Ancient DNA from Hungary-Christine Gamba et al

Robert6 said:
IR1 in Iron Age Hungary was N1a, he have these snps of haplogroup N1a tested
Y6503+, Y6511+, Y6559+, Y6560+, Y6561+, Y6562+, Y6564+, Y6566+, Y6470+, Y6482+, Y6494+, Y6515+, Y6518+, Y6521+, Y6523+, Y6525+, Y6536+, Y6537+, Y6541+, Y6542+, Y6543+, Y6544+, Y6546+, Y6548+, Y6549+, Y6553+, Y6557+, Y6569+, Y6570+, Y6571+, Y6572+, Y6576+, Y6577+, Y6586+, Y6587+, Y6589+
P189-, Y6466-, Y6498-, Y6504-, Y6505-, Y6508-, Y6509-, Y6512-, Y6565-, Y6468-, Y6471-, Y6473-, Y6476-, Y6478-, Y6481-, Y6486-, Y6488-, Y6514-, Y6522-, Y6528-, Y6533-, Y6539-, Y6540-, Y6550-, Y6551-, Y6556-, Y6558-, Y6573-, Y6580-, Y6581-, Y6583-
Click to expand...


where did you get that info?

I have N1c2b2-L665

http://genetiker.wordpress.com/y-snp-calls-for-an-iron-age-hungarian-genome/
 
bicicleur said:
where did you get that info?

I have N1c2b2-L665

http://genetiker.wordpress.com/y-snp-calls-for-an-iron-age-hungarian-genome/
Click to expand...

You're wrong too. :wary2:

Read Genetiker more closely: "The calls show that IR1 belonged to haplogroup N, but not to N1a or N1c." L665 is downstream of several SNPs that were negative, so it must be considered a false positive.

Looks like IR1 could be N1b-L732. Seems rare but within range.
 
sparkey said:
You're wrong too. :wary2:

Read Genetiker more closely: "The calls show that IR1 belonged to haplogroup N, but not to N1a or N1c." L665 is downstream of several SNPs that were negative, so it must be considered a false positive.

Looks like IR1 could be N1b-L732. Seems rare but within range.
Click to expand...

some state origins as gulf of bothnia

a Finnish particular clade that emerges after the Uralic mtDNA Z contribution) and an Y-DNA legacy (e.g. Y-DNA haplogroup N1b and N1c1).
also
18% in the lands of the Veps
Veps or Vepsians are Finnic people that speak the Veps language, which belongs to the Finnic branch of the Uralic languages.
 
bicicleur said:
where did you get that info?

I have N1c2b2-L665

http://genetiker.wordpress.com/y-snp-calls-for-an-iron-age-hungarian-genome/
Click to expand...
The Administrator of YFull compared his results from BAM File with other N1a
http://forum.molgen.org/index.php/topic,7459.msg261520.html#msg261520
And he shares these snps with other N1a
Y6503+, Y6511+, Y6559+, Y6560+, Y6561+, Y6562+, Y6564+, Y6566+, Y6470+, Y6482+, Y6494+, Y6515+, Y6518+, Y6521+, Y6523+, Y6525+, Y6536+, Y6537+, Y6541+, Y6542+, Y6543+, Y6544+, Y6546+, Y6548+, Y6549+, Y6553+, Y6557+, Y6569+, Y6570+, Y6571+, Y6572+, Y6576+, Y6577+, Y6586+, Y6587+, Y6589+

But he is negative for these snps that N1a from Serbia do have
P189-, Y6466-, Y6498-, Y6504-, Y6505-, Y6508-, Y6509-, Y6512-, Y6565-, Y6468-, Y6471-, Y6473-, Y6476-, Y6478-, Y6481-, Y6486-, Y6488-, Y6514-, Y6522-, Y6528-, Y6533-, Y6539-, Y6540-, Y6550-, Y6551-, Y6556-, Y6558-, Y6573-, Y6580-, Y6581-, Y6583-
 
The admixture run from the paper hasn't been referenced yet. I think it's interesting when you look at the comparison between the "Hunter-Gatherer", the Neolithic sample, the Bronze Age samples, and the Iron Age sample:
View attachment 6786

The green component is modal in the Neolithic samples, the royal blue in Armenians (and the Druze, but present at large levels throughout the Middle East), and the red component is strongest in the Bedouin. The yellow orange color is obviously the "hunter-gatherer".

