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Thread: Making drift-free northern European(Celtic, Baltic, Scandinavian, and Slavic) samples

  1. #11
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    Quote Originally Posted by Coldmountains View Post
    The EHG, which many East Europeans get in Global25 models, has rather something to do with overfitting and does not show up in qpAdm which is so far the only method that really can differentiate between direct genetic contribution and indirect one like in this case (EHG via Steppe groups). Davidski made a blog post about this https://eurogenes.blogspot.com/2020/...n-present.html, Even Saami seem not to have significant direct EHG ancestry in qpAdm and rather some WHG-rich HG ancestry on top of their Corded Ware-like and Kra_BA-like ancestry
    I don’t buy the overfitting explanation. There’s a fair amount of WHG in GAC but there’s a ton of EHG in Corded Ware, more than enough to offset the WHG in GAC. Them scoring EHG on top of it while they actually have WHG doesn’t make sense in the context of overfitting although you might know more about how the G25 algorithm works than I do.

    I’m not saying that it’s not WHG but the question is, why would both your and my models reveal eastern Euros to be closer to their steppe progenitors than NW/N Euros when drift is cancelled?

  2. #12
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    Quote Originally Posted by Cynic View Post
    I don’t buy the overfitting explanation. There’s a fair amount of WHG in GAC but there’s a ton of EHG in Corded Ware, more than enough to offset the WHG in GAC. Them scoring EHG on top of it while they actually have WHG doesn’t make sense in the context of overfitting although you might know more about how the G25 algorithm works than I do.

    I’m not saying that it’s not WHG but the question is, why would both your and my models reveal eastern Euros to be closer to their steppe progenitors than NW/N Euros when drift is cancelled?
    HGs in the South Baltics, East Poland and likely even the western half of Belarus were not EHG-like and very WHG-rich with some EHG, so direct EHG ancestry is pretty much out of question for Proto-Balto-Slavs. Maybe some Balt_BA pops around Estonia had HG ancestry from a much EHG-richer source but these pops are not ancestral to the vast majority of Balto-Slavs which orginated more in the south where HGs were definetly mostly WHG-like. EHGs in Central Russia were already in the Fatyanovo period either replaced or extremely decimated so the significant survival of their ancestry up to the early medieval period is extremely unlikely and than would only effect Russians and Volga-Ural groups.

    qpAdm is checking each snp if i correctly understand it and much more powerful than global25 or any gedmatch calc which analyze a tiny amount of aggregated data compared to qpAdm. So qpAdm can tell if someone has direct EHG ancestry from 1500-3000 B.C or only indirect EHG ancestry from Steppe_Eneolithic around 4000 B.C. So far qpAdm pretty much shows no direct EHG ancestry among East Europeans on top of the EHG which was brought by Corded Ware or Yamnaya.

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  4. #13
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    Quote Originally Posted by Coldmountains View Post
    HGs in the South Baltics, East Poland and likely even the western half of Belarus were not EHG-like and very WHG-rich with some EHG, so direct EHG ancestry is pretty much out of question for Proto-Balto-Slavs. Maybe some Balt_BA pops around Estonia had HG ancestry from a much EHG-richer source but these pops are not ancestral to the vast majority of Balto-Slavs which orginated more in the south where HGs were definetly mostly WHG-like. EHGs in Central Russia were already in the Fatyanovo period either replaced or extremely decimated so the significant survival of their ancestry up to the early medieval period is extremely unlikely and than would only effect Russians and Volga-Ural groups.

    qpAdm is checking each snp if i correctly understand it and much more powerful than global25 or any gedmatch calc which analyze a tiny amount of aggregated data compared to qpAdm. So qpAdm can tell if someone has direct EHG ancestry from 1500-3000 B.C or only indirect EHG ancestry from Steppe_Eneolithic around 4000 B.C. So far qpAdm pretty much shows no direct EHG ancestry among East Europeans on top of the EHG which was brought by Corded Ware or Yamnaya.
    Im going to take another stab at this. I used the reduce function+as many European HGs as possible to find the best ones. This model seems to be a slightly improved version of the first. Lithuanians and Belarusians aren't scoring as much CWC as other groups, which is how it should be.

