It is hard to believe in some ancestry results. FamilyTreeDna's new Ancient Origins give me following results
Metal Age Invader 12%
Farmer 30%
Hunter-Gatherer 54%
Non-European 4%
Regarding Metal Age Invaders they refer to the Metal Age Yamnaya culture, regarding Farmers to the Neolithic Anatolian migration to Europe and regarding Hunter-Gatherers to ancient LaBrana, Loschbour and Motala samples. Regarding non-European proportion they give a hint to look at myOrigins, which is FamilyTreeDna's admixture analysis based on present-day populations. My myOrigins give me only one non-European group, Middle Easterners. I doubt it, the non-European in my Ancient Origins test is likely Asian.
Going further in analyzing results I compared my Ancient Origin results to scientific papers, Haak et al. 2015 giving comparable results. Haak et al. gives following results for Finns:
EN (Farmers) 31.5%
Nganasan (Asian) 10.2%
WHG (Hunter-Gatherer) 7.9%
Yamnaya (Metal Age Intrurers) 50.4%
Respectively Norwegians get in this study
EN (Farmers) 48.2%
Nganasan (Asian) 4.2%
WHG (Hunter-Gatherer) 0%
Yamnaya (Metal Age Intrurers) 47.5%
We can see a huge transition between Yamnayas/Iron Age Intruders and Hunter-Gatherers between Ancient Origins and Haak et al. I know something about the method used by Haak et al., but I have no idea what FamilyTreeDna did. However, if I try to guess, I would say that they could have used a very drastic LD-pruning. I can get similar differences by heavily pruned data and it makes sense. Metal-Age invasion to Europe happened during the Bronze Age, thousands years later than the arrival of hunter-gatherers. So it is reasonable to assume that we have still much more Bronze Age genetic drift than drift from hunter-gatherers, thus removing LD removes more ancestry of Metal Age Intrurers. Pruning present-day samples does't have same effect due to more similar genetic composition.
I made also some admixture tests. Pruning LD gives a big change in ancient admixtures.
My result without pruning
Anatolian_Neolithic 31.4
BA_East_European_Steppe 44,8
East_and_Southeast_Asian 10,8
Western_Hunter_Gathrerer 13
and after pruning
Anatolian_Neolithic 27.5
BA_East_European_Steppe 25.9
East_and_Southeast_Asian 7.8
Western_Hunter_Gathrerer 38.8
I am not saying that the difference between results of FamilyTreeDna and Haak et al. is caused by pruning, because I don't know it. I only state that pruning ancient samples is risky.
Wednesday, November 16, 2016
Wednesday, November 9, 2016
Project admix results, revised
My previous test was missing of German reference samples. Together with the fact that my Swedish reference samples seem to be somewhat off, this gave results biased towards Balto-Slavs. I have now added German samples available from Pagani et al. 2016 and have rerun all project samples, plus two new Finnish samples. Additionally I tested three Finnish samples introduced by aforementioned study. Soon after downloading those samples I understood that they don't represent average Finns. So this point is included after project results.
I had difficulties in editing columns and after some useless efforts I copy-pasted all in plain text format.
A new grouping, Karelian-Finnic indicates a sum of Karelian and Veps people.
