Allentoft and Iron Age Sweden

[Anglesqueville]

I started using data from the big Allentoft study. For me, they are of major interest in having been calculated (by Glimpse) by professionals. I have in fact always had reservations about my own imputations (by Beagle) for data with very low coverage. This is particularly the case for the Finnish Iron Age micro-group (Levänluhta). In addition, Allentoft has given us, among other things, a gift of valuable new data, in particular from the Swedish Falköping group (between 2000 BC and 1700 BC). This group is of major importance for at least three reasons:
1) It contains the first representatives of I-M253 which have a reasonable chance of corresponding to the roots of this haplogroup as we know it today (TMRCA and location).
2) Falköping is located in the heart of the Swedish corridor to which I have often alluded on the late proto-Germanic thread. This corridor, which links the Lake Mälaren region and the southwest coast of Sweden, is the area where most of the early iron industries were distributed, as well as the finds of Mälar axes.
3) Isotopic analyzes attest that most of the individuals from Falköping are not native to this area, but to regions located in the northeast of Sweden. (see: Open Archeology 2018; 4:1–35 Malou Blank*, Anna Tornberg, and Corina Knipper "New Perspectives on the Late Neolithic of South-Western Sweden. An Interdisciplinary Investigation of the Gallery Grave Falköping Stad 5").
I first carried out a PCA (by Plink2) by projecting onto modern populations the groups Falköping (Sweden_N), Sweden_IronAge (which includes the outlier individual of Levänluhta), Sweden-BattleAxes, and finally the micro-group of Levänluhta (which merges with that of the modern Saamis). This PCA reveals an indisputable cline, with an obvious shift of the Sweden_N group relative to the Falköping group in the direction of Levänluhta.



I obviously wondered whether this shift was verifiable by qpAdm. I didn't have much hope, remembering the sad experiences I had previously had with Levänluhta. My pessimism was unwarranted, because what qpAdm gives me is nothing less than the best model I have ever gotten for Iron Age Swedes. This model absolutely converges with Allentoft's conclusions regarding the leading role of the Falköping group. As for the Iron Age, it undoubtedly points to a genetic influx from Finland.

left pops:
Sweden_IA.imputed_allentoft
Sweden_N_Falköping.imputed_Allentoft
Finland_IA.imputed_allentoft

right pops:
Russia_Ust_Ishim.DG
Cameroon_SMA.DG
Italy_North_Villabruna_HG
Czech_Vestonice16
Belgium_UP_GoyetQ116_1
Russia_MA1_HG.SG
Iran_GanjDareh_N
Kazakhstan_Botai_Eneolithic.SG
Russia_Kostenki14.SG
Ukraine_Mesolithic
Indian_GreatAndaman_100BP.SG
Russia_Arkhangelsk_Veretye_Mesolithic.SG
Israel_PPNB
Georgia_Kotias.SG
Turkey_N_I0707



best coefficients:    0.919    0.081
totmean:      0.919    0.081
boot mean:    0.919    0.081
      std. errors:    0.033    0.033

    fixed pat  wt  dof    chisq      tail prob
          00  0    13    6.435        0.928885    0.919    0.081
          01  1    14    12.129        0.595957    1.000    0.000
          10  1    14  318.653              0    0.000    1.000
best pat:          00        0.928885              -  -
best pat:          01        0.595957  chi(nested):    5.694 p-value for nested model:      0.0170234



Samples:

NEO221_A U Sweden_N_Falköping.imputed_Allentoft
NEO223_A U Sweden_N_Falköping.imputed_Allentoft
NEO224_A U Sweden_N_Falköping.imputed_Allentoft
NEO225_A U Sweden_N_Falköping.imputed_Allentoft
NEO226_A U Sweden_N_Falköping.imputed_Allentoft
NEO227_A U Sweden_N_Falköping.imputed_Allentoft
NEO228_A U Sweden_N_Falköping.imputed_Allentoft
NEO259_A U Sweden_N_Falköping.imputed_Allentoft