The whole chart can be found as Supplementary Figure 10, page 10:
http://www.nature.com/ncomms/2014/141021/ncomms6257/extref/ncomms6257-s1.pdf


It's interesting that there seems to be the beginning of a genetic change in the Copper Age, but the changes in culture in this area, at least, seem to stem more from cultural diffusion for that period, not migration, as LeBrok alluded to upthread. Of course, we're only looking at one sample, so it may not be representative, but according to the authors the archaeology does not show the arrival of intrusive elements.

The change in the Bronze Age is obvious, and then again in the pre-Scythian Iron Age sample.

Of course, we have to keep in mind that like any of the other admixture components they are made up of the three ancestral populations as per Lazaridis et al. So, that royal blue component is made up of EEF and perhaps larger percentages of ANE than we have currently in Europe? Perhaps some UHG as well? I know Lazaridis said that their algorithm couldn't be used for Near Easterners, so I don't know if we have a good handle on that. The Sardinians have, in this run, a bit of the blue "West Asian" and they have the yellow HG, at levels which seem similar to the levels for them in Lazaridis et al.

In this regard I searched this site for the discussion about the "Thracian" late Iron Age sample, K8. In that discussion, Sile published some admixture results which were apparently produced by Genetiker. These are the Dodecad K7 results for K8:
K7b

  • 46.44% Atlantic_Baltic
  • 36.25% West_Asian
  • 17.30% Southern
  • 0.00% African
  • 0.00% East_Asian
  • 0.00% Siberian
  • 0.00% South_Asian
Ed. The attachment is drawn from Figure 10 of the supplement, not Figure 4 of the body of the paper. The link is now correct.
 
Last edited:
The Administrator of YFull compared his results from BAM File, with other N1a
http://forum.molgen.org/index.php/topic,7459.msg261520.html#msg261520
And he shares these snps with other N1a
Y6503+, Y6511+, Y6559+, Y6560+, Y6561+, Y6562+, Y6564+, Y6566+, Y6470+, Y6482+, Y6494+, Y6515+, Y6518+, Y6521+, Y6523+, Y6525+, Y6536+, Y6537+, Y6541+, Y6542+, Y6543+, Y6544+, Y6546+, Y6548+, Y6549+, Y6553+, Y6557+, Y6569+, Y6570+, Y6571+, Y6572+, Y6576+, Y6577+, Y6586+, Y6587+, Y6589+

But he is negative for these snps that N1a from Serbia do have
P189-, Y6466-, Y6498-, Y6504-, Y6505-, Y6508-, Y6509-, Y6512-, Y6565-, Y6468-, Y6471-, Y6473-, Y6476-, Y6478-, Y6481-, Y6486-, Y6488-, Y6514-, Y6522-, Y6528-, Y6533-, Y6539-, Y6540-, Y6550-, Y6551-, Y6556-, Y6558-, Y6573-, Y6580-, Y6581-, Y6583-
 
sparkey said:
You're wrong too. :wary2:

Read Genetiker more closely: "The calls show that IR1 belonged to haplogroup N, but not to N1a or N1c." L665 is downstream of several SNPs that were negative, so it must be considered a false positive.

Looks like IR1 could be N1b-L732. Seems rare but within range.
Click to expand...

ok, I see
you're right
he hasn't been tested for N1b, and neither for N1
he couldn't have been pre-N1c either, as N1c1 is estimated 14000 years old
why do you think N1b and not simply N* or N1*?
is it because of present-day distributions?
 
bicicleur said:
ok, I see
you're right
he hasn't been tested for N1b, and neither for N1
he couldn't have been pre-N1c either, as N1c1 is estimated 14000 years old
why do you think N1b and not simply N* or N1*?
is it because of present-day distributions?
Click to expand...

N1b was the only alternative I saw at the project link Kristiina gave. Admittedly, I'm not an expert on haplogroup N. Where are N* and N1* found? China?
 
Angela said:
The whole chart is Figure 4 in the paper:
http://www.nature.com/ncomms/2014/141021/ncomms6257/fig_tab/ncomms6257_F4.html

It's interesting that there seems to be the beginning of a genetic change in the Copper Age, but the changes in culture in this area, at least, seem to stem more from cultural diffusion for that period, not migration, as LeBrok alluded to upthread. Of course, we're only looking at one sample, so it may not be representative, but according to the authors the archaeology does not show the arrival of intrusive elements.

The change in the Bronze Age is obvious, and then again in the pre-Scythian Iron Age sample.

