existed only couple of generations. Was it unsuccesful farming experiment by HGs, or more likely these first farmers/pioneers were wiped out by HGs? Wild West style.

There is a definitive slight shift in later farmers towards HGs. Definitely there was some mixing at the beginning, not much but there was some and it shows on PCA. After this initial mixing there is no change in Neolithic PCA values till Bronze Age. Even this blond farmer NE7 plots like Sardinians. Perhaps there were no more HGs left to mate with? At least in Hungary.
 
I'm not surprised by the shift from a Sardinian like population to one that includes some eastern mix by the Bronze Age, and the skin and eye colour results would suggest a dietary influence. And the Y haplotype I2 isn't surprising but the C certainly is - if C haplotype hunter gatherers made the transition to agriculture, why did C later become rare. And I'm surprised there's no R1a in the Bronze or Iron Age samples. I'd agree that maybe the Y haplotypes aren't going to prove to be typical examples.

These could be I-M26 haplotypes, or dead branches of I2a, which are not necessarily from the same movement of people as the I2-M423 Dinaric population haplotypes common in Hungary today. If I recall I2a* and I-M26 aren't very common at all in eastern Europe. I did not read the paper yet as I'm still working in the real world... Is there any indication these remains were separate burials from the other farmers of the time? Strange that all the LBK stuff turns up G-P15 or F-M89, then suddenly all this hunter-gatherer YDNA in a group together.
 
That's why her father thrown him into the garbage, lol, or whatever was left after he was done with him.

Seriously, KO1 lived in primitive farming village, which existed only couple of generations. Was it unsuccesful farming experiment by HGs, or more likely these first farmers/pioneers were wiped out by HGs? Wild West style.

There is a definitive slight shift in later farmers towards HGs. Definitely there was some mixing at the beginning, not much but there was some and it shows on PCA. After this initial mixing there is no change in Neolithic PCA values till Bronze Age. Even this blond farmer NE7 plots like Sardinians. Perhaps there were no more HGs left to mate with? At least in Hungary.

Its probably a situation similar to that of the R1b hotspot in sub-saharan africa (chad/cameroon). It would only take a few generations of a small group of HG's autosomal traits to be diluted out of existence in a much larger population.
 
That's why her father thrown him into the garbage, lol, or whatever was left after he was done with him.

Seriously, KO1 lived in primitive farming village, which existed only couple of generations. Was it unsuccesful farming experiment by HGs, or more likely these first farmers/pioneers were wiped out by HGs? Wild West style.

There is a definitive slight shift in later farmers towards HGs. Definitely there was some mixing at the beginning, not much but there was some and it shows on PCA. After this initial mixing there is no change in Neolithic PCA values till Bronze Age. Even this blond farmer NE7 plots like Sardinians. Perhaps there were no more HGs left to mate with? At least in Hungary.


Most of them are still south of Otzi though, and the Sardinians, so slightly less WHG even after whatever mixing went on. Until we get the precise figures from the new Lazaridis paper and/or the right ancient samples, we won't know how much of the WHG in modern Europeans is from the groups who were in Europe proper when the farmers arrived, and how much might have been picked up by Yamnaya or come down from the far north east, yes?

If the abstract from the new Sardinia paper is correct, there was very little Bronze Age movement into Sardinia, so their WHG is largely from the first "original" admixture. (Some must have come along with U-152.) I don't think there were any roving bands of fisher hunters left in southern Europe. I'm not sure about Central Europe. Maybe not. I bet there were some left in the far northeast, and maybe Ireland and Scotland?

Personally, in terms of Sardinia, I find it interesting how most Tuscans just look like eastern shifted Sardinians. Can the divergence really have been 10,000 years ago as one of the proposed models would have it? Isn't it more likely that until 2500 BC or even later all of southern Europe and most of Central Europe at least was Sardinian like? Still, of course, that means they've largely been their own breeding group for what,3500 years? (By the way, even though I complained that Hellenthal et al didn't, in their prior paper, explain their sampling conditions, I really want to see their new map...150 clusters in Europe!)

