PDA

View Full Version : Autosomal map : European admixture (from Dodecad)



Pages : 1 [2]

Nobody1
12-03-13, 04:47
at zanipolo

I consider Plaza (2003) to be a good study, its actually one of the first [after Maca-Meyer (2001)] that did a full mtDNA study. Yes, there are mistakes in his study like the one you pointed out, but its still pretty solid and corresponds with later studies - Pereira, Cerezo or Achilli.

L3 is East African (Horn of Africa - Abyssinia) and the oldest of the mtDNA Haplogroup L. The fact that it has a high frequency in N. Africa and Near East suggests a Migration from East Africa into these regions and in Neolithic times (from Near East) into Balkans and Italy.
acc. Maca-Meyer (2001)
"Likewise, African haplogroup L3 is more related to Eurasian haplogroups than to the most divergent African clusters L1 and L2."

L1 and L2 are West African and can only be linked to the Atlantic slave trade.
U6 is Berber - Mozabites and also in High frequency in Mauritania. The Presence of U6 in Portugal (5.6%), Spain (2%) and Sicily (0.6%) can be linked to the Islamic conquests in the Middle Ages.

Drac II
12-03-13, 11:50
at Dracc II
Correct, its 2 diff. places: 14* is NW Spain and 15* is Portugal, Brisighelli lumped the 2 together an evaluated the average of 7.1%
But if you LOOK at Figure2 (the chart) you can clearly see more Orange (African) at 14* NW Spain than 15* Portugal, meaning NW Spain is clearly above the average of 7.1% and Portugal below [factor2]. Apart from the fact that 7.1% isnt that far from 9.2% in the first place, the Brisighelli study isnt an AutosomalDNA study to begin with. its largely a Y-DNA and mtDNA study and the results on mtDNA and Y-DNA are identical (confirms) with other studies you call Debunked or Outdated - Pereira, Achilli, Cerezo, Ottoni etc.

as for Plaza et al (2003); Thanks for the link.
Acc. to the chart the Sub-Saharan mtDNA (L1,L2,L3) and North African mtDNA (U6 - Mauritania) levels in Italy are absolutely in line with all other mtDNA studies on Italy that show a range of 0%-2.9% - [Achilli, Pereira, Cerezo, Ottoni etc.] so not only Brisighelli but also Plaza CONFIRMS those studies.

Sicily = 0.6% L & 0.6 % U6
Tuscany = 2.0% L & 0% U6
Sardinia = 2.8% L & 0% U6
Central Ita. = 1.2% L & 0% U6
Italy total = 2.9% L & 0.1% U6

except for S. Italy which has an extremely small sample size of 37 samples (8.1% L = 3 samples & 0% U6)
comparing S.Italy to Ottoni et al. (2009) = 2.2% / or Cerezo et al. 2012 or Achilli et al. 2007 or even Brisighelli et al. (2012) = 1%-2%

The interesting part however is that Italy's largest L haplogroup is L3 (1.7% of the 2.9%), which is East African [largely also in N.Africa and Near East] as compared to L1 and L2 which are West African (slave trade) in comparison with Portugal and Spain which are more L2 and L1 (west african slave trade). Something also Cerezo et al. (2012) evaluated. Also U6 is far more common in Spain in Portugal, where as in Italy its almost absent except for Sicily at 0.6%.

Portugal total = 3.6% L & 5.6% U6
North Portugal = 5% L & 7% U6
Central Portugal = 6.1% L & 0% U6
South Portugal = 5.1% L & 0% U6
Central Spain = 4% L & 2% U6 (also small sample size)

I am not convinced by what you are pointing out in figure 2 because if you look at the size of the "squares" they seem to also represent sample size, which make the orange and other color-keys look like "more" or "less", depending on the length of the square. Look at square #9 representing Britain, for example, which is quite small. The orange is almost at the same level as that of the much larger square representing NW Spain. Are we to conclude that Britain has the same level of sub-Saharan African as NW Spain? Judging by all evidence (including the very statements of this study regarding northern vs southern Europe in this regard), certainly not. Not even other parts of Spain do, let alone Britain. Now look at the squares representing northern and central Italy and then look at the one representing southern Italy: they also seem to have more "orange". Are we to conclude that northern Italy has more sub-Saharan African than southern Italy? Again, judging by all evidence available so far, certainly not. "Coincidentally", the southern Italian square is also longer than the ones for northern and central Italy, so the "orange" is more spread out. So things seem a bit more complicated than just saying "the level of orange in X seems to be more than the one for Y on the graph!" If my interpretation is correct, it shows that, as I suspected, the Portuguese sample was larger than the NW Spanish sample, and likely more responsible for the combined 7.1% figure.

