New (July 3, 2015) Allentoft and Haak Analysis Comparison of DNA

Johannes

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http://eurogenes.blogspot.com.au/2015/07/direct-comparison-of-allentoft-et-al.html

This analysis clearly shows how the European populations are categorized according to DNA. The spreadsheet includes Native American Indian, Black, Australian, and other exotic DNA which some populations will have.

Friday, July 3, 2015

ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomes

"I haven't had a chance to study the output in detail yet, and I don't know what the cross-validation errors are for each of these unsupervised runs, but I'd say they all look pretty good. A Principal Component Analysis (PCA) of some of the K=10 data, showing how present-day Armenians compare to two Bronze Age Armenians, can be seen here."

There are some interesting results from this analysis. For example, Spaniards and Portuguese (and French?) have some Native American DNA. But as far as the rest its pretty consistent from previous studies.

K=6 spreadsheet


K=7 spreadsheet

K=8 spreadsheet

K=9 spreadsheet

K=10 spreadsheet

Check and see. If it was posted before then let me know and I will delete it.​



 
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http://eurogenes.blogspot.com.au/2015/07/direct-comparison-of-allentoft-et-al.html

This analysis clearly shows how the European populations are categorized according to DNA. The spreadsheet includes Native American Indian, Black, Australian, and other exotic DNA which some populations will have.

Friday, July 3, 2015

ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomes

"I haven't had a chance to study the output in detail yet, and I don't know what the cross-validation errors are for each of these unsupervised runs, but I'd say they all look pretty good. A Principal Component Analysis (PCA) of some of the K=10 data, showing how present-day Armenians compare to two Bronze Age Armenians, can be seen here."

There are some interesting results from this analysis. For example, Spaniards and Portuguese (and French?) have some Native American DNA. But as far as the rest its pretty consistent from previous studies.

K=6 spreadsheet


K=7 spreadsheet

K=8 spreadsheet

K=9 spreadsheet

K=10 spreadsheet

Check and see. If it was posted before then let me know and I will delete it.​




This "Native American" DNA shows up among a whole bunch of different groups, including people like Scots or Norwegians.
 
This "Native American" DNA shows up among a whole bunch of groups, including people like Scots and Norwegians.
 
Bell Beaker and Corded Ware folk had on average 2-3% Native American DNA.
 
According to this paper:

Lithuanians 61% 0% 38%
Estonians 61% 0% 37%
Russians 57% 1% 34%
Norway 53% 1% 38%
It seems very little EEF affected this area (0%-1%); Steppes (53%-61%); WHG/Neolithic Europeans (34%-38%)??

Scotland 51% 3% 45%
English 48% 6% 46%
Czechs 50% 7% 42%
French 40% 8% 52%
Spanish 32% 13% 53%
Croats 44% 15% 40%

Italians 24% 31% 43%
Greeks 30% 30% 36%
Bulgarians 37% 26% 36%
 
According to this paper:

Lithuanians 61% 0% 38%
Estonians 61% 0% 37%
Russians 57% 1% 34%
Norway 53% 1% 38%
It seems very little EEF affected this area (0%-1%); Steppes (53%-61%); WHG/Neolithic Europeans (34%-38%)??

Scotland 51% 3% 45%
English 48% 6% 46%
Czechs 50% 7% 42%
French 40% 8% 52%
Spanish 32% 13% 53%
Croats 44% 15% 40%

Italians 24% 31% 43%
Greeks 30% 30% 36%
Bulgarians 37% 26% 36%
What paper?
 
The Allentoft and Haak Analysis Comparison of DNA -- I meant the spreadsheet #6 analysis. I checked it and the guy who did this changed it. He eliminated EEF, Steppe, East African, and MN European and substituted Middle East, Siberian, Ameridian, European, and SSA.
 
The Allentoft and Haak Analysis Comparison of DNA -- I meant the spreadsheet #6 analysis. I checked it and the guy who did this changed it. He eliminated EEF, Steppe, East African, and MN European and substituted Middle East, Siberian, Ameridian, European, and SSA.

#6 spreadsheet doesn't measure ANE, EEF, and WHG.
 