FI1
Finland 57,0
AMBIG_Europe 25,0
Balto-Slavic 12,9
AMBIGUOUS 2,6
Baltic-Finnic 2,5
FI2
Finland 37,2
AMBIG_Europe 28,0
Balto-Slavic 14,8
NW-Atlantic-Europe 10,6
AMBIGUOUS 5,6
Saami 3,9
F3
Finland 62,3
AMBIG_Europe 33,0
AMBIGUOUS 2,4
Baltic-Finnic 2,3
F4
Finland 47,2
AMBIG_Europe 18,9
NW-Atlantic-Europe 18,1
Northeast-Europe 15,8
FI5
Finland 53,8
AMBIG_Europe 33,1
Baltic-Finnic 11,7
AMBIGUOUS 1,4
FI6
Finland 43,0
AMBIG_Europe 36,0
Baltic-Finnic 12,5
NW-Atlantic-Europe 7,9
FI7
Finland 78,7
AMBIG_Europe 17,4
TunNenets 3,4
FI8
Finland 56,5
Karelia 25,4
AMBIG_Europe 17,4
FI9
Finland 42,1
AMBIG_Europe 27,7
Karelia 24,5
Karelian-Finnic 5,0
FI10
Finland 43,1
Saami 21,5
AMBIG_Europe 10,9
Karelian-Finnic 10,2
AMBIGUOUS 10.0
AMBIG_Siberian 4,3
FI11
Finland 63,7
AMBIG_Europe 31,7
AMBIGUOUS 2,8
Baltic-Finnic 1,8
FI12
Finland 71,6
AMBIG_Europe 18,0
Central-Europe 10,2
FI14
Finland 69,8
Balto-Slavic 16,0
AMBIG_Europe 11,3
Baltic-Finnic 1,6
AMBIGUOUS 1,3
FI15
Finland 62,0
Karelian-Finnic 21,2
AMBIG_Europe 14,9
AMBIGUOUS 1,9
FI16
Finland 43,1
AMBIG_Europe 22,9
Estonia 21,8
Karelia 10,3
AMBIGUOUS 1,8
FI17
Finland 33,9
Central-Europe 24,0
Karelia 13,8
Baltic-Finnic 9,8
AMBIG_Europe 9,5
RU_Pinega 5,6
AMBIGUOUS 2,1
Karelian-Finnic 1,3
FI18
Finland 46,1
Karelian-Finnic 19,7
Balto-Slavic 14,5
AMBIG_Europe 8,8
Baltic-Finnic 6,5
Saami 3,7
FI19
Finland 0,62
AMBIG_Europe 0,20
Northeast-Europe 0,08
RU_Pinega 0,05
Saami 0,03
AMBIGUOUS 0,02
FI20
Finland 57,8
AMBIG_Europe 21,8
Balto-Slavic 10,9
AMBIGUOUS 5,1
Baltic-Finnic 4,3
FI21
Finland 53,1
Karelia 28,0
AMBIG_Europe 10,7
Northeast-Europe 4,8
AMBIGUOUS 2,2
Karelian-Finnic 1,2
SC2
NW-Atlantic-Europe 32,8
Central-Europe 32,5
Balto-Slavic 19,3
AMBIG_Europe 13,3
AMBIGUOUS 2,1
SC3
Baltic-Finnic 27,6
Central-Europe 21,2
AMBIG_Europe 19,3
Norway 17,5
NW-Atlantic-Europe 12,9
AMBIGUOUS 1,6
SC4
Norway 53,0
Central-Europe 18,3
Balto-Slavic 13,7
NW-Atlantic-Europe 8,1
AMBIG_Europe 6,5
SC5
AMBIG_Europe 28,9
NW-Atlantic-Europe 18,3
Central-Europe 18,3
Ireland 14,1
GermanyAustria 11,5
Northeast-Europe 7,9
AMBIGUOUS 1,0
SC6
Central-Europe 31,5
NW-Atlantic-Europe 24,7
AMBIG_Europe 16,5
Finland 14,5
Balto-Slavic 11,9
AMBIGUOUS 1,0
SC7
AMBIG_Europe 29,7
NW-Atlantic-Europe 26,1
Sweden 20,5
Orcadian 11,0
Central-Europe 10,7
AMBIGUOUS 1,9
Additionally some freely available genomes, only for checking the method.
Genomes Unzipped, VXP
North-Italy 24,9
Central-Europe 20,7
AMBIG_Europe 18,4
Norway 13,7
NW-Atlantic-Europe 12,0
South-Europe 6,6
AMBIGUOUS 3,8
Genomes Unzipped, JKP
Central-Europe 28,9
South-Europe 19,8
NW-Atlantic-Europe 19,1
Spain 12,5
AMBIG_Europe 11,3
AMBIG_WEURASIA 5,8
AMBIG_SEURASIA 2,0
Razib Khan, downloaded here.
Indian 35,6
Sindhi 22,3
Cambodian 12,8
AMBIGUOUS 10,6
Burusho 8,6
IndianJew 6,3
AMBIG_Southeast-Asian 2,4
AMBIG_EEURASIA 1,4
Blaine Bettinger, downloaded here.
He looks British, with a small portion of Native American.