The part of Brisighelli et al. under discussion was very clearly autosomal. The study deals with both autosomes and haplogroups. Their autosomal results are not as harmonious with haplogroup results as they like to claim, just like Moorjani et al.'s results were not, despite their claims to the contrary.

It is very common for some people trying to deny the results of Plaza et al. 2003 regarding southern Italy to use the argument that the sample size was too small. Fair enough. But what is good for the goose is also good for the gander. That means we can easily apply the exact same argument to some of those favorite papers used by anti-Spanish t-r-o-l-l-s trying desperately to inflate Spain's "sub-Saharan African influence", like the one for Sayago (Alvarez et al. 2010) with a sample size of only 33 (less than the southern Italian sample in Plaza et al. 2003.) So you can forget the much ballyhooed "even as high as 18% sub-Saharan mtDNA" in Spain.

U6 is prehistoric and its geographic origin is debated, either Near Eastern, North African or maybe even Iberian. It certainly is not sub-Saharan African.

Nobody1
12-03-13, 12:52
at Drac II

Exactly, WHO KNOWS. I dont know what the figure for Britain is, or what the exact figure for NW Spain is, because the Study simply doesnt include it or clearly explains the chart, so its a guessing game what the Orange clearly indicates.
it also doesnt explain how it obtained these figures or what method was used or anything regarding the 54 AIMs. And those results obtained (both the 7.1 and the 9.2) are nowhere in line with any other study. its not even in line with its own aDNA conclusion based on PCA observation.
Therefor i consider Moorjani et al. (2011) far more precise (detailed explanation on the SNPs used) and more credible than Brisighelli.

and Dude, i have no business with Sayago i seriously couldnt care less what the sub-saharan mtDNA rate is for that region, i just pointed out that there is a Study [Alvarez et al. (2010)] that has a result as high as 18.1% just like you pointed out (twice) that Plaza et al (2003) has a result as high as 8.1% for S. Italy. Now if the Sayago result is based on a small sample-set than thats an explanation for that high figure.
And thanks again for the Plaza et al (2003) link, good study.

Alexandros
12-05-13, 08:25
From the discussions I notice a misunderstanding regarding what does "looking European" mean, especially as regards Georgians vs. Sardinians, etc. A misconception I notice is that people tend to think "Europeaness" as having lighter skin and fairer hair, etc. In other words several traits differentiating Europeans from their closest neighbors, the Middle Easterns and North Africans. This is fair enough, but the confusion comes when maps like this appear showing that Georgians, for example, are not so European and here come the complaints by some. Of course the majority of Georgians have very light skin, even some with blonde hair, blue eyes, but this does not mean that they are European. Someone may argue that Russians also look 'European', but are they? The point is what is the definition of European? Where does the continent end?? How far east can we stretch the limits? Does the continent end in Greece, Bulgaria and Romania, or does it stretch eastern to include Ukraine, Belarus, Turkey or even Georgia and Azerbaijan? Indeed, Caucasus was the place of origin of great migrations into Europe and no one can argue that. This does not mean however that today we can consider the Caucasus region and even eastern from there as 'Europe'. We don't have to be considered all as 'Europeans' in order to be proud of our genetic ancestry. Just some thoughts..

Knovas
12-05-13, 13:28
The latest research seems to indicate that the most "European", "West Eurasian", or whatever...these are the Sardinians. At least, the Sardinians from the HGDP sample, who were probably so carefully selected. Judging from their phenotypes (images available all over google), one really doesn't know what to think, so it would worth to test other Sardinians to see how do they look in admixture analysis. But if we take the aforementioned sample as reference, there seems to be no question about it.

Still waiting to see the isolated samples from the Friulli region in detail though.

Toscano
15-08-13, 09:24
Is that map made by some Nordicist? If we italians are like 70% European. Please tell me what the rest 30% are? Arabic/negroid? don't think so!

Nobody1
15-08-13, 14:24
Is that map made by some Nordicist? If we italians are like 70% European. Please tell me what the rest 30% are? Arabic/negroid? don't think so!