     
    Target: Icelandic
    Distance: 3.2046% / 0.03204629 | R4P
    70.0 Corded_Ware_CZE
    26.6 POL_Globular_Amphora
    3.4 NOR_N_HG

    Target: Swedish
    Distance: 3.0066% / 0.03006637 | R4P
    67.2 Corded_Ware_CZE
    26.6 POL_Globular_Amphora
    6.2 NOR_N_HG

    Target: Norwegian
    Distance: 3.1249% / 0.03124879 | R4P
    71.0 Corded_Ware_CZE
    26.6 POL_Globular_Amphora
    2.4 NOR_N_HG

    Target: Ukrainian
    Distance: 5.8982% / 0.05898219 | R4P
    68.6 Corded_Ware_CZE
    23.6 POL_Globular_Amphora
    7.8 NOR_N_HG

    Target: Lithuanian_PZ
    Distance: 7.4529% / 0.07452857 | R4P
    59.0 Corded_Ware_CZE
    24.4 NOR_N_HG
    16.6 POL_Globular_Amphora

    Target: Belarusian
    Distance: 6.6650% / 0.06665038 | R4P
    63.6 Corded_Ware_CZE
    22.0 POL_Globular_Amphora
    14.4 NOR_N_HG

    Target: Russian_Voronez
    Distance: 6.2962% / 0.06296174 | R4P
    64.2 Corded_Ware_CZE
    24.2 POL_Globular_Amphora
    8.6 NOR_N_HG
    3.0 RUS_Karelia_HG

    Target: Russian_Tver
    Distance: 6.0994% / 0.06099423 | R4P
    68.4 Corded_Ware_CZE
    16.6 POL_Globular_Amphora
    13.0 NOR_N_HG
    2.0 RUS_Krasnoyarsk_BA

    Target: Russian_Smolensk
    Distance: 6.6981% / 0.06698133 | R4P
    65.4 Corded_Ware_CZE
    22.2 POL_Globular_Amphora
    12.4 NOR_N_HG

    Target: Russian_Pinega
    Distance: 5.7082% / 0.05708237 | R4P
    55.2 Corded_Ware_CZE
    22.4 NOR_N_HG
    13.0 POL_Globular_Amphora
    9.4 RUS_Krasnoyarsk_BA

    Target: Russian_Orel
    Distance: 6.1111% / 0.06111094 | R4P
    68.2 Corded_Ware_CZE
    21.4 POL_Globular_Amphora
    7.2 NOR_N_HG
    3.2 RUS_Karelia_HG

    Target: Russian_Kursk
    Distance: 6.0569% / 0.06056878 | R4P
    67.6 Corded_Ware_CZE
    20.6 POL_Globular_Amphora
    7.4 NOR_N_HG
    4.4 RUS_Karelia_HG

    Target: Russian_Kostroma
    Distance: 5.4980% / 0.05497989 | R4P
    65.4 Corded_Ware_CZE
    15.2 POL_Globular_Amphora
    13.6 NOR_N_HG
    5.8 RUS_Krasnoyarsk_BA

    Target: Polish
    Distance: 5.3653% / 0.05365275 | R4P
    66.0 Corded_Ware_CZE
    25.6 POL_Globular_Amphora
    8.4 NOR_N_HG


    The resulting ghost populations:
     
    Belarusdriftless2,0.125077242,0.121445878,0.070433 129,0.072782472,0.034478632,0.021508385,0.0022677, 0.00379412,0.003247146,-0.010418728,-0.000096176,0.000361976,-0.003446744,-0.016526096,0.01570776,0.013065819,0.00160751,0.00 2350036,0.003976004,0.009110072,0.005772494,0.0022 26749,-0.002529374,-0.010105678,0.0007024

    Icelanddriftless,0.12452475,0.128344029,0.05943338 3,0.056024528,0.033293622,0.014948926,0.002594649, 0.003614896,0.002031228,-0.002999915,-0.001046393,0.002939416,-0.008157747,-0.015307555,0.013808413,0.008894345,0.001602169,0. 002608018,0.004774484,0.006223354,0.003465689,0.00 1390158,-0.001996874,-0.004197429,0.000109407