RISE174_A U    Sweden_IA.imputed_allentoft
VK522_A U    Sweden_IA.imputed_allentoft
VK523_A U    Sweden_IA.imputed_allentoft

DA234_A U    Finland_IA.imputed_allentoft
DA238_A U    Finland_IA.imputed_allentoft

Here for once is a model of easy interpretation: the p-value of the alternative model is too low for this alternative model to be admissible. The intervention of the Finnish group is clearly essential. The monumental tail-prob of the complete model left little doubt as to this in any case.

[MrI1]

If the forefathers of modern I1 diverged apart from OST003 perhaps during the Ertebølle Culture at said time they would probably be primarily WHG. Perhaps when farming was introduced into Northern Europe the forefathers of Modern I1 moved to northeastern Scandinavia to completely avoid the Funnelbeaker Culture as opposed to the forefathers of Mr. OST003 who maintained their hunter-gathering lifestyle and genetics despite being surrounded by the farmers in Northern Germany for around 800 years?

I guess a few questions I still have are when and where did the forefathers of Modern I1 encounter the Corded Ware Culture? By the time they show up in Falköping during the Late Neolithic they have primarily Corded Ware autosomal dna correct? Did they have early contact with the Corded Ware somewhere in the Eastern Baltic? At said point how did they maintain their I1 patrilineal lines despite absorbing primarily Corded Ware autosomal dna?

[AimSmall]

Nice work.

You had me all excited thinking a new data drop was out there, but I see it's still 54.1.p1

[Anglesqueville]

Nice work.

You had me all excited thinking a new data drop was out there, but I see it's still 54.1.p1

The data is from Allentoft: https://erda.ku.dk/archives/917f1ac64148...chive.html. I did a bit of work to make this data usable, and recently uploaded the resulting eigenstrat file to my dropbox, but had to delete it because I was running out of space. Kale and Teepean downloaded it, I think you can call them if you're interested.

[Anglesqueville]

If the forefathers of modern I1 diverged apart from OST003 perhaps during the Ertebølle Culture at said time they would probably be primarily WHG. Perhaps when farming was introduced into Northern Europe the forefathers of Modern I1 moved to northeastern Scandinavia to completely avoid the Funnelbeaker Culture as opposed to the forefathers of Mr. OST003 who maintained their hunter-gathering lifestyle and genetics despite being surrounded by the farmers in Northern Germany for around 800 years?

I guess a few questions I still have are when and where did the forefathers of Modern I1 encounter the Corded Ware Culture? By the time they show up in Falköping during the Late Neolithic they have primarily Corded Ware autosomal dna correct? Did they have early contact with the Corded Ware somewhere in the Eastern Baltic? At said point how did they maintain their I1 patrilineal lines despite absorbing primarily Corded Ware autosomal dna?

Where did the Falköping guys pick their I1? Honestly, I don't know, even if I have some secret ideas about this question.

[teepean]

Nice work.

You had me all excited thinking a new data drop was out there, but I see it's still 54.1.p1

The data is from Allentoft: https://erda.ku.dk/archives/917f1ac64148...chive.html. I did a bit of work to make this data usable, and recently uploaded the resulting eigenstrat file to my dropbox, but had to delete it because I was running out of space. Kale and Teepean downloaded it, I think you can call them if you're interested.

I converted the dataset to plink:

https://drive.google.com/drive/folders/1...WEgEqXWcw2

[AimSmall]

Got is downloaded, thanks teepean.

[Anglesqueville]

Nice work.

You had me all excited thinking a new data drop was out there, but I see it's still 54.1.p1

The data is from Allentoft: https://erda.ku.dk/archives/917f1ac64148...chive.html. I did a bit of work to make this data usable, and recently uploaded the resulting eigenstrat file to my dropbox, but had to delete it because I was running out of space. Kale and Teepean downloaded it, I think you can call them if you're interested.