The numbers are from DODECAD:
https://docs.google.com/spreadsheet/ccc?key=0ArAJcY18g2GadDRCd0dva0dwTzc3a0JicjZmRE96b Gc&authkey=CPGxtqQM&hl=en&authkey=CPGxtqQM#gid=0


South Italy & Sicily [samples 14] -
Near East = 44.9 / N Europe = 13.7 / S Europe = 38.9 / N Africa = 2.2 / Sub-Sahara = 0.4

North Italy [samples 12] -
Near East = 21.2 / N Europe = 31.0 / S Europe = 47.5 / N Africa = 0.1 / Sub-Sahara = 0

Spain [samples 12] -
Near East = 11.3 / N Europe = 37.8 / S Europe = 47.7 / N Africa = 2.3 / Sub-Sahara = 0.6

Greece [samples 10] -
Near East = 40 / N Europe = 21.1 / S Europe = 38.6 / N Africa = 0.1 / Sub-Sahara = 0

Portugal [samples 7] -
Near East = 12.3 / N Europe = 36.1 / S Europe = 43.3 / N Africa = 5.8 / Sub-Sahara = 1.7

Sardinia [samples 28] -
Near East = 2.5 / N Europe = 0.6 / S Europe = 96.5 / N Africa = 0.1 / Sub-Sahara = 0


Keep in mind its an Internet Blogger; not a scientist at an institution;
But the numbers seem alright;

Knovas
15-08-13, 14:35
The map is based on K=12 v3 if I recall (the same as Epedia's autosomal maps). The figures you posted belong to the K=10 run. There many different genome interpretations using Admixture, so it's good to keep this in mind.

Sile
30-09-13, 08:31
Dodecad and BCA

My BCA pinpoint
http://img6.imageshack.us/img6/7950/jvty.png (http://imageshack.us/photo/my-images/6/jvty.png/)

Uploaded with ImageShack.us (http://imageshack.us)


Dodecad World data for me


#
Population
Percent


1
Amerindian
0.00


2
East_Asian
0.06


3
African
0.19


4
Atlantic_Baltic
56.29


5
Australasian
0.00


6
Siberian
0.00


7
Caucasus_Gedrosia
17.20


8
Southern
25.49


9
South_Asian
0.78




Pct. Calc. Option 1



1
N_Italian
92.05%


2
Mordovians
3.99%


3
Kalash
2.25%


4
Lezgins
1.51%


5
Romanians
0.15%


6
Greek
0.03%


7
O_Italian
0.01%


8
S_Italian
0.01%


9
Chechens
0.00%


10
Pathan
0.00%



Total RMSD: 0.269527

what about 2 pop mix
Using 2 populations approximation:
1 50% C_Italian +50% French @ 1.439
2 50% North_Italian +50% Bulgarians @ 1.458
3 50% Sicilian +50% Kent @ 1.547
4 50% Sicilian +50% Cornwall @ 1.584
5 50% Sicilian +50% British_Isles @ 1.626
6 50% S_Italian_Sicilian +50% British_Isles @ 1.670
7 50% N_Italian +50% Bulgarians @ 1.755
8 50% S_Italian_Sicilian +50% Cornwall @ 1.768
9 50% S_Italian_Sicilian +50% Kent @ 1.774
10 50% British +50% Sicilian @ 1.777
31375 iterations.

Is this 2 pop mix the only one that matches the BCA pinpoint from Doug.
Let me know which to use

Sile
30-09-13, 08:50
http://eurogenes.blogspot.com.au/

new finds on admixtures

Angela
01-10-13, 22:27
I took a look at Eurogenes' commentary about the latest Skoglund paper. I didn't personally find that this article added much to what Skoglund had already published other than confirming his results by adding more samples. The only additional piece of really new information that I could find is about the new sample from the Baltic Sea, which is older, and so is more firmly "Mesolithic" in terms of a time line than the Swedish hunter gatherer samples, which are only from about 3,000 B.C. This new sample carried mt dna U4b1.
See:http://uu.diva-portal.org/smash/get/diva2:645462/FULLTEXT01.pdf

I also took a look at the three Eurogenes maps. I'm not part of that project, and don't really follow it, so I can't comment really on whether I think the maps are totally accurate according to his population averages for a northern European like component, or what actually appears more to be a northeast European component and a Mediterranean component. (I don't even know if he now publishes his population averages for each component. Last time I heard, he didn't.) Generally though, the first two maps seem to depict what looks like a Northeast European cline and a Mediterranean cline. The third map looks generally like a map of Dienekes' West Asian component.

Clearly, though, modern European populations are a mix of all three components.

In this regard, I find it interesting to look at the Geno 2.0 results. Their labelling of the third component as "Southwest Asian" is unfortunate, because I think a lot of people are confused by it...I think what they're talking about is a sort of combined Gedrosia/West Asia component if we were to use Dienekes type terms, but it's difficult to tell as they don't explain it anywhere. The percentages seem to be within a point or two of each other for all the countries.
https://genographic.nationalgeographic.com/overview-of-regions-and-closest-populations/reference-populations/

Of the populations they published, the Finns have the highest percentage of north Euro at 57%, but they also contain a northeast Asian component, so a population like the Lithuanians would probably have even higher percentages. The lowest among the European populations for that component is a tie between the Greeks and the Tuscans at 28%.