    Lithdriftless2,0.125545836,0.114522909,0.08035777, 0.089216729,0.034686378,0.027992299,0.001987553,0. 003885427,0.003470188,-0.018369386,0.000738187,-0.002079355,0.000946484,-0.017791609,0.017825609,0.016979518,0.001562219,0. 002045089,0.003230104,0.011838905,0.007760773,0.00 2874351,-0.00280828,-0.015055688,0.001224616
    Nordriftless2,0.124462964,0.128747339,0.058407616, 0.054912937,0.032887396,0.014531383,0.002630235,0. 003574015,0.001617798,-0.002739574,-0.001142893,0.003140017,-0.008548088,-0.015250931,0.013770027,0.008556812,0.001584469,0. 002607297,0.004840204,0.005996813,0.003218625,0.00 1275335,-0.001878028,-0.00351575,4.9778E-05

    Polishdriftless2,0.124806038,0.125792318,0.0645005 46,0.062567362,0.034610953,0.017464138,0.00243074, 0.003760504,0.003374071,-0.005291851,-0.000588085,0.001855796,-0.006115335,-0.01572017,0.014321452,0.010681708,0.001649504,0.0 02553816,0.004429458,0.007441878,0.004611683,0.001 871564,-0.002422668,-0.007260124,0.000394055
    RusKosdriftless,0.119652769,0.086987781,0.07477075 6,0.073872083,0.020143045,0.017865256,0.00335735,0 .00533859,0.000566952,-0.01527253,0.004639098,-0.000128797,-0.001818063,-0.019126558,0.014052928,0.011140301,0.001325318,0. 002217726,0.003936661,0.008345629,0.006487223,0.00 1790311,-0.001356364,-0.007214557,0.001330425
    RusKurskdriftless2,0.124610807,0.119853668,0.06649 0606,0.072175996,0.02961113,0.02060403,0.001535374 ,0.002309261,4.23142E-05,-0.012515322,0.000088258,0.000777246,-0.004273582,-0.017214138,0.015741017,0.011684165,0.000754218,0. 002356433,0.004016946,0.007854316,0.003577579,0.00 2104908,-0.001176562,-0.006096152,-0.000169441
    RusOreldriftless2,0.124619264,0.121362319,0.065428 194,0.069585093,0.030380361,0.019791265,0.00180429 ,0.002652589,0.00034729,-0.010980345,-0.000155453,0.001120788,-0.004909277,-0.016852913,0.015516706,0.0113074,0.000966817,0.00 2377342,0.004151259,0.007683112,0.003692466,0.0019 34734,-0.00136529,-0.005896502,-5.17862E-05
    RusPinegadriftless,0.116916107,0.062931999,0.08712 3793,0.082892221,0.016463962,0.018621874,0.0036745 26,0.006796089,0.004210457,-0.018704559,0.008524236,-0.002135415,0.002638377,-0.021005376,0.012733786,0.012881585,0.001397895,0. 002259115,0.003334464,0.009803783,0.009408191,0.00 2774212,-0.002073503,-0.012455884,0.002303209
    Swedriftless2.0,0.12469775,0.127214761,0.062305531 ,0.059136983,0.034431055,0.016118046,0.002495008,0 .003729362,0.003188832,-0.00372887,-0.000776193,0.002377733,-0.007064792,-0.015466102,0.013915894,0.009839438,0.001651729,0. 002610036,0.004590468,0.006857669,0.004157468,0.00 1711662,-0.002329643,-0.00610613,0.000276564
    Ukrdriftless2,0.124713682,0.124963982,0.063761742, 0.063870165,0.032939619,0.018068606,0.002480134,0. 003618381,0.001677399,-0.007116108,-0.000694369,0.001814926,-0.006168125,-0.015945185,0.014940638,0.010678585,0.001556554,0. 002437769,0.004436038,0.007477591,0.004284793,0.00 1617252,-0.002014488,-0.006159716,0.000330541


    How they score:
     
    Distance to: KAZ_Oy_Dzhaylau_MLBA
    0.05072312 RusKosdriftless
    0.06043330 RusKurskdriftless2
    0.06268674 RusPinegadriftless
    0.06307940 RusOreldriftless2
    0.06421003 Lithdriftless2
    0.06730752 Belarusdriftless2
    0.07048104 Ukrdriftless2
    0.07382538 Polishdriftless2
    0.07626606 Swedriftless2.0
    0.07748141 Icelanddriftless
    0.07800759 Nordriftless2

