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View Full Version : New (July 3, 2015) Allentoft and Haak Analysis Comparison of DNA



Johannes
23-07-15, 02:06
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 (https://drive.google.com/file/d/0B9o3EYTdM8lQMURLSmZ3eTd4UVU/view?usp=sharing)."

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 (https://docs.google.com/spreadsheets/d/17FnR-OeYN4m-XCzWxChiLPJR6QW_ehmR3I0Mrz6OjDI/edit?usp=sharing)

K=7 spreadsheet (https://docs.google.com/spreadsheets/d/12AH4v-e7XmLfPI3my5q3H2RjOizmTECW3c162bgD9nE/edit?usp=sharing)

K=8 spreadsheet (https://docs.google.com/spreadsheets/d/1cdXAo7-_wAnncODW3Pn0s3DkARANQnj9Lu8PqAPPF6c/edit?usp=sharing)

K=9 spreadsheet (https://docs.google.com/spreadsheets/d/1ePhVUdXocymdHJShbBFHpdzu3c8LUWYnG5HxKXCy2E0/edit?usp=sharing)

K=10 spreadsheet (https://docs.google.com/spreadsheets/d/1MTm_wkLXkXGTZ6W6rgz-2PyQyqqxjRUNl1KkstjZ11w/edit?usp=sharing)

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

Drac II
23-07-15, 17:56
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 (https://drive.google.com/file/d/0B9o3EYTdM8lQMURLSmZ3eTd4UVU/view?usp=sharing)."

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 (https://docs.google.com/spreadsheets/d/17FnR-OeYN4m-XCzWxChiLPJR6QW_ehmR3I0Mrz6OjDI/edit?usp=sharing)

K=7 spreadsheet (https://docs.google.com/spreadsheets/d/12AH4v-e7XmLfPI3my5q3H2RjOizmTECW3c162bgD9nE/edit?usp=sharing)

K=8 spreadsheet (https://docs.google.com/spreadsheets/d/1cdXAo7-_wAnncODW3Pn0s3DkARANQnj9Lu8PqAPPF6c/edit?usp=sharing)

K=9 spreadsheet (https://docs.google.com/spreadsheets/d/1ePhVUdXocymdHJShbBFHpdzu3c8LUWYnG5HxKXCy2E0/edit?usp=sharing)

K=10 spreadsheet (https://docs.google.com/spreadsheets/d/1MTm_wkLXkXGTZ6W6rgz-2PyQyqqxjRUNl1KkstjZ11w/edit?usp=sharing)

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.

Drac II
23-07-15, 17:57
This "Native American" DNA shows up among a whole bunch of groups, including people like Scots and Norwegians.

arvistro
23-07-15, 22:44
EHG folks.

Johannes
24-07-15, 00:43
Bell Beaker and Corded Ware folk had on average 2-3% Native American DNA.

Johannes
31-07-15, 02:57
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%

LeBrok
31-07-15, 03:37
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?

Johannes
31-07-15, 12:49
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.

LeBrok
01-08-15, 02:00
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.

Johannes
01-08-15, 10:32
#6 spreadsheet doesn't measure ANE, EEF, and WHG.

ANE and EEF are simply Middle Eastern/European and WHG are European Hunter Gatherers.

Johannes
01-08-15, 10:33
K6
Allentoft and Haak Analysis of Comparisons of DNA 6-3-2015