I wish they provided figures for all the populations, but so far this is it.

I don't think that the timing of the arrival of the Mediterranean component in Europe is entirely a closed question, by the way. There are no samples as of yet from southern Spain, from Italy, or from the Balkans, although some are apparently in the pipeline. The possibility remains open, in my opinion, that it might have arrived in some of those areas in the Mesolithic. Time will tell...they are supposedly testing Mesolithic samples in the Balkans.

I wonder, also, how this will all fit with the findings of some recent papers that the major population expansion was actually pre-Neolithic, if indeed that is proven to be the case.
See: http://mbe.oxfordjournals.org/content/early/2013/09/20/molbev.mst156.abstract

Sile
02-10-13, 07:59
I took a look at Eurogenes' commentary about the latest Skoglund paper. I didn't personally find that this article added much to what Skoglund had already published other than confirming his results by adding more samples. The only additional piece of really new information that I could find is about the new sample from the Baltic Sea, which is older, and so is more firmly "Mesolithic" in terms of a time line than the Swedish hunter gatherer samples, which are only from about 3,000 B.C. This new sample carried mt dna U4b1.
See:http://uu.diva-portal.org/smash/get/diva2:645462/FULLTEXT01.pdf

I also took a look at the three Eurogenes maps. I'm not part of that project, and don't really follow it, so I can't comment really on whether I think the maps are totally accurate according to his population averages for a northern European like component, or what actually appears more to be a northeast European component and a Mediterranean component. (I don't even know if he now publishes his population averages for each component. Last time I heard, he didn't.) Generally though, the first two maps seem to depict what looks like a Northeast European cline and a Mediterranean cline. The third map looks generally like a map of Dienekes' West Asian component.

Clearly, though, modern European populations are a mix of all three components.

In this regard, I find it interesting to look at the Geno 2.0 results. Their labelling of the third component as "Southwest Asian" is unfortunate, because I think a lot of people are confused by it...I think what they're talking about is a sort of combined Gedrosia/West Asia component if we were to use Dienekes type terms, but it's difficult to tell as they don't explain it anywhere. The percentages seem to be within a point or two of each other for all the countries.
https://genographic.nationalgeographic.com/overview-of-regions-and-closest-populations/reference-populations/

Of the populations they published, the Finns have the highest percentage of north Euro at 57%, but they also contain a northeast Asian component, so a population like the Lithuanians would probably have even higher percentages. The lowest among the European populations for that component is a tie between the Greeks and the Tuscans at 28%.

I wish they provided figures for all the populations, but so far this is it.

I don't think that the timing of the arrival of the Mediterranean component in Europe is entirely a closed question, by the way. There are no samples as of yet from southern Spain, from Italy, or from the Balkans, although some are apparently in the pipeline. The possibility remains open, in my opinion, that it might have arrived in some of those areas in the Mesolithic. Time will tell...they are supposedly testing Mesolithic samples in the Balkans.

I wonder, also, how this will all fit with the findings of some recent papers that the major population expansion was actually pre-Neolithic, if indeed that is proven to be the case.
See: http://mbe.oxfordjournals.org/content/early/2013/09/20/molbev.mst156.abstract

Eurogenes K9 ( not the K9B which is used for GPS mesolithic placements) is its mesolithic data. You can check it out.

IberoAtlantid
09-12-14, 18:58
This map is definitive?

Pax Augusta
09-12-14, 19:30
This map is definitive?

No, of course not.

Angela
09-12-14, 19:48
Three years is an eon in the field of population genetics. See Lazaridis et al:
http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

This is the supplement, which is just as important:
http://www.nature.com/nature/journal/v513/n7518/extref/nature13673-s1.pdf

Gamba et al is also very important:
http://www.nature.com/ncomms/2014/141021/ncomms6257/full/ncomms6257.html

Skoglund et al 2012
http://211.144.68.84:9998/91keshi/Public/File/41/336-6080/pdf/466.full.pdf

Papers which should be out shortly will also refine our understanding of the population migrations which led to the creation of the "Europeans".

IberoAtlantid
10-12-14, 15:06
Not I have a inferior complex you are simply too mentally challenged to understand that a North European Russian is in the average Eye more European looking than anyone from the Mediterranean are you denying this? You are the only person here who tries to prove how even more European they are than Austrians or Germans. I am simply saying What is more European is based on the definition. The average Person would any day consider a Moldavian more European looking than a Spaniard or other Mediterraneans even though Moldavians are more West Asian.
You study taxonomy or what?

Oraliahenue
30-12-19, 02:54
No. It was not a going AWOL. They took their rifles away.I agree. Pretty much every government in the world would have reacted in the same way.