    Distance to: Yamnaya_RUS_Samara
    0.11876979 RusKosdriftless
    0.12353503 RusPinegadriftless
    0.12477374 Lithdriftless2
    0.12500196 RusKurskdriftless2
    0.12759397 RusOreldriftless2
    0.13170832 Belarusdriftless2
    0.13478859 Ukrdriftless2
    0.13851090 Polishdriftless2
    0.14072438 Swedriftless2.0
    0.14132498 Icelanddriftless
    0.14159213 Nordriftless2

    Distance to: Corded_Ware_CZE
    0.03729745 RusKurskdriftless2
    0.03888567 RusOreldriftless2
    0.04482790 Ukrdriftless2
    0.04549666 Belarusdriftless2
    0.04847544 RusKosdriftless
    0.04861453 Polishdriftless2
    0.05025885 Swedriftless2.0
    0.05056411 Icelanddriftless
    0.05082127 Nordriftless2
    0.05155580 Lithdriftless2
    0.07382206 RusPinegadriftless

    Distance to: RUS_Petrovka_MLBA
    0.05026161 RusKurskdriftless2
    0.05072943 RusOreldriftless2
    0.05376711 Ukrdriftless2
    0.05606086 Belarusdriftless2
    0.05621478 Polishdriftless2
    0.05673149 Icelanddriftless
    0.05680711 Nordriftless2
    0.05689154 Swedriftless2.0
    0.06451806 Lithdriftless2
    0.06509518 RusKosdriftless
    0.08893429 RusPinegadriftless

    Distance to: RUS_Sintashta_MLBA
    0.04000793 RusKurskdriftless2
    0.04177251 RusOreldriftless2
    0.04785163 Belarusdriftless2
    0.04790258 Ukrdriftless2
    0.05068705 RusKosdriftless
    0.05148599 Polishdriftless2
    0.05260675 Lithdriftless2
    0.05326296 Swedriftless2.0
    0.05378481 Icelanddriftless
    0.05410950 Nordriftless2
    0.07478745 RusPinegadriftless


    Unsurprisingly, Lithuanians wind up near the bottom for all except Yamnaya. Also unsurprisingly, Pinega Russians with their high Uralic ancestry remain the furthest from the steppe groups . But like with Lithuanians, they're not that far from Yamnaya. It's strange. Overall not a huge difference from my original model and ghosts, just a bit better.

  5. #14
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    Quote Originally Posted by Coldmountains View Post
    HGs in the South Baltics, East Poland and likely even the western half of Belarus were not EHG-like and very WHG-rich with some EHG, so direct EHG ancestry is pretty much out of question for Proto-Balto-Slavs. Maybe some Balt_BA pops around Estonia had HG ancestry from a much EHG-richer source but these pops are not ancestral to the vast majority of Balto-Slavs which orginated more in the south where HGs were definetly mostly WHG-like. EHGs in Central Russia were already in the Fatyanovo period either replaced or extremely decimated so the significant survival of their ancestry up to the early medieval period is extremely unlikely and than would only effect Russians and Volga-Ural groups.

    qpAdm is checking each snp if i correctly understand it and much more powerful than global25 or any gedmatch calc which analyze a tiny amount of aggregated data compared to qpAdm. So qpAdm can tell if someone has direct EHG ancestry from 1500-3000 B.C or only indirect EHG ancestry from Steppe_Eneolithic around 4000 B.C. So far qpAdm pretty much shows no direct EHG ancestry among East Europeans on top of the EHG which was brought by Corded Ware or Yamnaya.
    The Narva-culture foragers (which are also some of the last Hunter-Gatherers in Europe going by radiocarbon dating) are about 75% WHG and 25% EHG. The far older HGs from Zvejnieki in Latvia are more around 60%/40% WHG/EHG.

     


    Imho it's doubtful that even the Narva HGs contributed directly to Balto-Slavs. The more likely possibility is that that ancestry was mediated by Baltic_BA groups and ended up in modern Balts (mainly Latvians, far lesser extent Lithuanians, especially the further south you go in Lithuania). Most of the HG ancestry in Balto-Slavs is similar to what we find in GAC/TRB, which is 'pure' old WHG with very little EHG admixture.

    It's a relatively small sample size, but I think that it is very telling that the R1a subclade found in EHGs from Northern Russia and a more recently published HG sample from Latvia is virtually extinct in that area. Once post-CW groups expand into Northern Russia and the Baltics, we don't see any evidence of gene flow from local EHGs into the Corded-Ware people (i.e an increased EHG component).

