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Thread: Faire du vieux avec du neuf...

  1. #41
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    K1a4a1

    Italy 1861-1946 France-Ile-de-France Lorraine
    Quelle est la composition de "Balkans_ChL" avec ton K8?

  2. #42
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    Normandie Netherlands Friesland Finland Orkney
    Quote Originally Posted by Camulogène Rix View Post
    Quelle est la composition de "Balkans_ChL" avec ton K8?
    Tu as toutes les compositions dans le post #36
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  3. #43
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    Bon, j'ai ajouté des Beakers, avec pour effet que comme prévu 4mix fait une tambouille de campaniformes. Allez, autant le dire brutalement, je ne crois décidément pas à l'intérêt de cela. Mais bien sûr ce truc ne m'appartient pas, donc vous pouvez passer les individus ou groupes anciens que vous voulez au travers de nMonte avec le fichier voulu (que je vais publier dans ce post), et ajouter ces individus à la feuille d'oracles.

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
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    Anatolia_N:I1101,0.114961339458098,0.1797487070885 35,0.00641105139583204,-0.100776482970979,0.054779481925261,-0.0437858335537877,-0.000940042552228355,-0.000230759615184287,0.0425409581462383,0.07854376 3660777,0.00568359481314423,0.00869226322657109,-0.0228937458708705,0.00743162431773835,-0.0347443969583586,-0.0102093986110838,0.0168195422054228,0.0039273464 3238918,0.018729009584065,-0.0063780592659523,-0.0207134478057131,0.00469880410317349,-0.000616238590158065,-0.00313297302892955,-0.0102984775573868
    Anatolia_N:I1102,0.106993721871893,0.1706089423213 21,0.00527968938480286,-0.0975464674911398,0.0597034803005654,-0.0454591775112573,-0.0042301914850276,-0.00784582691626574,0.030474051748988,0.0845575553 099781,0.00519642954344615,0.00989119608540848,-0.0295834768071638,-0.00619302026478196,-0.0318942706453683,0.00185625429292433,0.029597178 91962,0.00202701751349119,0.0130725972935756,-0.00875419899248355,-0.00910892584227141,0.0106341356019189,-0.00382067925898,-0.00397646576748751,-0.0026344942588664
    Anatolia_N:I1103,0.112684877290611,0.1695934129027 42,-0.00641105139583204,-0.100130479875011,0.0440082354792827,-0.0468536308091486,-0.00705031914171266,-0.00553823076442288,0.0392685767503738,0.075992458 1126312,0.0113671896262885,0.0134879946619207,-0.0221504424335046,-0.00550490690202841,-0.0366444811670189,-0.0115352945346012,0.0194272231675039,-0.00202701751349119,0.0104329382246805,-0.0080038390788421,-0.0163461545936651,0.00568802601963106,-0.0113387900589084,-0.00939891908678865,-0.00706523460332352
    Anatolia_N:I1579,0.12520541921179,0.18482635418143 2,0.00829665474754735,-0.102068489162915,0.0569337312144567,-0.0504792093836661,-0.00493522339919886,-0.00484595191887002,0.0368142907034755,0.089295694 1851062,0.0116919664727538,0.0131882614472113,-0.0312187443693689,0.00344056681376775,-0.0472306646152688,-0.00676206920993863,0.0178626145902553,0.003673969 24320278,0.0115642206827784,-0.0157575581864704,-0.0139753382785534,0.00581167875918826,-0.00320444066882194,-0.00421746369278978,-0.00155674660751196
