(NEW) GenePlaza K12 Ancient Calculator Results

[Angela]

Does anyone know if Kurd has published precisely which samples, other than LBK, make up his "Eastern farmer" reference sample? LBK would have no Anatolia Chalcolithic/Anatolia Bronze. All I know, as I said, is that LBK is included, and that the samples are from 8,000 to 5,000 years ago.

 

[noman]

Of course, noman, if you wish it, and for what it's worth.

Either post your results here or send them to me by PM if you wish it to be private.

My results are on the first page - the very first post.

 

[Angela]

My results are on the first page - the very first post.

I'd guess Indian, and given the high "steppe", I'd say perhaps Northwest Indian and high caste? I don't know if Afghan would be possible.

It's interesting how the Iran Neo type farmer is so much higher but brought along Western (Anatolian) and Levant farmer genetic material along with it, probably because a certain amount of admixture had already taken place.

Another interesting thing is that the steppe substructure is divided pretty evenly. Could that mean that the steppe like groups that went to India were already pretty well admixed, for example perhaps in Bactria?

I wouldn't have guessed that the Southeast Eurasian component was the smallest, although not by much.

This is all speculation, but you did ask.

 

[Alan]

Here is my results, the results are okay. The only concern I have is that the "Western European Farmers" samples came from Neolithic Iberia;aka Atlantic Megalithic and a mixture of WHG and EFF themselves.

HOW RELATED ARE YOU TO ANCIENT CIVILIZATIONS

• • ANCIENT FARMERS54.2%
    • WEST EUROPEAN FARMERS (4000-5000 years)29.5%
    • LEVANT (4000-8000 years)5.2%
    • NEOLITHIC-CHALCOLITHIC IRAN-CHG (5000-12000 years)4.4%
    • EAST EUROPEAN FARMERS (5000-8000 years)15.2%
• STEPPE CULTURES32.3%
• WESTERN EUROPEAN & SCANDINAVIAN HUNTER GATHERERS (4000-5000 years)13.5%
• AFRICAN0.0%
• EASTERN NON AFRICANS (modern)0.0%
• SOUTHEAST EURASIAN0.0%

eh not really Western European Farmers are basically EEF from Central Europe to Iberia. Those were not really a "mix" of WHG- EEF but almost completely Anatolian_NEO with some WHG admixture (3-10%).

 

[Angela]

eh not really Western European Farmers are basically EEF from Central Europe to Iberia. Those were not really a "mix" of WHG- EEF but almost completely Anatolian_NEO with some WHG admixture (3-10%).

Some of the samples are Iberian Chalcolithic, so more WHG, maybe up to 20% for some of them. If he had early Cardial it would probably be different.

 

[Alan]

Some of the samples are Iberian Chalcolithic, so more WHG, maybe up to 20% for some of them. If he had early Cardial it would probably be different.

True, I have to correct myself. After seeing the datings. It seems those are Middle Neolithic samples. Those were indeed up to 15-25% admixed with WHG. Basically the main source of Basques and Sardinians. There seems to have come very little addition to these two populations after the middle Neolithic.

 

[Alan]

I see "East European" farmers are basically another wave of those earliest farmers that left Anatolia for Greece, the Balkans and northern Black Sea (CT culture).

 

[Alan]

Hmmm, what will you get when you pull Neolithic Iran/CHG genes from Yamnaya-Afansievo? What's left is pure EHG genes, not the BA Steppe Culture. You can't measure Yamnaya without Iran/CHG in it!
When you measure farmer genes on one side, you should measure h-gs on the other. Not the mixed cultures like Steppe BA or even Iron Age like in case of Scythians.
Likewise when you measure Steppe Cultures, you should compare them to their contemporaries. Like BA Hungary or Balkans or BA Levant.

I think what he is trying to do here, is measure ancestry based on post early Neolithic genomes. Means how we show up as a mix of populations that emerged from middle Neolithic to Bronze Age.

WHat he labeled here as Iran_CHL/CHG is actually Iran_CHL/CHG admixture that can not be explained via Steppe admixture. Thats how I understand it.

Unfortunately we don't have Bronze_Age or Neolithic samples from the North Caucasus. Therefore to counter confusion he should have used a different term or call it "extra Iran/CHG".