Of course, we have to keep in mind that like any of the other admixture components they are made up of the three ancestral populations as per Lazaridis et al. So, that royal blue component is made up of EEF and perhaps larger percentages of ANE than we have currently in Europe? Perhaps some UHG as well? I know Lazaridis said that their algorithm couldn't be used for Near Easterners, so I don't know if we have a good handle on that. The Sardinians have, in this run, a bit of the blue "West Asian" and they have the yellow HG, at levels which seem similar to the levels for them in Lazaridis et al.
Click to expand...

It looks to me like this admixture analysis in Figure 4 tends to group the "West-Asian EEF-ANE" mix under blue rather than EEF-like orange, which is misleading for Sardinians and neolithic farmers who likely posess no real ANE. Probably this blue is just a common mediterranean ancestry of both, "West Asian" and EEF farmers.
At the same time it tends to group other ANE mixtures with the orange WHG (approximation) color, as happened for BR1/2, French and Orcadians, which might be a hint for an admixture in these peoples from north-east (steppe? R1b?), because in the PCA plot they are actually heavily eastern-shifted compared to Sardinians, Basques and neolithic farmers.
In summary: I believe it subsumes north-eastern admixtures as orange and over-amplifies south-eastern admixture as blue (= false-positive "West Asian").

Also that WHG part which is part of K15 "Atlantic" seems to be subsumed under the green color (as happened in KO1 for example), indicating false-positive EEF-farmer admixture.
 
as per angela's post......the K8 thracian is contaminated due to modern human intervention, only focus on other 3 thracians

both gok4 and P192-1 form a clade with Sardinians like the Iceman, although with less bootstrap support (gok4 83%, P192-1 56%). Finally, although K8 clusters with Northern European populations, its position in the tree is not resolved (3% Bootstrap). We note however that despite the reduced number of SNPs for K8, the relationships among the modern populations are consistent with the full dataset and generally well supported (bootstrap >90%), except within the Southern European group (minimum bootstrap 53%). It is therefore possible that the inconclusive pattern for K8 either reflects a possible higher level of modern DNA contamination (see Table S4 in [15]) or a more complex relationship to the modern populations included in the analysis.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014435/
 
ElHorsto said:
It looks to me like this admixture analysis in Figure 4 tends to group the "West-Asian EEF-ANE" mix under blue rather than EEF-like orange, which is misleading for Sardinians and neolithic farmers who likely posess no real ANE. Probably this blue is just a common mediterranean ancestry of both, "West Asian" and EEF farmers.
At the same time it tends to group other ANE mixtures with the orange WHG (approximation) color, as happened for BR1/2, French and Orcadians, which might be a hint for an admixture in these peoples from north-east (steppe? R1b?), because in the PCA plot they are actually heavily eastern-shifted compared to Sardinians, Basques and neolithic farmers.
In summary: I believe it subsumes north-eastern admixtures as orange and over-amplifies south-eastern admixture as blue (= false-positive "West Asian").

Also that WHG part which is part of K15 "Atlantic" seems to be subsumed under the green color (as happened in KO1 for example), indicating false-positive EEF-farmer admixture.
Click to expand...

I'm sorry, El Horsto, in my original post I carelessly linked to Figure 8 in the body of the paper but was discussing Figure 10, p. 10 of the Supplement. I went back later and edited the post, but I guess you saw the original link. This is the correct one here:
http://www.nature.com/ncomms/2014/14...mms6257-s1.pdf

I deliberately was talking about Figure 10 because it made more sense to me than Figure 4.

If you have a chance to take a look at it I'd be interested to know your interpretation of it.
 
The Administrator of YFull, compared IR1 results from BAM File with other N1a
http://forum.molgen.org/index.php/topic,7459.msg261520.html#msg261520
And he shares these snps with other N1a
Y6503+, Y6511+, Y6559+, Y6560+, Y6561+, Y6562+, Y6564+, Y6566+, Y6470+, Y6482+, Y6494+, Y6515+, Y6518+, Y6521+, Y6523+, Y6525+, Y6536+, Y6537+, Y6541+, Y6542+, Y6543+, Y6544+, Y6546+, Y6548+, Y6549+, Y6553+, Y6557+, Y6569+, Y6570+, Y6571+, Y6572+, Y6576+, Y6577+, Y6586+, Y6587+, Y6589+

But he is negative for these snps that N1a from Serbia do have
P189-, Y6466-, Y6498-, Y6504-, Y6505-, Y6508-, Y6509-, Y6512-, Y6565-, Y6468-, Y6471-, Y6473-, Y6476-, Y6478-, Y6481-, Y6486-, Y6488-, Y6514-, Y6522-, Y6528-, Y6533-, Y6539-, Y6540-, Y6550-, Y6551-, Y6556-, Y6558-, Y6573-, Y6580-, Y6581-, Y6583-
 
Angela said:
I'm sorry, El Horsto, in my original post I carelessly linked to Figure 8 in the body of the paper but was discussing Figure 10, p. 10 of the Supplement. I went back later and edited the post, but I guess you saw the original link. This is the correct one here:
http://www.nature.com/ncomms/2014/14...mms6257-s1.pdf

I deliberately was talking about Figure 10 because it made more sense to me than Figure 4.