I converted the dataset to plink:

https://drive.google.com/drive/folders/1...WEgEqXWcw2

You should have asked me, I made the Plink first too, and kept it of course. Tell me if you see weird things with the names. I used R to rename the samples. I think it's OK but one never knows.

[AimSmall]

I've been spacing out on this thread...  doh!

This Allentoft is the Neolithic discussion from last October.  Totally wasn't making the connection.

Here is a family file I modified at Davidski's request. It's not as inclusive as the one above, but has population names and lat long data.

Code:

Russia_Mesolithic_Romanov-Ilmurzin NEO100 0 0 0 NEO100 51.566 53.683
Russia_Lower_Don_Eneolithic NEO113 0 0 0 NEO113 50.073 39.878
Russia_Zjindo_N NEO117 0 0 0 NEO117 49.9 108
France_Grotte_Mandrin_C NEO119 0 0 0 NEO119 44.466 4.766
France_Grotte_Mandrin_C NEO121 0 0 0 NEO121 44.466 4.766
Denmark_Mesolithic_Kongemose NEO122 0 0 0 NEO122 54.96 11.85
Denmark_Mesolithic_Kongemose NEO123 0 0 0 NEO123 54.96 11.85
Hungary_Koros_EN NEO137 0 0 0 NEO137 46.418 20.33
Hungary_Tisza_MN NEO140 0 0 0 NEO140 46.369 20.424
Hungary_Tisza_MN NEO142 0 0 0 NEO142 46.369 20.424
Hungary_Tisza_MN NEO145 0 0 0 NEO145 46.369 20.424
Hungary_Tisza_MN NEO147 0 0 0 NEO147 46.369 20.424
Russia_LN_Volosovo NEO158 0 0 0 NEO158 56.78 40.447
Russia_Eneolithic_Srednestogovskaya NEO160 0 0 0 NEO160 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO162 0 0 0 NEO162 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO163 0 0 0 NEO163 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO164 0 0 0 NEO164 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO166 0 0 0 NEO166 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO167 0 0 0 NEO167 52.9 40.03
Norway_Mesolithic NEO17 0 0 0 NEO17 58.064 7.743
Russia_Eneolithic_Srednestogovskaya NEO170 0 0 0 NEO170 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO171 0 0 0 NEO171 52.9 40.03
Russia_Eneolithic_Srednestogovskaya NEO173 0 0 0 NEO173 52.278 38.955
Russia_Eneolithic_Srednestogovskaya NEO174 0 0 0 NEO174 52.278 38.955
Russia_MBA_Catacomb NEO175 0 0 0 NEO175 52.278 38.955
Russia_LN_Volosovo NEO178 0 0 0 NEO178 56.78 40.447
Russia_LN_Volosovo NEO179 0 0 0 NEO179 56.78 40.447
Russia_LN_Volosovo NEO180 0 0 0 NEO180 56.781 40.447
Russia_LN_Volosovo NEO184 0 0 0 NEO184 56.776 40.443
Russia_MN_Lyalovo NEO185 0 0 0 NEO185 56.781 40.447
Russia_MN_Lyalovo NEO186 0 0 0 NEO186 56.781 40.447
Russia_MN_Lyalovo NEO187 0 0 0 NEO187 56.781 40.447
Russia_LN_Volosovo NEO189 0 0 0 NEO189 56.781 40.447
Russia_MN_Lyalovo NEO192 0 0 0 NEO192 56.78 40.447
Russia_LN_Volosovo NEO193 0 0 0 NEO193 56.781 40.447
Russia_LN_Volosovo NEO194 0 0 0 NEO194 56.781 40.447
Russia_LN_Volosovo NEO195 0 0 0 NEO195 56.781 40.447
Russia_LN_Volosovo NEO197 0 0 0 NEO197 56.781 40.447
Russia_Fofonovo_MN NEO199 0 0 0 NEO199 52.2 107
Russia_Fofonovo_MN NEO200 0 0 0 NEO200 52.2 107