 

[Alan]

I just ran GedrisiaDNA K13 for the RISE548 Temrta IV and it seems like he had 90% EHG. Just curious, how old do you think RISE548 is? . F999968

gedrosia K13 Oracle

Admix Results (sorted):

Population

EHG

[TD="align: center"] # [/TD]

[TD="align: right"] Percent [/TD]

[TD="align: center"]1[/TD]

[TD="align: right"]91.64[/TD]

[TD="align: center"]2[/TD]
[TD="width: 120"]CHG_EEF[/TD]
[TD="width: 50, align: right"]6.82[/TD]

[TD="width: 30, align: center"]3[/TD]
[TD="width: 120"]IRAN_NEOLITHIC[/TD]
[TD="width: 50, align: right"]1.03[/TD]

Finished reading population data. 145 populations found.
13 components mode.

--------------------------------

Least-squares method.

Using 1 population approximation:
1 Steppe_EMBA @ 8.332838
2 EHG @ 10.848113
3 Steppe_Eneolithic @ 15.332281
4 MA1 @ 35.752441
5 Steppe_MLBA @ 54.005684
6 Steppe_IA @ 57.893478
7 Europe_LNBA @ 68.595451
8 Mansi @ 81.844429
9 Russian @ 84.221184
10 Finnish @ 84.834053
11 Tajik @ 85.156075
12 Estonian @ 85.601242
13 Norwegian @ 86.192795
14 English @ 86.641441
15 Icelandic @ 86.720924
16 Ukrainian @ 86.735909
17 Lezgin @ 86.938011
18 Lithuanian @ 87.061974
19 Chechen @ 87.216942
20 Scottish @ 87.639229

Using 2 populations approximation:
1 50% Steppe_EMBA +50% Steppe_EMBA @ 8.332838


Using 3 populations approximation:
1 50% EHG +25% EHG +25% Steppe_MLBA @ 6.024658


Using 4 populations approximation:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 EHG + EHG + EHG + Steppe_MLBA @ 6.024658
2 EHG + EHG + Steppe_EMBA + Steppe_MLBA @ 6.929148
3 Steppe_EMBA + Steppe_EMBA + Steppe_EMBA + Steppe_Eneolithic @ 7.842470
4 EHG + Steppe_EMBA + Steppe_EMBA + Steppe_MLBA @ 7.931480
5 EHG + Steppe_EMBA + Steppe_EMBA + Steppe_Eneolithic @ 8.007501
6 Steppe_EMBA + Steppe_EMBA + Steppe_EMBA + Steppe_EMBA @ 8.332838
7 EHG + EHG + Steppe_EMBA + Steppe_Eneolithic @ 8.360223
8 EHG + EHG + EHG + MA1 @ 8.508878
9 EHG + EHG + MA1 + Steppe_EMBA @ 8.638973
10 EHG + Steppe_EMBA + Steppe_EMBA + Steppe_EMBA @ 8.761701
11 EHG + EHG + EHG + Steppe_Eneolithic @ 8.878288
12 EHG + MA1 + Steppe_EMBA + Steppe_EMBA @ 8.945330
13 Steppe_EMBA + Steppe_EMBA + Steppe_EMBA + Steppe_MLBA @ 8.997570
14 EHG + Steppe_EMBA + Steppe_Eneolithic + Steppe_Eneolithic @ 9.184469
15 EHG + EHG + Steppe_Eneolithic + Steppe_Eneolithic @ 9.242440
16 Steppe_EMBA + Steppe_EMBA + Steppe_Eneolithic + Steppe_Eneolithic @ 9.297512
17 EHG + EHG + Steppe_EMBA + Steppe_EMBA @ 9.339354
18 MA1 + Steppe_EMBA + Steppe_EMBA + Steppe_EMBA @ 9.410752
19 EHG + EHG + EHG + Steppe_EMBA @ 10.044287
20 EHG + EHG + EHG + Steppe_IA @ 10.053915

Done.

Gedrosia K12 had flaws with ancient samples. Kurd even mentioned that and it had been mentioned here several times too. It is impossible that a Yamnaya sample is 90% EHG even with variation. the samples were in variation between 40-60% EHG.

 

[Angela]

I see "East European" farmers are basically another wave of those earliest farmers that left Anatolia for Greece, the Balkans and northern Black Sea (CT culture).

As I said, I'd like to know which specific samples Kurd included in that "eastern" group other than LBK, so we can approximate how much Iran Neo/Chal. is sort of "hidden" in that, like WHG is hidden in the Spain Chalcolithic. I don't think the Portugal Neolithic which is also included in the western group has much WHG if I remember correctly, so I would doubt, if that's correct, that Western farmers in this calculator are 20-25% WHG.