    Anatolia_N:I1580,0.12520541921179,0.18279529534427 3,0.00301696536274449,-0.105298504642754,0.0532407324329784,-0.0468536308091486,-0.00282012765668507,-0.0110764615288458,0.0394731005876154,0.0781792914 396133,0.00730747904547115,0.0145370609134034,-0.0193258893715141,-0.00247720810591278,-0.0411232510874323,0,0.0357252291805105,-0.00164695172971159,0.0118156167845779,-0.00900431896369737,-0.00811068739380331,0.0040805404053875,0.002588202 07866387,-0.00120498962651137,-0.00490973930061465
    Anatolia_N:I1581,0.114961339458098,0.1797487070885 35,0,-0.111758535602432,0.0603189800974784,-0.0488058654261965,-0.00141006382834253,-0.00923038460737146,0.0433590534952044,0.085833208 084051,0.00552120638991154,0.0158858603795954,-0.0218531210585582,-0.00302769879611562,-0.043837657099804,-0.000132589592351738,0.0401582868160483,0.00354728 064860958,0.00879886356298358,-0.00375179956820724,-0.0104815037089151,0.00779012259210341,-0.0113387900589084,0.0036149688795341,-0.00359249217118145
    Anatolia_N:I1583,0.117237801625585,0.1827952953442 73,0.00301696536274449,-0.108205518574609,0.0523174827376089,-0.0510369907028226,-0.00587526595142722,-0.0117687403743986,0.0400866720993399,0.0854687358 628873,0.0128286854353827,0.00509546465005891,-0.0208124962462459,0.0027524534510142,-0.0335229142527913,-0.00424286695525561,0.0207310636485444,0.001013508 75674559,0.0138267855989742,-0.00300143965456579,-0.00923370564832993,0.00284401300981553,-0.00382067925898,-0.00819392946027729,-0.00311349321502392
    Anatolia_N:I1585,0.121790725960559,0.1807642365071 14,-0.00150848268137225,-0.100453481422995,0.0520097328391523,-0.0418335989367398,-0.00517023403725595,-0.00669202884034431,0.0353826238427847,0.075627985 8914675,0.00876897485456538,0.0170847932384328,-0.0212584783086655,0.00302769879611562,-0.042209013492381,-0.000132589592351738,0.0329871641703254,-0.00304052627023678,0.0135753894971747,-0.00600287930913158,-0.00623899030292563,0.00469880410317349,-0.00480666100323291,0.00240997925302273,-0.009100980166993
    CHG:KK1,0.0910584866994834,0.102568471276509,-0.0833436681458166,-0.00323001547983907,-0.0861699715678263,0.0206379088087917,0.0249111276 340514,-0.00184607692147429,-0.12823644595044,-0.0747168053385582,-0.006333148506075,0.0239786571767478,-0.0548557936776053,0.00440392552162273,0.026601178 9212433,-0.0327496293108792,0.0238602808030417,-0.0134289910268791,-0.0222485550092585,0.0347666759987204,0.0338153274 418569,-0.00704820615476023,0.00653212905567549,-0.0257867780073432,-0.00203574556366949
    Levant_N:I0867,0.0728467893595867,0.17264000115848 ,-0.030923894968131,-0.147934708976629,0.0344679886271305,-0.0686071022562533,-0.0164507446639962,-0.0119994999895829,0.0726059622207433,0.0488392776 359356,0.010555247510125,-0.0130383948398566,0.0294348161196906,-0.00825736035304261,-0.0248368150132017,0.00729242757934558,0.020991831 7447525,-0.00861482443233755,-0.00465082788329132,0.0237613972653125,-0.000374339418175538,0.00445149862405909,0.0001232 47718031613,-0.00530195435665001,-0.00682573512524475
    Levant_N:I1699,0.067155633940869,0.168577883484163 ,-0.0226272402205837,-0.150841722908484,0.0286207405564566,-0.0716748995116143,-0.0138656276453682,-0.0177684903691901,0.0777190581517815,0.0377228748 904428,0.006333148506075,-0.013338128054566,0.0325566905566275,-0.00027524534510142,-0.0149292330680447,0.00848573391051122,-0.000782304288624318,-0.00772800427018516,-0.0135753894971747,0.0123809385750839,-0.0101071642907395,0.0101395246436902,0.0029579452 3275871,0.00313297302892955,-0.00203574556366949
