What is the actual amount of Neolithic Farmer/EEF admixture in Saamis?

[Tsakhur]

I noticed that when the EHG component is included, the amount of Neolithic admixture (Barcin_N) in the Saami increase drastically. But when I removed them the Neolithic affinity decreased but at the same time, the fits got worse as well. Why does the EHG ancestry increase the amount of Neolithic in Saami? Is EHG component need to model the Saami?

Here is when I modelled them as a mix between Steppe_Herder+Hunter Gatherer+Farmer. Look at how little Neolithic they have compared to most Europeans.
https://i.imgur.com/x3NMKhZ.png

But when I added EHG to improve the distance, the Neolithic Farmer (Barcin_N) also increase massively...

https://i.imgur.com/swo523R.png

But it looks like Mereke also have minor Neolithic like other Yamnaya pops so because I want to find out the actual amount of Anatolian Neolithic admixture in the Saami, I decided to replace the Mereke with just the CHG and ANE to create the Steppe component without Neolithic (since Steppe= EHG+CHG with EHG being a mix of mostly ANE+ significant WHG).

So now the Anatolian Neolithic increase among the Saami. I also added RUS_Bolshoy_Oleni_Ostrov_o and SWE_Meso since it seem to improve the distance for the models.

https://i.imgur.com/EAQ5zyV.png

But later when the EHG is included again into the run which further makes the distance even better, the Anatolian increase even more.

https://i.imgur.com/DdVVzmx.png

However, when I decided to add the RUS_Progress_EN, the Neolithic Farmer (Barcin_N) decreases slightly again...
https://i.imgur.com/ZNmaqhk.png

And finally when I decided to remove EHG again from the run, the Neolithic Farmer decrease again. But the fit distance still remains decent...

https://i.imgur.com/aT6nTb1.png

My questions: is the EHG component really vital and relevant to model the Saami and why does EHG raise the amount of Neolithic Farmer in the Saamis?

Also what's the actual amount of Neolithic Farmer do the Saamis really have? Is it around 15-20%? In the models, it seems that even the most East Asian-shifted samples: Saami:GS000035025 and Saami:saami2 possessed around 15-16% EEF when adding the EHG but decrease to around 13-14% when removing that source?

Why does the EEF ancestry in Saamis varied and fluctuated widely when including certain pops into the run?

[Norfern-Ostrobothnian]

I noticed that when the EHG component is included, the amount of Neolithic admixture (Barcin_N) in the Saami increase drastically. But when I removed them the Neolithic affinity decreased but at the same time, the fits got worse as well. Why does the EHG ancestry increase the amount of Neolithic in Saami? Is EHG component need to model the Saami?

Here is when I modelled them as a mix between Steppe_Herder+Hunter Gatherer+Farmer. Look at how little Neolithic they have compared to most Europeans.
https://i.imgur.com/x3NMKhZ.png

But when I added EHG to improve the distance, the Neolithic Farmer (Barcin_N) also increase massively...

https://i.imgur.com/swo523R.png

But it looks like Mereke also have minor Neolithic like other Yamnaya pops so because I want to find out the actual amount of Anatolian Neolithic admixture in the Saami, I decided to replace the Mereke with just the CHG and ANE to create the Steppe component without Neolithic (since Steppe= EHG+CHG with EHG being a mix of mostly ANE+ significant WHG).

So now the Anatolian Neolithic increase among the Saami. I also added RUS_Bolshoy_Oleni_Ostrov_o and SWE_Meso since it seem to improve the distance for the models.

https://i.imgur.com/EAQ5zyV.png

But later when the EHG is included again into the run which further makes the distance even better, the Anatolian increase even more.

https://i.imgur.com/DdVVzmx.png

However, when I decided to add the RUS_Progress_EN, the Neolithic Farmer (Barcin_N) decreases slightly again...
https://i.imgur.com/ZNmaqhk.png


My questions: is the EHG component really vital and relevant to model the Saami and why does EHG raise the amount of Neolithic Farmer in the Saamis?

Also what's the actual amount of Neolithic Farmer do the Saamis really have? Is it around 15-20%? In the models, it seems that even the most East Asian-shifted samples: Saami:GS000035025 and Saami:saami2 possessed around 15-16% EEF when adding the EHG.

You could try with a Baltic and a Germanic source as well and then try infer their EEF admixture.

[Tsakhur]

You could try with a Baltic and a Germanic source as well and then try infer their EEF admixture.