 

[Angela]

I personally haven't seen any Western European farmer scores higher than these two. Since a poster from Romagna who also has some Emilian? has much less western farmer than I do, either full Emilians like my father have a lot more western farmer than people from Romagna because of the later Adriatic and Greek influence on the latter, and/or Ligurians have a lot of western farmer. The latter, at least, makes absolute sense to me, as Cardial/Impressa may have passed through Liguria (and coastal Toscana) to get to southern France and Spain. It would be nice to see the scores of a Sardinian and of some Spanish testees.

Basque poster:
Ancient Farmers: 70.3
Western European Farmers: 43.2%
Levant: 3.7%
Neolithic & Chalcolithic Iran: 3%
Eastern European Farmers: 20.4%


These are my scores:
ANCIENT FARMERS

74.3%​

• WEST EUROPEAN FARMERS (4000-5000 years)
  39.2%​
• LEVANT (4000-8000 years)
  3.3%​
• NEOLITHIC-CHALCOLITHIC IRAN-CHG (5000-12000 years)
  3.4%​
• EAST EUROPEAN FARMERS (5000-8000 years)
  28.4%
  
  
  ​

 

[Alan]

These are my results:

Ancient Farmers: 70.3
Western European Farmers: 43.2%
Levant: 3.7%
Neolithic & Chalcolithic Iran: 3%
Eastern European Farmers: 20.4%

Steppe Cultures: 22.7%

Karasuk-Scythian: 5%
Andronovo-Srubnaya: 9.6%
Yamnaya-Afanasievo-Poltavka: 8.1%

​Western European & Scandinavian Hunter-Gatherers: 7%

Nice to have a Basque result too.

 

[davef]

I personally haven't seen any Western European farmer scores higher than these two. Since a poster from Romagna who also has some Emilian? has much less western farmer than I do, either full Emilians like my father have a lot more western farmer than people from Romagna because of the later Adriatic and Greek influence on the latter, and/or Ligurians have a lot of western farmer. The latter, at least, makes absolute sense to me, as Cardial/Impressa may have passed through Liguria (and coastal Toscana) to get to southern France and Spain. It would be nice to see the scores of a Sardinian and of some Spanish testees.

Basque poster:
Ancient Farmers: 70.3
Western European Farmers: 43.2%
Levant: 3.7%
Neolithic & Chalcolithic Iran: 3%
Eastern European Farmers: 20.4%


These are my scores:
ANCIENT FARMERS

74.3%​

• WEST EUROPEAN FARMERS (4000-5000 years)
  39.2%​
• LEVANT (4000-8000 years)
  3.3%​
• NEOLITHIC-CHALCOLITHIC IRAN-CHG (5000-12000 years)
  3.4%​
• EAST EUROPEAN FARMERS (5000-8000 years)
  28.4%
  
  
  ​

Did you make that map?

 

[davef]

Does anyone know if Kurd has published precisely which samples, other than LBK, make up his "Eastern farmer" reference sample? LBK would have no Anatolia Chalcolithic/Anatolia Bronze. All I know, as I said, is that LBK is included, and that the samples are from 8,000 to 5,000 years ago.

I copied this from Dibran's post:

"References consist of genomes from Turkey, Greece, and other parts of SE Europe from the Neolithic period. These represent descendants of the first farmers to colonize Europe from the Near East."

I guess this is copied from the instruction manual that came with the cotton swab and whatever else is in the kit you ordered from gene plaza. It says that it's made of Neolithic farmers from Greece and Turkey. This is from a wiki:

"Neolithic settlements include Çatalhöyük, Çayönü, Nevali Cori, Aşıklı Höyük, Boncuklu Höyük Hacilar, Göbekli Tepe, Norsuntepe, Kosk, and Mersin."

So I guess it's comprised of the genomes of these people.

The western component is western farmer, which is from ancient Spanish farmers.

Peace out

 

[Alan]

Not weird as in wrong, of course, or bad. I apologize if it came across that way. I just didn't expect any African to show up in mainland Greece. I would have thought even the East African would have disappeared by now. I don't understand the southeast Eurasian either. I normally see it as a trace of the South Asian in some steppe ancestry. Perhaps that's what happened. You just happen to have kept a trace of it.

Still, I'd wait a day or so and maybe try it again.

The East African didn't disappear because it is indeed Natufian related DNA in East Africans. As written previously the calculator tries to model people as a mix of post early Neolithic populations. The East African component in this calculator is actually of modern samples as it is written by the component.