    Morocco_Iberomaurusian:TAF009,-0.162767,0.07718,-0.024513,-0.079135,0.009848,-0.047969,-0.052877,0.020538,0.13294,0.002005,0.025333,-0.026676,0.057978,-0.052985,0.072882,-0.034076,0.002347,-0.05625,-0.130475,0.04152,-0.026204,-0.120314,0.067909,-0.016508,0.012334
    Morocco_Iberomaurusian:TAF010,-0.193499,0.083273,-0.03017,-0.088502,0.034776,-0.055499,-0.076378,0.019384,0.163619,0.008565,0.02111,-0.030573,0.07879,-0.046104,0.077496,-0.046141,-0.00665,-0.069805,-0.144176,0.036518,-0.042924,-0.129217,0.07629,-0.015303,0.018322
    Morocco_Iberomaurusian:TAF011,-0.194638,0.085304,-0.021873,-0.088825,0.026774,-0.059961,-0.072148,0.019845,0.161165,0.002551,0.016564,-0.035818,0.080574,-0.051196,0.066367,-0.037523,0.012126,-0.071199,-0.14493,0.035767,-0.041427,-0.12662,0.068279,-0.011447,0.018441
    Morocco_Iberomaurusian:TAF013,-0.196914,0.082258,-0.026398,-0.088502,0.032314,-0.057173,-0.074733,0.017768,0.156665,0.002369,0.02111,-0.036717,0.077898,-0.052159,0.072746,-0.038584,0.000913,-0.069552,-0.141285,0.039894,-0.035687,-0.125384,0.075428,-0.011206,0.020477
    Morocco_Iberomaurusian:TAF014,-0.201467,0.079211,-0.018479,-0.083011,0.034468,-0.055499,-0.076848,0.014538,0.162596,0.002005,0.020461,-0.029374,0.078344,-0.054223,0.066503,-0.025192,0.017602,-0.063724,-0.151215,0.04127,-0.042176,-0.126126,0.077153,-0.014339,0.012693
    Ethiopia_4500BP:mota,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
    Bolshoy_Oleni_Ostrov:BOO001,0.084229,-0.150298,0.121433,0.098515,-0.066782,-0.003347,-0.003995,-0.000923,0.002863,-0.045923,0.027119,-0.008542,0.021407,-0.052159,-0.0076,0.006232,-0.004824,0.003167,-0.000503,0.003377,-0.010981,0.007914,0.005793,-0.007591,-0.001916
    Bolshoy_Oleni_Ostrov:BOO002,0.093335,-0.14319,0.122187,0.105945,-0.05878,0.001673,-0.00282,0.007846,-0.00859,-0.044648,0.038486,-0.010491,0.020367,-0.052572,0.002579,0.006099,-0.000913,0.004054,-0.003645,0.004377,0.001497,0.009521,0.003574,-0.008314,0.002155
    Bolshoy_Oleni_Ostrov:BOO003,0.097888,-0.129988,0.121056,0.103683,-0.059088,-0.000837,-0.00235,0.003231,0.005727,-0.053577,0.035401,-0.01079,0.023786,-0.049544,-0.005972,0.009016,-0.003912,-0.001394,-0.004022,0.001751,0.007112,0.00643,0.006655,-0.018436,0.001557
    Bolshoy_Oleni_Ostrov:BOO004,0.088782,-0.144205,0.112759,0.112405,-0.059703,0.000558,-0.003995,-0.005538,0.000409,-0.043372,0.026632,-0.014987,0.024826,-0.049131,-0.001493,0.009812,-0.001695,-0.002027,-0.006662,-0.005253,0.006863,0.003091,0.007641,-0.009037,0.001916
    Bolshoy_Oleni_Ostrov:BOO005,0.092197,-0.136081,0.121433,0.114666,-0.061858,-0.001952,-0.00658,-0.005077,-0.001432,-0.040274,0.035888,-0.009142,0.021407,-0.04514,-0.002036,0.012596,-0.004303,0.004687,0,0.008254,0.005615,0.004699,0.0 08751,-0.022533,-0.000958
    Bolshoy_Oleni_Ostrov:BOO006,0.080814,-0.207168,0.120301,0.085272,-0.076322,-0.010598,0.003055,0.001846,0.002659,-0.03991,0.042708,-0.008692,0.019772,-0.04748,-0.015065,0.001193,0.000913,0.003547,-0.00176,-5e-04,0.000374,0.009274,0.000739,-0.009399,0.003233
    C'est bien sûr le même que le premier, à la seule différence que BOO est venu remplacer Botai.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  5. #44
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    Quote Originally Posted by anglesqueville View Post
    Pour Camu: juste un début d'esquisse de velleité de réponse à ta proposition.