Aberdeen:And the Y haplotype I2 isn't surprising but the C certainly is - if C haplotype hunter gatherers made the transition to agriculture, why did C later become rare.

That "C" is definitely a shocker. Before they found it in a WHG sample, other stray sightings were put down to easterners wandering west but it seems some C is "home grown". I don't know why it disappeared, but Aaron 1981 makes a good point...those I2a lineages may either be of the "Sardinian" variety or an extinct variety. Either way, they may have nothing to do with the I2a in the area now. Without more resolution we just won't know.

I bet they wish they had known about this new extraction procedure for ancient dna. Which reminds me...the Lazaridis authors are still in the process of doing the y DNA analysis, or so the rumor goes, although we know how well that can turn out! Never again. :) Anyway, that may mean it will be a while till we get it.I definitely have a lot of questions about those Razib Khan tweets about Lazaridis' oral presentation.

Oh, doesn't the paper say that it was a very small group in the Mesolithic, or words to that effect? I've always held to the old formulation that it takes a lot of territory to support hunter/gatherers, although I suppose fisher/gatherers might have needed less.
 
we know r1a and r1b were in bronze age Germany, but nowhere else so far! Not even in bronze-age/Iron-Age Hungary, Ucraine, or Bulgaria! It sure looks like they're not the original IE haplogroups after all, which are leading more towards J2a/J2b.
 
[h=1]Table 1: Result summary from 13 Hungarian petrous bone samples.[/h] [h=2]From Genome flux and stasis in a five millennium transect of European prehistory[/h]
Nature Communications 5,Article number:5257doi:10.1038/ncomms6257 back to article
Table 1: Result summary from 13 Hungarian petrous bone samples.
IndividualMean coverageHuman DNA (%)Period and cultureSiteAge (cal BC)SexmtDNA haplogroupY Haplogroup
ALP, Alföld Linear Pottery; E.,early; F, female; KO1, Körös Neolithic; L., late; LBK, Linearbandkeramik; M, male; M., middle; mtDNA, mitochondrial DNA; Neol., Neolithic.

Dates are in calibrated years BC at 2 s.d., 95.4% confidence interval calibrated using OxCal 4.2 and rounded to the decade. For the individual NE4 two dates were obtained.

KO11.2462.80E. Neol. KörösTiszaszőlős-Domaháza5,650–5,780MR3I2a
KO20.1310.13E. Neol. KörösBerettyóújfalu-Morotva-liget5,570–5,710FK1
NE122.1286.85M. Neol. ALPPolgár-Ferenci-hát5,070–5,310FU5b2c
NE20.1945.85M. Neol. ALP Esztár GroupDebrecen Tócópart Erdõalja5,060–5,290FH
NE30.1337.60M. Neol. Bükk CultureGaradna5,010–5,210FX2b
NE40.1015.16M. Neol. Tiszadob-Bükk CulturePolgár-Ferenci-hát5,050–5,290
5,030–5,280
FJ1c
NE51.0471.02M. Neol. Late ALPKompolt-Kigyósér4,990–5,210MJ1c1C6
NE61.1880.36M. Neol. LBK CultureApc-Berekalja I.4,950–5,300MK1a3a3C6
NE71.1462.81L. Neol. Lengyel CultureApc-Berekalja I.4,360–4,490MN1a1a1aI2a
CO11.1334.57L. Copper Age, Baden CultureApc-Berekalja I.2,700–2,900FH
BR10.8170.85E. Bronze, Makó CultureKompolt-Kigyósér1,980–2,190FK1c1
BR221.2555.31L. Bronze, Kyjatice CultureLudas-Varjú-dűlő1,110–1,270MK1a1aJ2a1
IR11.3156.37Iron Age, Pre-Scythian Mezőcsát CultureLudas-Varjú-dűlő830–980MG2a1N



The mtdna is interesting...many K's
 

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