#6 spreadsheet doesn't measure ANE, EEF, and WHG.

ANE and EEF are simply Middle Eastern/European and WHG are European Hunter Gatherers.
 
K6Allentoft and Haak Analysis of Comparisons of DNA 6-3-2015
SteppeEEF/M EMN EuropeE. AfricaSC AsiaSSA
Lithuania61%0%38% 0% 0%0%
Finland56%0%36%7%
Estonians61%0%37%1%
Russia57%1%34%8%
Norway53%1%38%
Scotland51%3%45%
England48%6%46%
Czechs50%7%42%
French40%8%52%
Basques34%1%65%
Spanish32%13%53%2%
Croats44%15%40%
Italians23%30%40%7%
Greeks30%31%36%3%
Bulgarians37%37%36%1%
Bell Beaker51%49%
CW77%23%
Algerians1%34%33%24%6%
Mozabite0%27%41%30%2%
K6 RevisedMiddle EastEuropeE. EurasiaAmeridiansSSA
Finland4%85%7%4%
Lithuania5%91%1%3%
Estonians4%91%2%3%
Belarus10%85%2%2%
Iceland11%88%2%
Norway11%86%3%
Ukraine13%81%2%2%
Scotland14%83%2%
England16%82%1%
Czechs16%80%1%2%
Hungarians19%75%1%2%
French22%80%1%
Spanish24%72%
Croats24%74%1%1%
N. Italians38%62%
S. Italians50%49%1%
Greeks42%55%
Yamnaya11%78%1%8%
Bell Beaker9%90%1%
CW6%86%6%
Algerians50%29%20%
Mozabites50%28%22%
K7SiberianEuropeanMiddle EastAmeridianSSA
Estonia4%92%1%1%
Finland9%87%1%1%
Lithuania3%94%2%1%
Iceland6%90%0%1%
Norway2%89%7%2%
Belarus3%89%5%2%
Ukraine4%83%10%1%
Scotland88%11%1%
Basques88%10%
England85%12%1%
French1%83%13%
Czechs2%84%13%1%
Hungary78%18%1%
Croatia80%19%
N Spain80%19%1%
S Spain77%22%1%
N Italy65%33%
S Italy53%45%
Greeks57%40%
BB93%3%1%
CW3%87%3%3%
Yamnaya5%77%11%6%
Algeria34%43%21%
Mozabites32%45%22%
K8Hindu KushHG EuropeMiddle EastAmeridiansSSA
Estonia9%75%13%2%
Finland8%72%12%7%
Lithuania9%77%13%1%
Iceland9%71%18%0%
Belarus10%70%17%0%
Norway9%71%20%0%
Ukraine11%69%20%
Scotland10%67%21%0%
EN Spain0%41%59%
MN Spain0%47%53%
N Spain4%60%36%
S Spain4%58%38%
Czechs10%66%23%
England10%66%24%
Hungary10%64%28%
Croatia11%60%29%
French6%62%32%
Greece15%42%43%
N Italy7%50%43%
S Italy15%34%50%
Algeria18%59%1%20%
Mozabites15%61%21%

OK here are the results of Europeans and some North Africans. Can some one explain to me what are the "Hindu-Kush", "Ameridians", and "Siberian" results?
 
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very imaginative and diverse breaking down! but it seems carots-potatoes are sometimes replaced by beans-turnips and sometimes potatoes are not the same potatoes nor are the carots or turnips; globally we can see some constant rough results for some categories but in detail it is not concluding, for me at least;
Hindue Kush is a strange grouping: 'gedrosia' (more) + 'caucasus' (lesser) + something else of other poolings (verylesser: 'southasian'???)?
I'm slightly confused. By chance I'm going to eat to strengthen my poor brain. Good appetite! Debrit gant kalon! ("Do eat with hart")
 
ANE and EEF are simply Middle Eastern/European and WHG are European Hunter Gatherers.
They contain admixtures but in different proportions. For example, in what they call European there is EEF, WHG and ANE. Now could you please separate them for exact calculations of said admixtures.
 
They contain admixtures but in different proportions. For example, in what they call European there is EEF, WHG and ANE. Now could you please separate them for exact calculations of said admixtures.