    J'obtiens sans surprise des choses cohérentes avec des individus qui sont des cas faciles, comme ma mère:

    Using 4 populations approximation:
    1 France_MLN+Beaker_NL+Beaker_NL+Beaker_NL @ 4,411349
    2 GAC+Beaker_NL+Beaker_NL+Beaker_NL @ 4,710626
    3 Baden_LCA+Beaker_NL+Beaker_NL+Beaker_NL @ 5,421254
    4 GAC+Beaker_NL+Beaker_NL+Battle_Axe @ 5,689463

    Avec toi on retombe sur un simple barycentre qui ne t'apprendra rien:

    Using 4 populations approximation:
    1 France_MLN+Balkans_ChL+Battle_Axe+Battle_Axe @ 5,395831
    2 GAC+Balkans_ChL+Battle_Axe+Battle_Axe @ 5,426785
    3 France_MLN+Baden_LCA+Battle_Axe+Battle_Axe @ 5,913966
    4 GAC+Baden_LCA+Battle_Axe+Battle_Axe @ 6,390618
    5 France_MLN+Balkans_ChL+Beaker_NL+Battle_Axe @ 6,488065


    Je jetterai un oeil sur ce qui se passe quand on ajoute des Ibériques et des Beakers italiens, mais je n'y crois pas beaucoup. Mais peut-être suis-je déformé par mes préjugés fortement en faveur de qpAdm quand il est question d'Anciens.
    Cela m' intrigue un petit peaux:

    Beaker Dutch :

    EEF 32,6
    WHG 37,4
    ANE 16,6
    CHG (like parce que il n'est pas vraiment south caucasus )13,4

    et sourtout

    Battle axe
    EEF 32,6
    WHG 33
    ANE 20,6
    CHG 13,8

    Mais le composant "locale" EEF+WHG ( Funnel Beaker and GAC respectivement) sont dans ce cas presque 70%. Et la composant steppique (ANE+CHG) seulment 30% ( plus ou moins). Je pensais que le Yamnaia c'etait plus ou moins 70% dans le dutch beaker and CWC. Ce qui s'est passé?

    Une seconde question :

    J'ai lu differentes interpretations sur l'exact niveau du WHG dans le AHG: quelque fois 30%. Selon ton post c'est presque de 0 ( j'ai entendu bien?)
    Dans le papier il semble que AHG= 75% WHG+ 25 BASAL EURASIAN.
    41467_2019_9209_Fig3_HTML.png

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  7. #45
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    ruderico: tu poses des questions de transitivité des modèles. Mon idée est que cela marche le plus souvent mal, et parfois pas du tout, pour des raisons diverses qui dépendent des instruments de modélisation. Pour G25+nMonte, c'est tellement vrai que quand cela a l'air de marcher je suis très méfiant, et qu'il m'est arrivé de poser comme un postulat méthodologique que les comparaisons n'ont de sens qu'à l'intérieur d'un modèle déterminé. Cela dit:

    [1] "distance%=0.96"

    Beaker_The_Netherlands

    Yamnaya_Samara,60.4
    Poland_GAC,39.6


    Voyons, si l'on pose "à la louche": Yamna_Samara = 60%EHG+30%CHG+10%EEF d'une part, et GAC=70%EEF+30%WHG, on obtient sauf erreur:

    Beaker_NL = 60%(60%EHG+30%CHG+10%EEF)+40%(70%EEF+30%WHG) = 36%EHG + 18%CHG + 6%EEF + 28%EEF + 12%WHG, soit finalement:
    Beaker_NL = 36% EHG + 34% EEF + 12% WHG + 18% CHG. Si l'on prend le HG de Samara comme proxy de EHG, il n'a sûrement pas plus d'un tiers d'affinité ANE avec G25+nMonte (à vérifier), ce qui nous donnerait quelque chose comme 36% WHG + 10% ANE + 34% EEF + 20% CHG. Compte-tenu des réserves exprimées plus haut quant à la validité d'un tel calcul par transitivité (auquel encore une fois je ne crois pas un instant) ce résultat n'est pas monstrueusement différent de celui qui apparaît dans mon "truc".