Russia_Fofonovo_MN NEO201 0 0 0 NEO201 52.2 107
Sweden_LN NEO220 0 0 0 NEO220 58.166 13.573
Sweden_LN NEO224 0 0 0 NEO224 58.166 13.573
Sweden_LN NEO226 0 0 0 NEO226 58.166 13.573
Sweden_LN NEO227 0 0 0 NEO227 58.166 13.573
Sweden_LN NEO228 0 0 0 NEO228 58.166 13.573
Denmark_MN NEO25 0 0 0 NEO25 56.433 10.789
Denmark_Mesolithic_Maglemose NEO254 0 0 0 NEO254 55.404 10.133
Ukraine_Neolithic_Mariupol NEO270 0 0 0 NEO270 47.433 34.268
Sweden_Mesolithic NEO28 0 0 0 NEO28 55.91 12.307
Georgia_Kotias_UP NEO283 0 0 0 NEO283 42.22 43.32
Denmark_EN NEO29 0 0 0 NEO29 55.134 10.903
Russia_Dolgoe_Ozero_EN NEO292 0 0 0 NEO292 56.2 95.7
Ukraine_N_Dnieper-Donetsk NEO304 0 0 0 NEO304 47.95 35.39
Latvia_Mesolithic_Kunda NEO307 0 0 0 NEO307 57.775 25.229
Turkmenistan_C_Anau NEO310 0 0 0 NEO310 36.848 60.418
Sweden_MN NEO38 0 0 0 NEO38 55.565 13.036
Sweden_MN NEO39 0 0 0 NEO39 55.565 13.036
Denmark_EN NEO43 0 0 0 NEO43 55.994 10.248
Sweden_Battle_Axe NEO44 0 0 0 NEO44 55.564 12.946
Sweden_EN_TRB NEO46 0 0 0 NEO46 55.588 13.113
Ukraine_Mesolithic NEO501 0 0 0 NEO501 48.2 35.216
Ukraine_Neolithic NEO502 0 0 0 NEO502 48.132 35.081
Ukraine_Neolithic NEO503 0 0 0 NEO503 48.132 35.081
Ukraine_Neolithic NEO507 0 0 0 NEO507 48.132 35.081
Sweden_Battle_Axe NEO51 0 0 0 NEO51 55.555 13.023
Ukraine_Neolithic NEO516 0 0 0 NEO516 48.396 35.161
Ukraine_Igren_LBA NEO518 0 0 0 NEO518 48.396 35.161
Sweden_LN NEO52 0 0 0 NEO52 55.503 13.009
Ukraine_Mesolithic NEO521 0 0 0 NEO521 48.396 35.161
Ukraine_Mesolithic NEO522 0 0 0 NEO522 48.305 35.136
Ukraine_Neolithic NEO524 0 0 0 NEO524 48.132 35.081
Ukraine_Neolithic NEO528 0 0 0 NEO528 48.122 35.096
Russia_Minino_Mesolithic NEO536 0 0 0 NEO536 59.7 39.5
Russia_Minino_Mesolithic NEO537 0 0 0 NEO537 59.7 39.5
Russia_Minino_Mesolithic NEO539 0 0 0 NEO539 59.7 39.5
Ukraine_Neolithic NEO552 0 0 0 NEO552 48.122 35.096
Russia_Karavaikha_Mesolithic NEO555 0 0 0 NEO555 60.414 38.932
Russia_Karavaikha_Mesolithic NEO556 0 0 0 NEO556 60.414 38.932
Russia_Karavaikha_Mesolithic NEO557 0 0 0 NEO557 60.414 38.932
Russia_Karavaikha_Mesolithic NEO558 0 0 0 NEO558 60.414 38.932
Russia_Karavaikha_Mesolithic NEO559 0 0 0 NEO559 60.414 38.932
Russia_Karavaikha_Mesolithic NEO560 0 0 0 NEO560 60.414 38.932
Russia_Karavaikha_Mesolithic NEO561 0 0 0 NEO561 60.414 38.932
Denmark_BA NEO563 0 0 0 NEO563 55.76 11.798
Denmark_Mesolithic_Ertebolle NEO569 0 0 0 NEO569 56.812 9.179
Kazakhstan_EBA_Sintashta NEO57 0 0 0 NEO57 52.166 64.533
Denmark_Mesolithic_Ertebolle NEO583 0 0 0 NEO583 56.371 10.573
Denmark_Mesolithic_Ertebolle NEO586 0 0 0 NEO586 56.371 10.573
Denmark_Mesolithic_Kongemose NEO587 0 0 0 NEO587 55.583 11.551
Denmark_BA NEO590 0 0 0 NEO590 55.34 11.161
Denmark_EN NEO595 0 0 0 NEO595 55.789 11.292
Denmark_MN NEO597 0 0 0 NEO597 55.587 11.574
Denmark_Mesolithic_Ertebolle NEO598 0 0 0 NEO598 55.948 11.897