Central-Europe 24,9
Kent 24,1
AMBIG_Europe 21,2
Welsh 9,3
AMBIGUOUS 7,9
Ireland 7,3
Atlantic-Europe 3,3
Native-American 1,9
Tests using Pagani et al. Finns as a Finnish reference
Pagani-FI12
Karelia 28,0
AMBIG_Europe 23,8
Central-Europe 17,8
Baltic-Finnic 12,6
Finland 12,1
Karelian-Finnic 3,4
AMBIGUOUS 2,4
Pagani-FI14
Estonia 23,7
AMBIG_Europe 22,5
Karelia 18,6
Central-Europe 18,5
Finland 7,9
Karelian-Finnic 4,7
AMBIGUOUS 4,1
Pagani-FI21
Karelia 46,3
AMBIG_Europe 16,1
Finland 10,4
Baltic-Finnic 8,7
Northeast-Europe 8,5
Saami 4,3
AMBIGUOUS 2,9
Karelian-Finnic 2,8
I tested three Finns, seen above, two of them typical Western Finns without any obvious foreign admixture and one should be a typical Finn from East Finland. The first row below shows the average result using average Finnish reference picked from 1000-genomes and the second row shows the average result after changing the reference to Finnish samples of Pagani et al.
FI12, FI14 and FI21, average Finnish result when using average Finnsh reference 64,8
FI12, FI14 and FI21, average Finnish result when using Pagani Finnish samples as a reference 10,1
In this particular case, while Pagani Finns almost fully mismatch with average Finns, it also eliminates Finnish admixture of Swedish results where it is present in analyses based on average Finnish reference, in some cases substituting Finnish admixture by Karelian and Veps. This is really odd.
A map giving an estimate of admixture regions in Europe
I had difficulties in editing columns and after some useless efforts I copy-pasted all in plain text format.
A new grouping, Karelian-Finnic indicates a sum of Karelian and Veps people.
FI1
Finland 57,0
AMBIG_Europe 25,0
Balto-Slavic 12,9
AMBIGUOUS 2,6
Baltic-Finnic 2,5
FI2
Finland 37,2
AMBIG_Europe 28,0
Balto-Slavic 14,8
NW-Atlantic-Europe 10,6
AMBIGUOUS 5,6
Saami 3,9
F3
Finland 62,3
AMBIG_Europe 33,0
AMBIGUOUS 2,4
Baltic-Finnic 2,3
F4
Finland 47,2
AMBIG_Europe 18,9
NW-Atlantic-Europe 18,1
Northeast-Europe 15,8
FI5
Finland 53,8
AMBIG_Europe 33,1
Baltic-Finnic 11,7
AMBIGUOUS 1,4
FI6
Finland 43,0
AMBIG_Europe 36,0
Baltic-Finnic 12,5
NW-Atlantic-Europe 7,9
FI7
Finland 78,7
AMBIG_Europe 17,4
TunNenets 3,4
FI8
Finland 56,5
Karelia 25,4
AMBIG_Europe 17,4
FI9
Finland 42,1
AMBIG_Europe 27,7
Karelia 24,5
Karelian-Finnic 5,0
FI10
Finland 43,1
Saami 21,5
AMBIG_Europe 10,9
Karelian-Finnic 10,2
AMBIGUOUS 10.0
AMBIG_Siberian 4,3
FI11
Finland 63,7
AMBIG_Europe 31,7
AMBIGUOUS 2,8
Baltic-Finnic 1,8
FI12
Finland 71,6
AMBIG_Europe 18,0
Central-Europe 10,2
FI14
Finland 69,8
Balto-Slavic 16,0
AMBIG_Europe 11,3
Baltic-Finnic 1,6
AMBIGUOUS 1,3
FI15
Finland 62,0
Karelian-Finnic 21,2
AMBIG_Europe 14,9
AMBIGUOUS 1,9
FI16
Finland 43,1
AMBIG_Europe 22,9
Estonia 21,8
Karelia 10,3
AMBIGUOUS 1,8
FI17
Finland 33,9
Central-Europe 24,0
Karelia 13,8
Baltic-Finnic 9,8
AMBIG_Europe 9,5
RU_Pinega 5,6
AMBIGUOUS 2,1
Karelian-Finnic 1,3
FI18
Finland 46,1
Karelian-Finnic 19,7
Balto-Slavic 14,5
AMBIG_Europe 8,8
Baltic-Finnic 6,5
Saami 3,7
FI19
Finland 0,62