So it is Levant-Neo/Natufian DNA that can not be explained by Levant_Neo/CHL. It could even have come from Bronze Age East Africa when East Africans where already heavily mixed with Levant-Neo like ancestry.

 

[Ghani]

As I said, I'd like to know which specific samples Kurd included in that "eastern" group other than LBK, so we can approximate how much Iran Neo/Chal. is sort of "hidden" in that, like WHG is hidden in the Spain Chalcolithic. I don't think the Portugal Neolithic which is also included in the western group has much WHG if I remember correctly, so I would doubt, if that's correct, that Western farmers in this calculator are 20-25% WHG.

Here are the references for E European Farmer that Dilawer me:


Anatolia_N I0707
Anatolia_N I0708
Anatolia_N I0709
Anatolia_N I0744
Anatolia_N I0745
Anatolia_N I0746
Anatolia_N I1580
Anatolia_N I1581
Anatolia_N I1583
Anatolia_N I1585
Anatolia_N_Imputed Bar8
Anatolia_N_Imputed Bar31
Central_LNBA_Imputed RISE150
Central_LNBA_Imputed RISE577
Europe_EN CB13
Europe_EN I1505
Europe_EN I1506
Europe_LNBA I0099
Europe_LNBA I0103
Europe_LNBA I0104
Europe_LNBA I0112
Europe_LNBA I0117
Europe_LNBA I0118
Europe_LNBA I0164
Europe_MNChL I1497
Europe_MNChL Matojo
Greek_EN_Imputed Rev5
Greek_LN_Imputed Klei10
Greek_LN_Imputed Pal7
Stuttgart_Imputed LBK


These are for the W European Farmer:

Europe_MNChL I0172
Europe_MNChL I0408
Portugal_BA_Imputed MonteGato104
Portugal_BA_Imputed TV3831
Portugal_BA_Imputed TV32032
Portugal_LN_Imputed CabecoArruda122A
Portugal_LN_Imputed CovaMoura9B
Portugal_LN_Imputed CovaMoura364
Portugal_LN_Imputed DolmenAnsiao96B
Portugal_MN_Imputed LugarCanto41
Portugal_MN_Imputed LugarCanto42
Portugal_MN_Imputed LugarCanto44
Spain_Chl_Imputed ATP2
Spain_Chl_Imputed ATP12-1420
Spain_Chl_Imputed ATP16

 

[Alan]

My results
ANCIENT FARMERS71.8%
WEST EUROPEAN FARMERS (4000-5000 years)14.8%
LEVANT (4000-8000 years)6.8%
NEOLITHIC-CHALCOLITHIC IRAN-CHG (5000-12000 years)21.4%
EAST EUROPEAN FARMERS (5000-8000 years)28.8%

STEPPE CULTURES21.7%
KARASUK-E SCYTHIAN (2000-3000 years)11.2%
ANDRONOVO-SRUBNAYA (3000-4000 years)5.6%
YAMNAYA-AFANASIEVO-POLTAVKA (4000-5000 years)4.9%

SOUTHEAST EURASIAN 4.4%

AFRICAN 2.1%
EAST AFRICAN (modern)2.1%
WEST AFRICAN (modern)0.0%

WESTERN EUROPEAN & SCANDINAVIAN HUNTER GATHERERS (4000-5000 years)0.0%

EASTERN NON AFRICANS (modern)0.0%



Angela you are the only one beside Noman who has little more Karasuk Scythian scores. Noman make sense him being also a Indo_Iranian speaker. But your results are out of the ordinary. There is definitely something Alan like going on in your heritage.

I also score the East African 2.1% it is very similar figure to matadworf and Nomans s so I doubt his has anything to do with ancient Ethopians in Greece or Rajasthan. Rather ancient Natufian/Levant_Neo like DNA in East Africa.

What else I have in common with matadworfs is the South Eurasian. Greek and Indo_Iranian speakers must be from a similar source that still had traces of this ancestry?

I am the person with the highest extra Iran_Neo/CHG scores here so far.

And not atypical for a non European, I have zero real WHG ancestry.

 

[Ghani]

Does anyone know if Kurd has published precisely which samples, other than LBK, make up his "Eastern farmer" reference sample? LBK would have no Anatolia Chalcolithic/Anatolia Bronze. All I know, as I said, is that LBK is included, and that the samples are from 8,000 to 5,000 years ago.