    So how would have additional EHG gotten into Balto-Slavs if even the Baltic Corded-Ware/Fatyanovo that predated them in that area by a few thousand years lack any increased EHG ancestry compared to other Corded-Ware groups in Europe? It would appear to me that most local HGs left little to no genetic trace once CW-derived people start showing up in these territories the foragers inhabited. More contemporary ethnographic examples show that hunter-gatherers generally don't fare too well in direct competition with farmer/pastoralists.
    YDNA (P): R-Y33
    YDNA (P, maternal line): R-Y20756
    YDNA(M): E-Y6938

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  7. #15
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    Quote Originally Posted by altvred View Post
    The Narva-culture foragers (which are also some of the last Hunter-Gatherers in Europe going by radiocarbon dating) are about 75% WHG and 25% EHG. The far older HGs from Zvejnieki in Latvia are more around 60%/40% WHG/EHG.

     


    Imho it's doubtful that even the Narva HGs contributed directly to Balto-Slavs. The more likely possibility is that that ancestry was mediated by Baltic_BA groups and ended up in modern Balts (mainly Latvians, far lesser extent Lithuanians, especially the further south you go in Lithuania). Most of the HG ancestry in Balto-Slavs is similar to what we find in GAC/TRB, which is 'pure' old WHG with very little EHG admixture.

    It's a relatively small sample size, but I think that it is very telling that the R1a subclade found in EHGs from Northern Russia and a more recently published HG sample from Latvia is virtually extinct in that area. Once post-CW groups expand into Northern Russia and the Baltics, we don't see any evidence of gene flow from local EHGs into the Corded-Ware people (i.e an increased EHG component).

    So how would have additional EHG gotten into Balto-Slavs if even the Baltic Corded-Ware/Fatyanovo that predated them in that area by a few thousand years lack any increased EHG ancestry compared to other Corded-Ware groups in Europe? It would appear to me that most local HGs left little to no genetic trace once CW-derived people start showing up in these territories the foragers inhabited. More contemporary ethnographic examples show that hunter-gatherers generally don't fare too well in direct competition with farmer/pastoralists.
    Latvians and Lithuanians score 80% Baltic_BA. Slavs score a lot less but its still essential to their ethnogenesis. Its not hard to see how some EHG can sneak into the eastern European genepool.

    Moreover, if GAC was solely WHG+EEF, why then are both Sintashta and Yamnaya closer to GAC than they are to either pure ANF or WHG? They are furthest from WHG. If anything, the extra WHG admixture should put GAC right in between ANF and WHG in terms of proximity.

    Distance to: RUS_Sintashta_MLBA
    0.19619835 POL_Globular_Amphora
    0.26269470 TUR_Barcin_N
    0.33642648 WHG

    Distance to: Yamnaya_RUS_Samara
    0.28437448 POL_Globular_Amphora
    0.33822432 TUR_Barcin_N
    0.37744914 WHG

    You can argue that because Sintashta partially descends directly from GAC, it can explain the distance. But Yamnaya doesn’t. Yet, when modeling GAC, it picks up only ANF and WHG and not EHG in any appreciable amount. G25 is extremely confusing and probably flawed.
    Last edited by Cynic; 07-29-2021 at 05:01 AM.

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    Quote Originally Posted by Cynic View Post
    Latvians and Lithuanians score 80% Baltic_BA. Slavs score a lot less but its still essential to their ethnogenesis. Its not hard to see how some EHG can sneak into the eastern European genepool.
    Populations like Lativa_BA are tangentially related not only to Slavs but to Balts as well, their HG ancestry exceeds 30% which isn't something observable even in the most HG-rich modern Latvian. Lithuania_BA more closely resembles a population one would expect proto-Balto-Slavs to originate from (less HG, more EEF) but it's still not a perfect fit as far as qpAdm is concerned.

    Most modern 'North' Slavic-speaking populations can be modeled almost exclusively as a mixture of GAC/TRB and CW/Steppe while Latvia_BA requires additional WHG input.


     


     


     


    I don't believe it's entirely unreasonable to assume that to the south of Lithuania_BA there existed a more suitable source population, possibly in present-day Belarus which is a blank space in terms of aDNA samples. Hopefully, that will change soon but until then I don't believe we have a true ancestral population for Balto-Slavs currently genotyped. There's an entire 50+ page thread on a related topic if you're interested.

    https://anthrogenica.com/showthread....dieval-Moravia

    Moreover, if GAC was solely WHG+EEF, why then are both Sintashta and Yamnaya closer to GAC than they are to either pure ANF or WHG? They are furthest from WHG. If anything, the extra WHG admixture should put GAC right in between ANF and WHG in terms of proximity.