Denmark_EN_TRB NEO599 0 0 0 NEO599 55.553 11.684
Russia_Bolshoy_Oleni_Ostrov_BA NEO60 0 0 0 NEO60 68.966 33.083
Denmark_Mesolithic_Kongemose NEO600 0 0 0 NEO600 55.848 12.56
Portugal_LN NEO609 0 0 0 NEO609 38.676 -9.164
Scotland_Orkney_N NEO625 0 0 0 NEO625 58.734 -2.937
Scotland_Orkney_N NEO626 0 0 0 NEO626 58.734 -2.937
Scotland_Orkney_N NEO627 0 0 0 NEO627 58.734 -2.937
Scotland_Orkney_N NEO630 0 0 0 NEO630 58.734 -2.937
Russia_Eneolithic_Bolshoy_Mys NEO64 0 0 0 NEO64 52.713 84.692
Poland_MN_TRB NEO640 0 0 0 NEO640 50.267 20.45
Poland_MN_TRB NEO641 0 0 0 NEO641 50.267 20.45
Denmark_EN NEO645 0 0 0 NEO645 55.914 11.091
Spain_Mesolithic NEO648 0 0 0 NEO648 43.402 -4.707
Spain_Mesolithic NEO649 0 0 0 NEO649 43.402 -4.707
Spain_Mesolithic NEO653 0 0 0 NEO653 43.402 -4.707
Serbia_IronGates_Mesolithic NEO655 0 0 0 NEO655 44.5355833 22.0444444
Serbia_IronGates_Mesolithic NEO657 0 0 0 NEO657 44.5355833 22.0444444
Serbia_IronGates_Mesolithic NEO658 0 0 0 NEO658 44.5355833 22.0444444
Serbia_IronGates_Mesolithic NEO669 0 0 0 NEO669 44.5555278 22.02742
Russia_N_Kuznetks-Altai NEO67 0 0 0 NEO67 52.18 85.965
Romania_IronGates_Mesolithic NEO671 0 0 0 NEO671 44.635 22.66
Romania_IronGates_Mesolithic NEO672 0 0 0 NEO672 44.635 22.66
Romania_Baile_Herculane_N NEO674 0 0 0 NEO674 44.896 22.428
Serbia_IronGates_Mesolithic NEO677 0 0 0 NEO677 44.5355833 22.0444444
Denmark_Mesolithic_Ertebolle NEO679 0 0 0 NEO679 55.386 13.481
Denmark_Mesolithic_Kongemose NEO683 0 0 0 NEO683 55.395 9.826
Russia_Kumyshanskaya_N NEO687 0 0 0 NEO687 57.58 58.2
Spain_Mesolithic NEO694 0 0 0 NEO694 38.73 -0.463
Italy_Maddalena_di_Muccia_N NEO695 0 0 0 NEO695 43.075 13.059
Scotland_Orkney_N NEO717 0 0 0 NEO717 58.734 -2.937
Russia_N_Koshkino NEO72 0 0 0 NEO72 56.019 69.31
Spain_C NEO721 0 0 0 NEO721 40.439 -3.501
Russia_N_Koshkino NEO73 0 0 0 NEO73 56.019 69.31
Denmark_Mesolithic_Ertebolle NEO732 0 0 0 NEO732 55.768 11.388
Denmark_Mesolithic_Ertebolle NEO733 0 0 0 NEO733 55.768 11.388
Denmark_LN NEO735 0 0 0 NEO735 55.225 11.303
Denmark_LN NEO737 0 0 0 NEO737 55.225 11.303
Denmark_LN NEO738 0 0 0 NEO738 56.362 10.593
Denmark_EN NEO744 0 0 0 NEO744 55.856 11.59
Denmark_Mesolithic_Ertebolle NEO745 0 0 0 NEO745 55.853 12.559
Denmark_Mesolithic_Ertebolle NEO746 0 0 0 NEO746 55.853 12.559
Denmark_Mesolithic_Ertebolle NEO747 0 0 0 NEO747 55.853 12.559
Russia_Omskaya_Stoyanka_N NEO75 0 0 0 NEO75 54.971 73.366
Denmark_Mesolithic_Ertebolle NEO751 0 0 0 NEO751 56.874 9.215
Denmark_EN NEO753 0 0 0 NEO753 55.772 12.213
Russia_Okunevo_N NEO77 0 0 0 NEO77 56.438 74.907
Russia_Omskaya_Stoyanka_N NEO78 0 0 0 NEO78 54.971 73.366
Russia_Okunevo_N NEO79 0 0 0 NEO79 56.438 74.907
Denmark_EN NEO790 0 0 0 NEO790 55.711 12.274
Denmark_LN_Single_Grave_Culture NEO792 0 0 0 NEO792 54.87 12.116
Russia_Borovyanka_Eneolithic NEO80 0 0 0 NEO80 55.733 74.285
Italy_Grotta_Delle_Mura_BA NEO806 0 0 0 NEO806 40.957 17.29