AMBIG_Europe 0,20
Northeast-Europe 0,08
RU_Pinega 0,05
Saami 0,03
AMBIGUOUS 0,02
FI20
Finland 57,8
AMBIG_Europe 21,8
Balto-Slavic 10,9
AMBIGUOUS 5,1
Baltic-Finnic 4,3
FI21
Finland 53,1
Karelia 28,0
AMBIG_Europe 10,7
Northeast-Europe 4,8
AMBIGUOUS 2,2
Karelian-Finnic 1,2
SC2
NW-Atlantic-Europe 32,8
Central-Europe 32,5
Balto-Slavic 19,3
AMBIG_Europe 13,3
AMBIGUOUS 2,1
SC3
Baltic-Finnic 27,6
Central-Europe 21,2
AMBIG_Europe 19,3
Norway 17,5
NW-Atlantic-Europe 12,9
AMBIGUOUS 1,6
SC4
Norway 53,0
Central-Europe 18,3
Balto-Slavic 13,7
NW-Atlantic-Europe 8,1
AMBIG_Europe 6,5
SC5
AMBIG_Europe 28,9
NW-Atlantic-Europe 18,3
Central-Europe 18,3
Ireland 14,1
GermanyAustria 11,5
Northeast-Europe 7,9
AMBIGUOUS 1,0
SC6
Central-Europe 31,5
NW-Atlantic-Europe 24,7
AMBIG_Europe 16,5
Finland 14,5
Balto-Slavic 11,9
AMBIGUOUS 1,0
SC7
AMBIG_Europe 29,7
NW-Atlantic-Europe 26,1
Sweden 20,5
Orcadian 11,0
Central-Europe 10,7
AMBIGUOUS 1,9
Additionally some freely available genomes, only for checking the method.
Genomes Unzipped, VXP
North-Italy 24,9
Central-Europe 20,7
AMBIG_Europe 18,4
Norway 13,7
NW-Atlantic-Europe 12,0
South-Europe 6,6
AMBIGUOUS 3,8
Genomes Unzipped, JKP
Central-Europe 28,9
South-Europe 19,8
NW-Atlantic-Europe 19,1
Spain 12,5
AMBIG_Europe 11,3
AMBIG_WEURASIA 5,8
AMBIG_SEURASIA 2,0
Razib Khan, downloaded here.
Indian 35,6
Sindhi 22,3
Cambodian 12,8
AMBIGUOUS 10,6
Burusho 8,6
IndianJew 6,3
AMBIG_Southeast-Asian 2,4
AMBIG_EEURASIA 1,4
Blaine Bettinger, downloaded here.
He looks British, with a small portion of Native American.
Central-Europe 24,9
Kent 24,1
AMBIG_Europe 21,2
Welsh 9,3
AMBIGUOUS 7,9
Ireland 7,3
Atlantic-Europe 3,3
Native-American 1,9
Tests using Pagani et al. Finns as a Finnish reference
Pagani-FI12
Karelia 28,0
AMBIG_Europe 23,8
Central-Europe 17,8
Baltic-Finnic 12,6
Finland 12,1
Karelian-Finnic 3,4
AMBIGUOUS 2,4
Pagani-FI14
Estonia 23,7
AMBIG_Europe 22,5
Karelia 18,6
Central-Europe 18,5
Finland 7,9
Karelian-Finnic 4,7
AMBIGUOUS 4,1
Pagani-FI21
Karelia 46,3
AMBIG_Europe 16,1
Finland 10,4
Baltic-Finnic 8,7
Northeast-Europe 8,5
Saami 4,3
AMBIGUOUS 2,9
Karelian-Finnic 2,8
I tested three Finns, seen above, two of them typical Western Finns without any obvious foreign admixture and one should be a typical Finn from East Finland. The first row below shows the average result using average Finnish reference picked from 1000-genomes and the second row shows the average result after changing the reference to Finnish samples of Pagani et al.
FI12, FI14 and FI21, average Finnish result when using average Finnsh reference 64,8
FI12, FI14 and FI21, average Finnish result when using Pagani Finnish samples as a reference 10,1
In this particular case, while Pagani Finns almost fully mismatch with average Finns, it also eliminates Finnish admixture of Swedish results where it is present in analyses based on average Finnish reference, in some cases substituting Finnish admixture by Karelian and Veps. This is really odd.
A map giving an estimate of admixture regions in Europe