If you have a chance to take a look at it I'd be interested to know your interpretation of it.
Click to expand...

Yes, Supplementary Figure 10 makes more sense to me as well. It shows the eastern admixture (blue) in BR1/2 and contemporary West Europeans (excl. Basques, Sardinians) in accordance with their east-shift in the PCA plot and our historic model. Also the blue traces still visible in Basques makes sense considering their R1b and assuming our theory of eastern R1b origin is true. I remember K12b was suggesting this too by showing lower WGH/EEF ("North-euro"/"Atlantic-med") ratio than the neighbours, indicating a more northern than southern east-admixture in non-basques, while basques probably possess rather local WHG.
In general I find the results not surprising and well supportive of our main theory here of bronze-age expansion into west and east europe, while mostly omitting the Basques and Sardinians. Although PCA plots reduce information, this one makes much sense.

The iron age IR1 was already WHG admixed, but his ancestors were probably dinaric looking I guess (not having seen his skull), somewhat similar to some carpathian East-Europeans and Armenians, and probably also South-Eastern europe in general, incl. Greece and Italy, and some continental celts. Such iron age people are probably the main responsibles for the much higher "West Asian" admixture in SE europe, although dinarics were also already present during Bronze-Age, as attested by Bell-Beaker skeletons.
 
ElHorsto said:
The iron age IR1 was already WHG admixed, but his ancestors were probably dinaric looking I guess (not having seen his skull), somewhat similar to some carpathian East-Europeans and Armenians, and probably also South-Eastern europe in general, incl. Greece and Italy, and some continental celts. Such iron age people are probably the main responsibles for the much higher "West Asian" admixture in SE europe, although dinarics were also already present during Bronze-Age, as attested by Bell-Beaker skeletons.
Click to expand...

IR1 lacks EEF (green) admixture like a caucasian.
 
sparkey said:
N1b was the only alternative I saw at the project link Kristiina gave. Admittedly, I'm not an expert on haplogroup N. Where are N* and N1* found? China?
Click to expand...

N* is Chinese
N1* moved north toward Manchuria probably long time ago, also some Turkic people are N1*, but Turkic probably hadn't reached Europe by 1100 BC
so, it depends whether the IR1 tribe survived or not
I guess, if they have descendants today, they probably were N1b, if not N1*
 
ElHorsto said:
Yes, Supplementary Figure 10 makes more sense to me as well. It shows the eastern admixture (blue) in BR1/2 and contemporary West Europeans (excl. Basques, Sardinians) in accordance with their east-shift in the PCA plot and our historic model. Also the blue traces still visible in Basques makes sense considering their R1b and assuming our theory of eastern R1b origin is true. I remember K12b was suggesting this too by showing lower WGH/EEF ("North-euro"/"Atlantic-med") ratio than the neighbours, indicating a more northern than southern east-admixture in non-basques, while basques probably possess rather local WHG.
In general I find the results not surprising and well supportive of our main theory here of bronze-age expansion into west and east europe, while mostly omitting the Basques and Sardinians. Although PCA plots reduce information, this one makes much sense.

The iron age IR1 was already WHG admixed, but his ancestors were probably dinaric looking I guess (not having seen his skull), somewhat similar to some carpathian East-Europeans and Armenians, and probably also South-Eastern europe in general, incl. Greece and Italy, and some continental celts. Such iron age people are probably the main responsibles for the much higher "West Asian" admixture in SE europe, although dinarics were also already present during Bronze-Age, as attested by Bell-Beaker skeletons.
Click to expand...

I think this admixture chart correlates very well with the Lazaridis figures for EEF if you add up the green, blue and red. The Hungarians are at about 50% (the Germans would be about the same then if the pattern holds?), the North Italians and Bulgarians at 71-72%, the Tuscans at 75%, the Ukrainians here look about 40% when they're actually at about 46%, but it's pretty darn close.