    Distance to: RUS_Sintashta_MLBA
    0.19619835 POL_Globular_Amphora
    0.26269470 TUR_Barcin_N
    0.33642648 WHG

    Distance to: Yamnaya_RUS_Samara
    0.28437448 POL_Globular_Amphora
    0.33822432 TUR_Barcin_N
    0.37744914 WHG
    Not sure I understand you. GAC can be modeled as purely EEF and WHG on qpAdm with EHG as right/reference pop, if GAC did have any EHG related ancestry then the model should have failed.

     


     



    Sintashta definitely descends partially from something like GAC/TRB (as do all later CW groups), in the case of some of the more western Yamnaya samples, there is evidence of EEF/Barcin admixture pretty early on which might partially explain what you're referring to.
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  10. #17
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    Quote Originally Posted by altvred View Post
    Populations like Lativa_BA are tangentially related not only to Slavs but to Balts as well, their HG ancestry exceeds 30% which isn't something observable even in the most HG-rich modern Latvian. Lithuania_BA more closely resembles a population one would expect proto-Balto-Slavs to originate from (less HG, more EEF) but it's still not a perfect fit as far as qpAdm is concerned.

    Most modern 'North' Slavic-speaking populations can be modeled almost exclusively as a mixture of GAC/TRB and CW/Steppe while Latvia_BA requires additional WHG input.


     


     


     


    I don't believe it's entirely unreasonable to assume that to the south of Lithuania_BA there existed a more suitable source population, possibly in present-day Belarus which is a blank space in terms of aDNA samples. Hopefully, that will change soon but until then I don't believe we have a true ancestral population for Balto-Slavs currently genotyped. There's an entire 50+ page thread on a related topic if you're interested.

    https://anthrogenica.com/showthread....dieval-Moravia



    Not sure I understand you. GAC can be modeled as purely EEF and WHG on qpAdm with EHG as right/reference pop, if GAC did have any EHG related ancestry then the model should have failed.

     


     



    Sintashta definitely descends partially from something like GAC/TRB (as do all later CW groups), in the case of some of the more western Yamnaya samples, there is evidence of EEF/Barcin admixture pretty early on which might partially explain what you're referring to.
    In other words can we just chalk this up to G25 being unreliable? If formal stats do indeed show Balto-Slavs to have very little EHG and instead much more WHG, then there shouldn't really be a reason they're closer to MLBA steppe groups with or without drift being present.

    Also, what calculator/software did you use in the image you posted?

  11. #18
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    Quote Originally Posted by Cynic View Post
    In other words can we just chalk this up to G25 being unreliable? If formal stats do indeed show Balto-Slavs to have very little EHG and instead much more WHG, then there shouldn't really be a reason they're closer to MLBA steppe groups with or without drift being present.

    Also, what calculator/software did you use in the image you posted?
    I'm using the admixtools2 package, which is a more sleek version of the original admixtools developed by Nick Patterson from the Reich team (qpAdm, qpGraph, and all that stuff in a box with a pretty interface).

    I wouldn't completely write G25 off but it does have its disadvantages specifically concerning overfitting, the elevated EHG in Eastern Europeans as well as Slavs being modeled as a mixture of Latvia_BA + EEF rich Balkan population being two clear examples.

    Btw, using formal statistics some Volga-Ural populations like Udmurts appear EHG shifted but I'm not sure if it's some weird byproduct of their high Siberian + low EEF/GAC ancestry.

     
    Last edited by altvred; 07-29-2021 at 05:47 AM.
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    I'm getting additional EHG for Uralic populations in qpAdm models that include Corded Ware in left populations, like for example the first model below. But then in models with Yamnaya and Turkey_N in place of Corded Ware, like the fifth model below, often I don't get extra EHG.