[ANIEXCAVATOR]

I started using data from the big Allentoft study. For me, they are of major interest in having been calculated (by Glimpse) by professionals. I have in fact always had reservations about my own imputations (by Beagle) for data with very low coverage. This is particularly the case for the Finnish Iron Age micro-group (Levänluhta). In addition, Allentoft has given us, among other things, a gift of valuable new data, in particular from the Swedish Falköping group (between 2000 BC and 1700 BC). This group is of major importance for at least three reasons:
1) It contains the first representatives of I-M253 which have a reasonable chance of corresponding to the roots of this haplogroup as we know it today (TMRCA and location).
2) Falköping is located in the heart of the Swedish corridor to which I have often alluded on the late proto-Germanic thread. This corridor, which links the Lake Mälaren region and the southwest coast of Sweden, is the area where most of the early iron industries were distributed, as well as the finds of Mälar axes.
3) Isotopic analyzes attest that most of the individuals from Falköping are not native to this area, but to regions located in the northeast of Sweden. (see: Open Archeology 2018; 4:1–35 Malou Blank*, Anna Tornberg, and Corina Knipper "New Perspectives on the Late Neolithic of South-Western Sweden. An Interdisciplinary Investigation of the Gallery Grave Falköping Stad 5").
I first carried out a PCA (by Plink2) by projecting onto modern populations the groups Falköping (Sweden_N), Sweden_IronAge (which includes the outlier individual of Levänluhta), Sweden-BattleAxes, and finally the micro-group of Levänluhta (which merges with that of the modern Saamis). This PCA reveals an indisputable cline, with an obvious shift of the Sweden_N group relative to the Falköping group in the direction of Levänluhta.