Steppe

EEF/M E

MN Europe
E. Africa

SC Asia

SSA


Lithuania
61%

0%

38%

0%

0%

0%


Finland
56%

0%

36%



7%




Estonians
61%

0%

37%



1%




Russia
57%

1%

34%



8%




Norway
53%

1%

38%








Scotland
51%

3%

45%








England
48%

6%

46%








Czechs
50%

7%

42%








French
40%

8%

52%








Basques
34%

1%

65%








Spanish
32%

13%

53%

2%






Croats
44%

15%

40%








Italians
23%

30%

40%

7%






Greeks
30%

31%

36%



3%




Bulgarians
37%

37%

36%



1%




Bell Beaker
51%



49%








CW
77%



23%








Algerians
1%

34%

33%

24%



6%


Mozabite
0%

27%

41%

30%



2%
















K6 Revised
Middle East
Europe

E. Eurasia

Ameridians


SSA


Finland
4%

85%

7%

4%






Lithuania
5%

91%

1%

3%






Estonians
4%

91%

2%

3%






Belarus
10%

85%

2%

2%






Iceland
11%

88%



2%






Norway
11%

86%



3%






Ukraine
13%

81%

2%

2%






Scotland
14%

83%



2%






England
16%

82%



1%






Czechs
16%

80%

1%

2%






Hungarians
19%

75%

1%

2%






French
22%

80%



1%






Spanish
24%

72%










Croats
24%

74%

1%

1%






N. Italians
38%

62%










S. Italians
50%

49%

1%








Greeks
42%

55%










Yamnaya
11%

78%

1%

8%






Bell Beaker
9%

90%



1%






CW
6%

86%



6%






Algerians
50%

29%







20%


Mozabites
50%

28%







22%
















K7
Siberian

European

Middle East
Ameridian


SSA


Estonia
4%

92%

1%

1%






Finland
9%

87%

1%

1%






Lithuania
3%

94%

2%

1%






Iceland
6%

90%

0%

1%






Norway
2%

89%

7%

2%






Belarus
3%

89%

5%

2%






Ukraine
4%

83%

10%

1%






Scotland


88%

11%

1%






Basques


88%

10%








England


85%

12%

1%






French
1%

83%

13%








Czechs
2%

84%

13%

1%






Hungary


78%

18%

1%






Croatia


80%

19%








N Spain


80%

19%

1%






S Spain


77%

22%

1%






N Italy


65%

33%








S Italy


53%

45%








Greeks


57%

40%








BB


93%

3%

1%






CW
3%

87%

3%

3%






Yamnaya
5%

77%

11%

6%






Algeria


34%

43%





21%


Mozabites

32%

45%





22%






























K8
Hindu Kush
HG Europe
Middle East
Ameridians


SSA


Estonia
9%

75%

13%

2%






Finland
8%

72%

12%

7%






Lithuania
9%

77%

13%

1%






Iceland
9%

71%

18%

0%






Belarus
10%

70%

17%

0%






Norway
9%

71%

20%

0%






Ukraine
11%

69%

20%








Scotland
10%

67%

21%

0%






EN Spain
0%

41%

59%








MN Spain
0%

47%

53%








N Spain
4%

60%

36%








S Spain
4%

58%

38%








Czechs
10%

66%

23%








England
10%

66%

24%








Hungary
10%

64%

28%








Croatia
11%

60%

29%








French
6%

62%

32%








Greece
15%

42%

43%








N Italy
7%

50%

43%








S Italy
15%

34%

50%








Algeria


18%

59%

1%



20%


Mozabites

15%

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?

MOESAN
01-08-15, 12:18
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")

LeBrok
01-08-15, 16:46
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.

Johannes
02-08-15, 00:57
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:



K6
Allentoft and Haak Analysis of Comparisons of DNA MIXTURE 6-3-2015







Steppe

EEF/Middle Eastern

MN Europe (EEF+EHG)
E. Africa

SC Asia

SSA


Lithuania
61%

0%

38%

0%

0%

0%


Finland
56%

0%

36%

0%

7%

0%


Estonians
61%

0%

37%

0%

1%

0%


Russia
57%

1%

34%

0%

8%

0%


Norway
53%

1%

38%

0%

0%

0%


Scotland
51%

3%

45%

0%

0%

0%


England
48%

6%

46%

0%

0%

0%


Czechs
50%

7%

42%

0%

0%

0%


French
40%

8%

52%

0%

0%

0%


Basques
34%

1%

65%

0%

0%

0%


Spanish
32%

13%

53%

2%

0%

0%


Croats
44%

15%

40%

0%

0%

0%


Italians
23%

30%

40%

7%

0%

0%


Greeks
30%

31%

36%

0%

3%

0%


Bulgarians
37%

37%

36%

0%

1%

0%


Bell Beaker
51%

0%

49%

0%

0%

0%


CW
77%

0%

23%

0%

0%

0%


Algerians
1%

34%

33%

24%

0%

0%


Mozabite
0%

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???



K6
Allentoft and Haak Analysis of Comparisons of DNA MIXTURE 6-3-2015






K6 Revised
Middle East
Europe

E. Eurasia

Ameridians


SSA


Finland
4%

85%

7%

4%



0%


Lithuania
5%

91%

1%

3%



0%


Estonians
4%

91%

2%

3%



0%


Belarus
10%

85%

2%

2%



0%


Iceland
11%

88%

0%

2%



0%


Norway
11%

86%

0%

3%



0%


Ukraine
13%

81%

2%

2%



0%


Scotland
14%

83%

0%

2%



0%


England
16%

82%

0%

1%



0%


Czechs
16%

80%

1%

2%



0%


Hungarians
19%

75%

1%

2%



0%


French
22%

80%

0%

1%



0%


Spanish
24%

72%

0%

0%



0%


Croats
24%

74%

1%

1%



0%


N. Italians
38%

62%

0%

0%



0%


S. Italians
50%

49%

1%

0%



0%


Greeks
42%

55%

0%

0%



0%


Yamnaya
11%

78%

1%

8%



0%


Bell Beaker
9%

90%

0%

1%



0%


CW
6%

86%

0%

6%



0%


Algerians
50%

29%

0%

0%



20%


Mozabites
50%

28%

0%

0%



22%


Yemen
73%

15%

0%

0%



10%


Yemen Jew
87%

8%

0%

0%



4%


Bedouin A
73%

16%

0%

0%



9%


BedouinB
92%

4%

0%

0%



4%

Johannes
02-08-15, 01:25
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.