According to the notes I have before some guy named "David" changed the #6 spreadsheet: it stated that ANE (Ancient North Eurasians) as Steppe people, EEF (Early European Farmers) as Middle Eastern people, and MN Europeans (Middle Neolithic Europeans) as EEF and WHG mixed.

This is the original spreadsheet #6:

K6Allentoft and Haak Analysis of Comparisons of DNA MIXTURE 6-3-2015
Steppe EEF/Middle Eastern MN Europe (EEF+EHG)E. Africa SC AsiaSSA
Lithuania61%0%38%0%0%0%
Finland56%0%36%0%7%0%
Estonians61%0%37%0%1%0%
Russia57%1%34%0%8%0%
Norway53%1%38%0%0%0%
Scotland51%3%45%0%0%0%
England48%6%46%0%0%0%
Czechs50%7%42%0%0%0%
French40%8%52%0%0%0%
Basques34%1%65%0%0%0%
Spanish32%13%53%2%0%0%
Croats44%15%40%0%0%0%
Italians23%30%40%7%0%0%
Greeks30%31%36%0%3%0%
Bulgarians37%37%36%0%1%0%
Bell Beaker51%0%49%0%0%0%
CW77%0%23%0%0%0%
Algerians1%34%33%24%0%0%
Mozabite0%27%41%30%0%2%

This is the revised #6 Spreadsheet: I think it explains it better. Middle East is mostly EEF and Europe is a mix of ANE and WHG. Thus he was trying to make it more accurate. East Eurasia is Mongoloid people and Ameridians are eatern Siberians???

K6Allentoft and Haak Analysis of Comparisons of DNA MIXTURE 6-3-2015
K6 RevisedMiddle EastEuropeE. EurasiaAmeridiansSSA
Finland4%85%7%4%0%
Lithuania5%91%1%3%0%
Estonians4%91%2%3%0%
Belarus10%85%2%2%0%
Iceland11%88%0%2%0%
Norway11%86%0%3%0%
Ukraine13%81%2%2%0%
Scotland14%83%0%2%0%
England16%82%0%1%0%
Czechs16%80%1%2%0%
Hungarians19%75%1%2%0%
French22%80%0%1%0%
Spanish24%72%0%0%0%
Croats24%74%1%1%0%
N. Italians38%62%0%0%0%
S. Italians50%49%1%0%0%
Greeks42%55%0%0%0%
Yamnaya11%78%1%8%0%
Bell Beaker9%90%0%1%0%
CW6%86%0%6%0%
Algerians50%29%0%0%20%
Mozabites50%28%0%0%22%
Yemen73%15%0%0%10%
Yemen Jew87%8%0%0%4%
Bedouin A73%16%0%0%9%
BedouinB92%4%0%0%4%
 
very imaginative and diverse breaking down! but it seems carots-potatoes are sometimes replaced by beans-turnips and sometimes potatoes are not the same potatoes nor are the carots or turnips; globally we can see some constant rough results for some categories but in detail it is not concluding, for me at least; Hindue Kush is a strange grouping: 'gedrosia' (more) + 'caucasus' (lesser) + something else of other poolings (verylesser: 'southasian'???)? I'm slightly confused. By chance I'm going to eat to strengthen my poor brain. Good appetite! Debrit gant kalon! ("Do eat with hart")

Sorry Moesan: I have been changing things and its a little messy. The data is enormous. Here is a better way to read it. If you want to see other people simply check the spreadsheet on the top page and you can see all the people studied.