Here are the references for E European Farmer that Dilawer emailed me:

Anatolia_N I0707
Anatolia_N I0708
Anatolia_N I0709
Anatolia_N I0744
Anatolia_N I0745
Anatolia_N I0746
Anatolia_N I1580
Anatolia_N I1581
Anatolia_N I1583
Anatolia_N I1585
Anatolia_N_Imputed Bar8
Anatolia_N_Imputed Bar31
Central_LNBA_Imputed RISE150
Central_LNBA_Imputed RISE577
Europe_EN CB13
Europe_EN I1505
Europe_EN I1506
Europe_LNBA I0099
Europe_LNBA I0103
Europe_LNBA I0104
Europe_LNBA I0112
Europe_LNBA I0117
Europe_LNBA I0118
Europe_LNBA I0164
Europe_MNChL I1497
Europe_MNChL Matojo
Greek_EN_Imputed Rev5
Greek_LN_Imputed Klei10
Greek_LN_Imputed Pal7
Stuttgart_Imputed LBK


These are for W European Farmer:

Europe_MNChL I0172
Europe_MNChL I0408
Portugal_BA_Imputed MonteGato104
Portugal_BA_Imputed TV3831
Portugal_BA_Imputed TV32032
Portugal_LN_Imputed CabecoArruda122A
Portugal_LN_Imputed CovaMoura9B
Portugal_LN_Imputed CovaMoura364
Portugal_LN_Imputed DolmenAnsiao96B
Portugal_MN_Imputed LugarCanto41
Portugal_MN_Imputed LugarCanto42
Portugal_MN_Imputed LugarCanto44
Spain_Chl_Imputed ATP2
Spain_Chl_Imputed ATP12-1420
Spain_Chl_Imputed ATP16

 

[Angela]

Here are the references for E European Farmer that Dilawer me:


Anatolia_N I0707
Anatolia_N I0708
Anatolia_N I0709
Anatolia_N I0744
Anatolia_N I0745
Anatolia_N I0746
Anatolia_N I1580
Anatolia_N I1581
Anatolia_N I1583
Anatolia_N I1585
Anatolia_N_Imputed Bar8
Anatolia_N_Imputed Bar31
Central_LNBA_Imputed RISE150
Central_LNBA_Imputed RISE577
Europe_EN CB13
Europe_EN I1505
Europe_EN I1506
Europe_LNBA I0099
Europe_LNBA I0103
Europe_LNBA I0104
Europe_LNBA I0112
Europe_LNBA I0117
Europe_LNBA I0118
Europe_LNBA I0164
Europe_MNChL I1497
Europe_MNChL Matojo
Greek_EN_Imputed Rev5
Greek_LN_Imputed Klei10
Greek_LN_Imputed Pal7
Stuttgart_Imputed LBK


These are for the W European Farmer:

Europe_MNChL I0172
Europe_MNChL I0408
Portugal_BA_Imputed MonteGato104
Portugal_BA_Imputed TV3831
Portugal_BA_Imputed TV32032
Portugal_LN_Imputed CabecoArruda122A
Portugal_LN_Imputed CovaMoura9B
Portugal_LN_Imputed CovaMoura364
Portugal_LN_Imputed DolmenAnsiao96B
Portugal_MN_Imputed LugarCanto41
Portugal_MN_Imputed LugarCanto42
Portugal_MN_Imputed LugarCanto44
Spain_Chl_Imputed ATP2
Spain_Chl_Imputed ATP12-1420
Spain_Chl_Imputed ATP16

Thank you very much Ghani. This is very useful. So, the western farmer component is definitely cloaking perhaps 20-25% WHG. Given those eastern farmer samples, I don't think there's going to be much cloaked Iran Neo in there, i.e. no Anatolian Chl/BA samples are included.

A word of caution here: I've heard that the creator says that the Levant samples we have aren't very good, so that number may be higher, but perhaps the relative percentages are still useful. Does anyone know if that's also the case for the Iran like ancestry?

 

[Angela]

Did you make that map?

That's a map posted on the internet by academics. Nothing unusual about it other than the fact that the "eastern" farmers are included along with the "western" farmers. Of course, as is now clear, the only farmers from outside of Europe included in this calculator are Anatolia Neolithic farmers.

Here's another version: This shared ancestry may partly explain how Tuscans and Albanians plot in relationship to one another, with Tuscans being "western" shifted. That western shift could be due to later Celtic/Germanic admixture in Tuscans as well, with Albanians and Balkan people in general getting, instead, a bit of Slavic ancestry.