K6
Allentoft and Haak Analysis of Comparisons of DNA MIXTURE 6-3-2015






K6 Revised
Middle East
Europe

E. Eurasia

Ameridians


SSA


Finland
4%

85%

7%

4%



0%


Lithuania
5%

91%

1%

3%



0%


Estonians
4%

91%

2%

3%



0%


Belarus
10%

85%

2%

2%



0%


Iceland
11%

88%

0%

2%



0%


Norway
11%

86%

0%

3%



0%


Ukraine
13%

81%

2%

2%



0%


Scotland
14%

83%

0%

2%



0%


England
16%

82%

0%

1%



0%


Czechs
16%

80%

1%

2%



0%


Hungarians
19%

75%

1%

2%



0%


French
22%

80%

0%

1%



0%


Spanish
24%

72%

0%

0%



0%


Croats
24%

74%

1%

1%



0%


N. Italians
38%

62%

0%

0%



0%


S. Italians
50%

49%

1%

0%



0%


Greeks
42%

55%

0%

0%



0%


Yamnaya
11%

78%

1%

8%



0%


Bell Beaker
9%

90%

0%

1%



0%


Corded Ware
6%

86%

0%

6%



0%


Algerians
50%

29%

0%

0%



20%


Mozabites
50%

28%

0%

0%



22%


Yemen
73%

15%

0%

0%



10%


Yemen Jew
87%

8%

0%

0%



4%


Bedouin A
73%

16%

0%

0%



9%


BedouinB
92%

4%

0%

0%



4%
















K7
Siberian

European

Middle East
Ameridian


SSA


Estonia
4%

92%

1%

1%



0%


Finland
9%

87%

1%

1%



0%


Lithuania
3%

94%

2%

1%



0%


Iceland
6%

90%

0%

1%



0%


Norway
2%

89%

7%

2%



0%


Belarus
3%

89%

5%

2%



0%


Ukraine
4%

83%

10%

1%



0%


Scotland
0%

88%

11%

1%



0%


Basques
0%

88%

10%

0%



0%


England
0%

85%

12%

1%



0%


French
1%

83%

13%

0%



0%


Czechs
2%

84%

13%

1%



0%


Hungary
0%

78%

18%

1%



0%


Croatia
0%

80%

19%

0%



0%


N Spain
0%

80%

19%

1%



0%


S Spain
0%

77%

22%

1%



0%


N Italy
0%

65%

33%

0%



0%


S Italy
0%

53%

45%

0%



0%


Greeks
0%

57%

40%

0%



0%


Bell Beaker
0%

93%

3%

1%



0%


Corded Ware
3%

87%

3%

3%



0%


Yamnaya
5%

77%

11%

6%



0%


Algeria
0%

34%

43%

0%



21%


Mozabites
0%

32%

45%

0%



22%


Yemen
0%

13%

70%

0%



15%


Yemen Jew
0%

14%

82%

0%



4%


Bedouin A
0%

19%

70%

0%



11%


Bedouin B
0%

5%

90%

0%



5%
















K8
Hindu Kush
HG Europe
Middle East
Ameridians


SSA


Estonia
9%

75%

13%

2%



0%


Finland
8%

72%

12%

7%



0%


Lithuania
9%

77%

13%

1%



0%


Iceland
9%

71%

18%

0%



0%


Belarus
10%

70%

17%

0%



0%


Norway
9%

71%

20%

0%



0%


Ukraine
11%

69%

20%

0%



0%


Scotland
10%

67%

21%

0%



0%


EN Spain
0%

41%

59%

0%



0%


MN Spain
0%

47%

53%

0%



0%


N Spain
4%

60%

36%

0%



0%


S Spain
4%

58%

38%

0%



0%


Czechs
10%

66%

23%

0%



0%


England
10%

66%

24%

0%



0%


Hungary
10%

64%

28%

0%



0%


Croatia
11%

60%

29%

0%



0%


French
6%

62%

32%

0%



0%


Greece
15%

42%

43%

0%



0%


N Italy
7%

50%

43%

0%



0%


S Italy
15%

34%

50%

0%



0%


Algeria
0%

18%

59%

1%



20%


Mozabites
0%

15%

61%

0%



21%


Yemen
25%

1%

56%

0%



15%


Yemen Jew
22%

0%

72%

0%



5%


Bedouin A
23%

7%

61%

0%



9%


Bedouin B
16%

0%

80%

0%



4%

Johannes
02-08-15, 01:34
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??

LeBrok
02-08-15, 07:31
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.

joeyc
02-08-15, 07:44
Half of those numbers posted by Johanned are wrong. For first Italy is not 7% African, but 0.7%.

Sile
02-08-15, 08:47
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

Johannes
02-08-15, 09:27
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.

Johannes
02-08-15, 09:28
how did the spanish get 2% east-african...............maybe he meant north-african

Yes, it's North-African. But don't follow that table. Look at the revised tables.