I obviously wondered whether this shift was verifiable by qpAdm. I didn't have much hope, remembering the sad experiences I had previously had with Levänluhta. My pessimism was unwarranted, because what qpAdm gives me is nothing less than the best model I have ever gotten for Iron Age Swedes. This model absolutely converges with Allentoft's conclusions regarding the leading role of the Falköping group. As for the Iron Age, it undoubtedly points to a genetic influx from Finland.

left pops:
Sweden_IA.imputed_allentoft
Sweden_N_Falköping.imputed_Allentoft
Finland_IA.imputed_allentoft

right pops:
Russia_Ust_Ishim.DG
Cameroon_SMA.DG
Italy_North_Villabruna_HG
Czech_Vestonice16
Belgium_UP_GoyetQ116_1
Russia_MA1_HG.SG
Iran_GanjDareh_N
Kazakhstan_Botai_Eneolithic.SG
Russia_Kostenki14.SG
Ukraine_Mesolithic
Indian_GreatAndaman_100BP.SG
Russia_Arkhangelsk_Veretye_Mesolithic.SG
Israel_PPNB
Georgia_Kotias.SG
Turkey_N_I0707



best coefficients:    0.919    0.081
totmean:      0.919    0.081
boot mean:    0.919    0.081
      std. errors:    0.033    0.033

    fixed pat  wt  dof    chisq      tail prob
          00  0    13    6.435        0.928885    0.919    0.081
          01  1    14    12.129        0.595957    1.000    0.000
          10  1    14  318.653              0    0.000    1.000
best pat:          00        0.928885              -  -
best pat:          01        0.595957  chi(nested):    5.694 p-value for nested model:      0.0170234



Samples:

NEO221_A U Sweden_N_Falköping.imputed_Allentoft
NEO223_A U Sweden_N_Falköping.imputed_Allentoft
NEO224_A U Sweden_N_Falköping.imputed_Allentoft
NEO225_A U Sweden_N_Falköping.imputed_Allentoft
NEO226_A U Sweden_N_Falköping.imputed_Allentoft
NEO227_A U Sweden_N_Falköping.imputed_Allentoft
NEO228_A U Sweden_N_Falköping.imputed_Allentoft
NEO259_A U Sweden_N_Falköping.imputed_Allentoft


RISE174_A U    Sweden_IA.imputed_allentoft
VK522_A U    Sweden_IA.imputed_allentoft
VK523_A U    Sweden_IA.imputed_allentoft

DA234_A U    Finland_IA.imputed_allentoft
DA238_A U    Finland_IA.imputed_allentoft

Here for once is a model of easy interpretation: the p-value of the alternative model is too low for this alternative model to be admissible. The intervention of the Finnish group is clearly essential. The monumental tail-prob of the complete model left little doubt as to this in any case.

Great work Anglesqueville! 

If we believe that the expansion of the final stage of the proto-Germanic took place with an subtle shift in the direction of Uralic populations, because of people migrating from Malaren, it will be even more convincing if you can show that Danish or Norwegian Iron Age samples around 0AD are shifted from Danish or Norwegian samples from the I1 cluster 4,000 years ago in the direction of Finns as well. Are there enough samples for you to do this?

[Codaman]

It's my understanding that some of these Levänluhta samples(specifically DA234 and JK1968, although not so much JK1970 and not at all DA238) which are of course ancestrally Saami have relatively high levels of Germanic ancestry which is in line with proto-Germanics being the primary contact group of ancestral Saami along with Baltic Finns and I wonder if this could affect the results presented.
The following models may illuminate this.