What Baltic or Germanic source should I used and how much EEF/Anatolian do they score?

The funny thing is when I decided to remove EHG (Karelia_HG) from the run, the Neolithic Farmer decrease again for the Saami but this time the fit of the distance remains the same. And now they are back to being around 17.9% EEF from 19.4% EEF. The two most East Asian-shifted samples which are Saami:GS000035025 and Saami:saami2 now have around 13 and 13.6% EEF.

https://i.imgur.com/aT6nTb1.png

So now I'm confused which numbers are more accurate for the Neolithic admix in the Saami:GS000035025 and Saami:saami2: 13% EEF when removing the EHG (Karelia_HG) or 15-16% when including the latter into the run?

Why does the EEF ancestry in Saamis varied and fluctuated widely when including certain pops into the run?

[Norfern-Ostrobothnian]

What Baltic or Germanic source should I used and how much EEF/Anatolian do they score?

The funny thing is when I decided to remove EHG (Karelia_HG) from the run, the Neolithic Farmer decrease again for the Saami but this time the fit of the distance remains the same. And now they are back to being around 17.9% EEF from 19.4% EEF. The two most East Asian-shifted samples which are Saami:GS000035025 and Saami:saami2 now have around 13 and 13.6% EEF.

https://i.imgur.com/aT6nTb1.png

So now I'm confused which numbers are more accurate for the Neolithic admix in the Saami:GS000035025 and Saami:saami2: 13% EEF when removing the EHG (Karelia_HG) or 15-16% when including the latter into the run?

Why does the EEF ancestry in Saamis varied and fluctuated widely when including certain pops into the run?

I guess the Progress eneolithic eats up the EEF. I think Baltic Bronze Age would be the best baltic and some Norwegian or Swedish sample for the Germanic.

[Tsakhur]

I guess the Progress eneolithic eats up the EEF. I think Baltic Bronze Age would be the best baltic and some Norwegian or Swedish sample for the Germanic.

The Progress Eneolithic average is only 1.4% EEF though:

Target: RUS_Progress_En
Distance: 5.9942% / 0.05994216
46.4 GEO_CHG
36.6 RUS_AfontovaGora3
15.6 SWE_Meso
1.4 TUR_Barcin_N

And there are two samples: one sample is around 4% EEF while the other one is virtually free of EEF aka zero.

Target: RUS_Progress_En:PG2001
Distance: 5.8540% / 0.05854031
48.0 GEO_CHG
34.8 RUS_AfontovaGora3
13.2 SWE_Meso
4.0 TUR_Barcin_N


Target: RUS_Progress_En:PG2004
Distance: 6.3704% / 0.06370426
43.8 GEO_CHG
38.6 RUS_AfontovaGora3
17.6 SWE_Meso

I have tried to use the Progress Eneolithic individual that lacked EEF aka the PG2004 sample to model the Saamis but it doesn't allow me to; it only allowed the Progress_EN average (of the two samples) which is around 1.4% EEF to model the Saamis.


Thus, I don't think the Progress Eneolithic actually eats that much EEF when they barely score any Neolithic themselves. I still don't understand why the EHG (Karelia_HG) results in a notable increase of EEF in Saamis? I have tried with the Samara_HG as another EHG source and the EEF still increase in the Saamis...

Or is it possible that the "EEF" that increased massively in the Saamis isn't EEF at all but some type of Anatolian-related affinity?

How much EEF does the Baltic Bronze Age have? And are them EST_BA, LTU_BA and LVA_BA?

I think I have run Norwegian and Swedish samples before and I was astonished at how much EEF they possessed. It makes up approximately 40% of their autosomal DNA. :eek: :eek:

The following are the averages of all the samples.

Target: Norwegian
Distance: 7.1913% / 0.07191289
43.6 TUR_Barcin_N
33.4 SWE_Meso
13.4 RUS_AfontovaGora3
9.6 GEO_CHG


When I included EHG (Karelia_HG), Progress_EN and Bolshoy_Oleni_Ostrov_o into the run:

Target: Norwegian
Distance: 5.8258% / 0.05825807
40.6 TUR_Barcin_N
30.0 RUS_Progress_En
21.0 Baltic_LVA_HG
8.4 RUS_Karelia_HG


Target: Swedish
Distance: 6.8034% / 0.06803397
41.2 TUR_Barcin_N
37.0 SWE_Meso
11.2 GEO_CHG
10.6 RUS_AfontovaGora3

When adding EHG (Karelia_HG), Progress_EN and Bolshoy_Oleni_Ostrov_o for the Swedish:

Target: Swedish
Distance: 5.3950% / 0.05394977
38.8 TUR_Barcin_N
30.8 RUS_Progress_En
16.4 Baltic_LVA_HG
10.2 SWE_Meso
3.8 RUS_Karelia_HG

I didn't utilize the Yamnaya pops because they have some Neolithic and I want to gauge the actual amount of EEF in the Norwegian and Swedish samples.