Interesting also that the "Bedouin" component is at roughly similar levels? The really nice part is that it shows the varying proportions of what perhaps we could call a more "LBK" and "Cardial" like EEF, and a more eastern "shifted" EEF? Perhaps, as you say, more Caucasus like? I'm not sure how to interpret that though. From everything we've seen so far, the EEF are a pretty homogenous group. Is it just drift? Unless, just as Stuttgart has some small percentage of WHG, the eastern shifted farmers picked up some small portion of ANE? I think there might have been some ANE there in the east before the "Indo-Europeans" started moving east.

In that regard, this article purportedly recounts a conversation with Lazaridis:
"By examining admixture levels in these groups, they found that an early European farmer split off from the rest of the European farmers early on and mixed with eastern European hunter-gatherers to form the Yamnaya population, which lived on the Steppes, Lazaridis said."

Now, I'm always a little leery of reports from journalists, even science journalists, plus it's a little vague. Does he mean that the EEF component in Yamnaya came only from the west, or was some of it from the Caucasus region?

As to the "Dinaric" component, (if it can be partly identified with the "blue" component) I'm not sure that it came only from Iron Age migrations. As you pointed out, that blue is already present in the Bronze Age, and Beaker skulls show it, as do the ones in the early northern Italian sites. The Iron Age might just have increased it. I do think it was present in the Continental Celts as well, going by the proportions in the French. I think what the chart also shows is that since it came from the east it grows progressively less as you move west. Note how the proportions in Ukraine, and the Balkans, which would have been the first affected, are higher for the "eastern" component. (Interestingly enough, though, in this admixture chart the Spaniards and the Northern Italians have about the same amount.)

The Russians and the northeastern Europeans seem to have gotten the great majority of their farmer ancestry from these later migrations, although I don't know offhand whether the archaeology would show when more of it came, the Bronze Age migrations or the Iron Age ones. Btw, I think we have a clue now as to how those "African" mtDna haplogroups wound up all the way in Finland. Speaking of mtDna, although I don't have time to go back over all the papers and the frequency distributions, I think we can see why there is an "eastern" type of farmer mtDna, and a "western" type in Europe.

Physical Anthropology is not my forte, but isn't "Dinaric" supposed to fit with "mountain" origin? The Caucasus would certainly fit with that.
 
Interesting that modern Lithuanians in that chart is the only population that absolutely lacks Bedoine red.
Modern Russians roughly equal IR1.
Modern Central Europeans - BR1 and BR2.
Since I am Baltic as well, what is this shiny red bedoine thing that everyone has except Lithuanians? If I read chart correct half of Basques, Orcadians, Belarussians also dont have it.
 
arvistro said:
Interesting that modern Lithuanians in that chart is the only population that absolutely lacks Bedoine red.
Modern Russians roughly equal IR1.
Modern Central Europeans - BR1 and BR2.
Since I am Baltic as well, what is this shiny red bedoine thing that everyone has except Lithuanians? If I read chart correct half of Basques, Orcadians, Belarussians also dont have it.
Click to expand...

Actually, a few Lithuanians do have a smidgen of it, but generally that's correct. (I think it's the Ukrainians, and therefore central Russia probably by implication that's so much like IR1, but even then there is a difference in that they do have some of the "green" component.) I don't know what the red is. It can't be the "Red Sea" component that Dienekes was chasing, can it? It's a huge portion of the Bedouin genome. Maybe just far southwest Asian?

At any rate, when you have such a small component, and then you have small, isolated populations, it's easy to lose it just through drift, I think. I understand all of this in the far northeastern and northwestern populations. What I don't understand is the Basques. I've been in the Pyrennees. They're by no means impassable. Unless they were isolated by their language.

What puzzles me is how the Bronze Age people coming in from the steppe can be so similar to, as you say, modern central Europeans. Were the population crashes so extreme that there were very few people of any variety left there when the incursions began? I guess we'll get a better handle on it when the Lazaridis paper comes out.
 
Angela said:
What puzzles me is how the Bronze Age people coming in from the steppe can be so similar to, as you say, modern central Europeans. Were the population crashes so extreme that there were very few people of any variety left there when the incursions began? I guess we'll get a better handle on it when the Lazaridis paper comes out.
Click to expand...
For that reason I believe that BR1&2 are not fresh arrivals from the East. They have been their for few generations (beginning of Bronze Age) and already had mixed with locals well, same way modern Europeans are. If they were the fresh arrivals they would have looked more like IR1, the extreme outlier.
 
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