Target: Vologda_EIA:NEO538
Distance: 3.0806% / 0.03080646
41.0 Russia_Krasnoyarsk_BA.SG
24.2 Russia_Vologda_Veretye_Mesolithic.SG
19.4 Kazakhstan_MLBA_Karagash
9.8 Estonia_IA.SG
3.0 Estonia_BA.SG
2.6 Sweden_Motala_HG
0.0 Norway_N_HG.SG
0.0 Sweden_LN:NEO221

Target: FIN_Levanluhta_IA:DA234
Distance: 2.1313% / 0.02131308
52.2 Vologda_EIA:NEO538
27.6 Sweden_LN:NEO221
20.2 Estonia_BA.SG
0.0 Sweden_Motala_HG
0.0 Norway_N_HG.SG
0.0 Kazakhstan_MLBA_Karagash
0.0 Russia_Vologda_Veretye_Mesolithic.SG
0.0 Estonia_IA.SG

[Anglesqueville]

It's my understanding that some of these Levänluhta samples(specifically DA234 and JK1968, although not so much JK1970 and not at all DA238) which are of course ancestrally Saami have relatively high levels of Germanic ancestry which is in line with proto-Germanics being the primary contact group of ancestral Saami along with Baltic Finns and I wonder if this could affect the results presented.

I doubt. If the sources (Falköping and Levänluhta) shared enough alleles for the qpAdm model presented to be disrupted, this would be seen in the standard errors. However, these standard errors are very low. No, I believe these sources are as close to orthogonal as possible. With qpAdm Levänluhta (at least the two proto-Saamis imputed by Allentoft) can be modelled very well as combinations of VolgaOka_IA, kra001 and Motala_HG, and the addition of Falköping to these sources does not bring anything good in terms of tail prob. That there was a proto-Germanic lexical contribution to Saami languages is indisputable. But that doesn't reflect in the autosomal constitution of the Saami-like guys from Levänluhta.

[Anglesqueville]

Great work Anglesqueville! 

If we believe that the expansion of the final stage of the proto-Germanic took place with an subtle shift in the direction of Uralic populations, because of people migrating from Malaren, it will be even more convincing if you can show that Danish or Norwegian Iron Age samples around 0AD are shifted from Danish or Norwegian samples from the I1 cluster 4,000 years ago in the direction of Finns as well. Are there enough samples for you to do this?

The Denmark_IronAge micro-group is represented by 4 individuals, who come from the Margaryan study. Nothing is simple with them. In fact, this quartet is as heterogeneous as the Swedes micro-group is homogeneous. Thus, among these two individuals we find two males, both I1, VK521 and VK532. VK521 could come from Sweden (perhaps we have isotopic analyses for him, we should check), in any case "my" model applies perfectly to him. But this is not the case with VK532, which cannot be modelled with any Scandinavian source. In any case, I didn't find anything convincing for him. For the Norwegians, I have to work.

[Codaman]

With qpAdm Levänluhta (at least the two proto-Saamis imputed by Allentoft) can be modelled very well as combinations of VolgaOka_IA, kra001 and Motala_HG, and the addition of Falköping to these sources does not bring anything good in terms of tail prob. That there was a proto-Germanic lexical contribution to Saami languages is indisputable. But that doesn't reflect in the autosomal constitution of the Saami-like guys from Levänluhta.

The amount of Siberian ancestry from NEO538 to Levänluhta halves yet it is not due to an increase of 50% in SHG and certainly it's not Volga-Oka either because that makes no sense so what is the cause? the sources can not be chosen without considering their plausibility

What if you instead of these you used the following sources
NEO538
NEO62(Bolshoy Oleni Ostrov)
NEO225
and any source from the BA/IA Baltics which has the highest coverage

[Anglesqueville]

^^ I haven't been interested in NEO538 at all so far, so I don't have anything to say about it. As for using VolgaOka_IA as a source for the Saamis (including the two from Levänluhta) this is a perfectly justified choice if one follows Lang's theories (which is my case, at least on this point). This choice requires to be completed by a bonus from Krasnoyarsk_BA, and gives very satisfactory adjustments with qpAdm.