[Tsakhur]

I guess the Progress eneolithic eats up the EEF. I think Baltic Bronze Age would be the best baltic and some Norwegian or Swedish sample for the Germanic.

Here are the individual Norwegian and Swedish samples score btw:

https://i.imgur.com/njd2724.png

https://i.imgur.com/NUyLHbn.png

[Tsakhur]

This Viking Age sample from Norway seems to be Saami. Only 14.8% Anatolian and around 30% East Asian?

VK2020_NOR_North_VA_o1:VK518,0.104717,-0.079211,0.118039,0.079458,-0.034776,0,-0.00282,0.011307,-0.000205,-0.031527,0.033614,-0.010491,0.018583,-0.026699,-0.010043,0.003315,-0.012778,0.005448,-0.006536,-0.013506,0.0141,-0.001978,0.000986,0.002771,-0.00455

Target: VK2020_NOR_North_VA_o1
Distance: 4.1425% / 0.04142473
28.4 RUS_Karelia_HG
26.6 Nganassan
21.0 RUS_Khvalynsk_En
14.8 TUR_Barcin_N
4.8 VK2020_NOR_North_LN_HG
4.4 RUS_Devils_Gate_Cave_N

Closest pops:
Distance to: VK2020_NOR_North_VA_o1
0.06462205 Saami
0.07825823 Udmurt
0.09102267 Bashkir
0.09144585 Mari
0.09373786 Besermyan
0.09925064 Chuvash
0.10650201 Yukagir_Forest
0.10727664 Tatar_Siberian_Zabolotniye
0.10972508 Tatar_Siberian
0.11115392 Saami_Kola
0.12145246 Mansi
0.12573201 Tatar_Kazan
0.12644533 Tlingit
0.12764787 Komi
0.13096755 Tatar_Lipka
0.13394601 Khanty
0.14319266 Tatar_Crimean_steppe
0.15108655 Ket
0.15129487 Tatar_Mishar
0.15879129 Nogai
0.16415093 Uzbek
0.16728275 Russian_Pinega
0.16890719 Turkmen_Uzbekistan
0.17105258 Turkmen
0.17678970 Tubalar

While this other Viking Age sample from Norway seems to be Komi or some other Uralic speaking minorities from Russia?

VK2020_NOR_North_VA_o2:VK519,0.120652,0.033512,0.0 9692,0.075905,-0.005232,0.020917,0.00893,0.014999,-0.006749,-0.025878,0.01153,-0.003147,0.009514,-0.001101,-0.007872,0.01127,0.010561,0.002787,-0.00264,-0.006253,0.010232,-0.003339,-0.011462,0.003615,-0.010179

Target: VK2020_NOR_North_VA_o2
Distance: 4.9093% / 0.04909323
28.0 VK2020_NOR_North_LN_HG
26.0 TUR_Barcin_N
18.8 RUS_Progress_En
12.6 RUS_Karelia_HG
9.8 Nganassan
3.0 RUS_Devils_Gate_Cave_N
1.8 RUS_Khvalynsk_En

Closest Distance:
Distance to: VK2020_NOR_North_VA_o2
0.03433891 Komi
0.03864378 Saami_Kola
0.05586476 Russian_Pinega
0.05687966 Tatar_Mishar
0.06189647 Tatar_Kazan
0.06222097 Vepsian
0.06474965 Karelian
0.06627552 Finnish_East
0.07044728 Besermyan
0.07184553 Mordovian
0.07413956 Russian_Kostroma
0.07627761 Saami
0.07758599 Ingrian
0.07909076 Finnish
0.07915476 Udmurt
0.08373633 Chuvash
0.08598585 Cossack_Kuban
0.09630055 Russian_Tver
0.10363583 Russian_Kursk
0.10432828 Estonian
0.10652837 Tatar_Lipka
0.10724844 Russian_Orel
0.10827397 Cossack_Ukrainian
0.11041293 Russian_Voronez
0.11207440 Moldovan_o