    Also in these models for Saami, the first model which doesn't include Corded Ware doesn't get EHG, but the third model which is the highest-p model with Corded Ware gets high EHG:



    Code:
    library(admixtools)
    library(tidyverse)
    library(colorspace)
    library(cowplot)
    
    right=c("Russia_Kostenki14","Karitiana","Russia_Ust_Ishim.DG","Iran_GanjDareh_N","Spain_HG_published.SG","Han")
    left=c("Turkey_N.DG","Russia_Samara_EBA_Yamnaya","Estonia_CordedWare.SG","Hungary_EN_HG_Koros_published.SG","Russia_HG_Samara","Nganasan")
    target="Saami.DG"
    
    qp=qpadm("v44.3_HO_public",left,right,target)
    
    t=qp$popdrop%>%filter(feasible==T&f4rank!=0)%>%arrange(desc(p))%>%select(1,4,5,7:last_col(5))
    t2=melt(t[-c(2,3)],id.vars="pat")
    
    lab=sub("e-0","e-",sub("^0","",sprintf(ifelse(t$p<.001,"%.0e","%.3f"),t$p)))
    # lab=paste0(lab," (",ifelse(t$chisq<10,sub("^0","",sprintf("%.1f",t$chisq)),round(t$chisq)),")")
    
    subtit=str_wrap(paste("Outgroups:",paste(sort(right),collapse=", ")),width=50)
    
    legcols=1
    
    p=ggplot(t2,aes(x=fct_rev(factor(pat,level=t$pat)),y=value,fill=variable))+
    geom_bar(stat="identity",width=1,position=position_fill(reverse=T),size=.1,color="gray20")+
    geom_text(aes(label=round(100*value)),position=position_stack(vjust=.5,reverse=T),size=3.5)+
    ggtitle(paste("Target:",target),subtitle=subtit)+
    coord_flip()+
    scale_x_discrete(expand=c(0,0),labels=rev(lab))+
    scale_y_discrete(expand=c(0,0))+
    scale_fill_manual(values=colorspace::hex(HSV(c(30,60,90,200,230,280),.5,1)))+ # manual colors
    # scale_fill_manual(values=colorspace::hex(HSV(head(seq(0,360,length.out=ncol(t)-2),-1),.5,1)))+ # automatic colors
    guides(fill=guide_legend(ncol=legcols,byrow=F))+
    theme(
      axis.text=element_text(color="black",size=11),
      axis.text.x=element_blank(),
      axis.ticks=element_blank(),
      axis.title=element_blank(),
      legend.direction="horizontal",
      legend.key=element_rect(fill=NA),
      legend.margin=margin(-4,0,1,0),
      legend.text=element_text(size=11),
      legend.title=element_blank(),
      plot.subtitle=element_text(size=11),
      plot.title=element_text(size=16)
    )
    
    ggdraw(p)
    hei=c(.5+.2*(str_count(subtit,"\n")+1)+.25*nrow(t),+.1+.23*ceiling(length(unique(t2[!is.na(t2$value),2]))/legcols))
    ggdraw(cowplot::plot_grid(p+theme(legend.position="none"),cowplot::get_legend(p),ncol=1,rel_heights=hei))
    ggsave("a.png",width=4,height=sum(hei))

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  14. #20
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    Quote Originally Posted by altvred View Post
    I'm using the admixtools2 package, which is a more sleek version of the original admixtools developed by Nick Patterson from the Reich team (qpAdm, qpGraph, and all that stuff in a box with a pretty interface).

    I wouldn't completely write G25 off but it does have its disadvantages specifically concerning overfitting, the elevated EHG in Eastern Europeans as well as Slavs being modeled as a mixture of Latvia_BA + EEF rich Balkan population being two clear examples.

    Btw, using formal statistics some Volga-Ural populations like Udmurts appear EHG shifted but I'm not sure if it's some weird byproduct of their high Siberian + low EEF/GAC ancestry.

     
    Afaik (i could be wrong) some Uralics especially people like Khanty and Mansi have significant WSHG and more western Uralics may have some small WSHG ancestry brought by early Uralic speakers and Steppe_IA (Steppe Iranics) from the east. EHG on the other side looks pretty much like a pop getting replaced from almost all directions. I mean we see a lot of Indo-Iranians since 2000 B.C rich in WSHG but so far nobody rich in extra EHG despite them living earlier in EHG territories of Central-East Russia. WSHG ancestry persisted much longer than EHG it seems and up to 0-500 A.D we get pops very rich in WSHG ancestry in Central Asia/Siberia unlike EHG which pretty much seems to be insignificant after Fatyanovo and CWC (maybe survived better in unsampled regions north of Fatyanovo?).

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