K6Allentoft and Haak Analysis of Comparisons of DNA MIXTURE 6-3-2015
K6 RevisedMiddle EastEuropeE. EurasiaAmeridiansSSA
Finland4%85%7%4%0%
Lithuania5%91%1%3%0%
Estonians4%91%2%3%0%
Belarus10%85%2%2%0%
Iceland11%88%0%2%0%
Norway11%86%0%3%0%
Ukraine13%81%2%2%0%
Scotland14%83%0%2%0%
England16%82%0%1%0%
Czechs16%80%1%2%0%
Hungarians19%75%1%2%0%
French22%80%0%1%0%
Spanish24%72%0%0%0%
Croats24%74%1%1%0%
N. Italians38%62%0%0%0%
S. Italians50%49%1%0%0%
Greeks42%55%0%0%0%
Yamnaya11%78%1%8%0%
Bell Beaker9%90%0%1%0%
Corded Ware6%86%0%6%0%
Algerians50%29%0%0%20%
Mozabites50%28%0%0%22%
Yemen73%15%0%0%10%
Yemen Jew87%8%0%0%4%
Bedouin A73%16%0%0%9%
BedouinB92%4%0%0%4%
K7SiberianEuropeanMiddle EastAmeridianSSA
Estonia4%92%1%1%0%
Finland9%87%1%1%0%
Lithuania3%94%2%1%0%
Iceland6%90%0%1%0%
Norway2%89%7%2%0%
Belarus3%89%5%2%0%
Ukraine4%83%10%1%0%
Scotland0%88%11%1%0%
Basques0%88%10%0%0%
England0%85%12%1%0%
French1%83%13%0%0%
Czechs2%84%13%1%0%
Hungary0%78%18%1%0%
Croatia0%80%19%0%0%
N Spain0%80%19%1%0%
S Spain0%77%22%1%0%
N Italy0%65%33%0%0%
S Italy0%53%45%0%0%
Greeks0%57%40%0%0%
Bell Beaker0%93%3%1%0%
Corded Ware3%87%3%3%0%
Yamnaya5%77%11%6%0%
Algeria0%34%43%0%21%
Mozabites0%32%45%0%22%
Yemen0%13%70%0%15%
Yemen Jew0%14%82%0%4%
Bedouin A0%19%70%0%11%
Bedouin B0%5%90%0%5%
K8Hindu KushHG EuropeMiddle EastAmeridiansSSA
Estonia9%75%13%2%0%
Finland8%72%12%7%0%
Lithuania9%77%13%1%0%
Iceland9%71%18%0%0%
Belarus10%70%17%0%0%
Norway9%71%20%0%0%
Ukraine11%69%20%0%0%
Scotland10%67%21%0%0%
EN Spain0%41%59%0%0%
MN Spain0%47%53%0%0%
N Spain4%60%36%0%0%
S Spain4%58%38%0%0%
Czechs10%66%23%0%0%
England10%66%24%0%0%
Hungary10%64%28%0%0%
Croatia11%60%29%0%0%
French6%62%32%0%0%
Greece15%42%43%0%0%
N Italy7%50%43%0%0%
S Italy15%34%50%0%0%
Algeria0%18%59%1%20%
Mozabites0%15%61%0%21%
Yemen25%1%56%0%15%
Yemen Jew22%0%72%0%5%
Bedouin A23%7%61%0%9%
Bedouin B16%0%80%0%4%
 
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They contain admixtures but in different proportions. For example, in what they call European there is EEF, WHG and ANE. Now could you please separate them for exact calculations of said admixtures.

Yes but how did he get this "Hindu-Kush" and "Ameridians"??? How for example did Ameridians end up in Scandinavia?? I mean #6, #7, and #8 in Finland, Iceland, and Norway??
 
Yes but how did he get this "Hindu-Kush" and "Ameridians"??? How for example did Ameridians end up in Scandinavia?? I mean #6, #7, and #8 in Finland, Iceland, and Norway??
It must be a shared admixture, which came from ANE portion of common ancestors who lived in Syberia, like Mal'ta boy from 24kya.
 
Half of those numbers posted by Johanned are wrong. For first Italy is not 7% African, but 0.7%.
 
Half of those numbers posted by Johanned are wrong. For first Italy is not 7% African, but 0.7%.

how did the spanish get 2% east-african...............maybe he meant north-african
 
Half of those numbers posted by Johanned are wrong. For first Italy is not 7% African, but 0.7%.

No. All the numbers are correct. It's not 7% African but East African or E1b1. The author meant North African or Berbers mixture. But he revised his analysis. Had I not copied the first #6 table I would not have known what he did. Look at the "revised" tables #6 - #8 for a more accurate analysis.
 

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