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

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

    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.


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



    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.



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



    However, when I decided to add the RUS_Progress_EN, the Neolithic Farmer (Barcin_N) decreases slightly again...


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



    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?
    Last edited by Tsakhur; 01-04-2021 at 10:06 AM.

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    Quote Originally Posted by Tsakhur View Post
    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.


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



    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.



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



    However, when I decided to add the RUS_Progress_EN, the Neolithic Farmer (Barcin_N) decreases slightly again...



    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.

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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    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.



    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?

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    Quote Originally Posted by Tsakhur View Post
    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.



    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.

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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    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_EnG2001
    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_EnG2004
    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.

    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.
    Last edited by Tsakhur; 01-04-2021 at 10:38 AM.

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    Quote Originally Posted by Norfern-Ostrobothnian View Post
    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:




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    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
    Last edited by Tsakhur; 01-18-2021 at 02:38 PM.

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