    Maintenant à propos de qpAdm et de AHG. L'affinité de AHG avec WHG, et surtout l'évaluation que tu rappelles, n'ont pas été testées avec qpAdm. En particulier tu sais bien que l'on n'a pas de génome "basal". AHG peut très bien dériver de la même souche que WHG, et même avoir subi une influence post-séparation, cela n'empêche que la dérive génétique peut parfaitement avoir joué suffisamment pour rendre les specimens respectifs parfaitement distinguables par qpAdm, et c'est ce que je pense. En tout cas il est en l'état actuel de nos données simplement impossible d'afficher un modèle qpAdm de AHG en fonction de WHG. Ce qui est possible est de comparer des modèles faisant intervenir WHG et AHG.
    Je te renvoie au modèle que je donnais dans le grenier des EEF, qui donne Anatolia_N comme un mixe AHG/Natufian avec un ajustement statistiquement acceptable (bien qu'on pourrait espérer mieux). Il est simplement impossible d'obtenir un tel modèle en remplaçant AHG par WHG (unfeasible model, avec coefficients -0.087 et 1.087, chi2 de 324!). Pour en avoir confirmation, on peut tenter un modèle oecuménique.

    left pops:
    Anatolia_N
    WHG
    AHG
    Natufian

    Si WHG et AHG étaient dans une certaine mesure interchangeables (autrement dir s'ils overlappaient de manière significative), on s'attendrait à au moins un modèle acceptable marqué par de grosses erreurs-standards sur WHG et AHG. Or ce n'est pas du tout ce qui arrive.

    numsnps used: 164754

    best coefficients: -0.077 0.950 0.127
    Jackknife mean: -0.076295329 0.946826136 0.129469194
    std. errors: 0.016 0.061 0.059

    fixed pat wt dof chisq tail prob
    000 0 12 47.504 3.81083e-06 -0.077 0.950 0.127 infeasible
    001 1 13 51.352 1.74394e-06 -0.078 1.078 -0.000 infeasible

    qpAdm rejette catégoriquement WHG, pourtant assorti d'une erreur-standard faible.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  9. #46
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    je pose ma question ici car c'est aussi un produit dérivé du G25 . (désolé de polluer un peu ton post Angles)
    Vous avez suivi ce post :
    https://anthrogenica.com/showthread....s-in-Global-25 ?
    Je partage assez son diagnostique sur les labels, mais Il a fait quoi exactement ? je ne comprend pas bien.. il fait tourner avec admixture? comment il a pu définir/obtenir les trois composants dont il parle ?

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    Quote Originally Posted by fabrice E View Post
    je pose ma question ici car c'est aussi un produit dérivé du G25 . (désolé de polluer un peu ton post Angles)
    Vous avez suivi ce post :
    https://anthrogenica.com/showthread....s-in-Global-25 ?
    Je partage assez son diagnostique sur les labels, mais Il a fait quoi exactement ? je ne comprend pas bien.. il fait tourner avec admixture? comment il a pu définir/obtenir les trois composants dont il parle ?
    Il faut que tu lui poses la question. Il parle d'un "ADMIXTURE look-alike". Cela mériterait en effet d'ête éclairci. Faire tourner ADMIXTURE avec K=3 ne présente aucune difficulté si l'on dispose des data des individus impliqués, mais je ne pense pas que Ger soit très familier d'Admixture. Mais je peux me tromper. Je ne suis pas encore allé au-delà des premiers posts.

    edit: tous les résultats qu'il donne sont sur la base de G25 et nMonte, donc je soupçonne quelque chose du même tonneau que ce que j'ai tenté ici. Je ne comprends pas bien où il va.
    Last edited by anglesqueville; 05-01-2019 at 07:51 PM.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  11. #48
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    Quote Originally Posted by anglesqueville View Post
    edit: tous les résultats qu'il donne sont sur la base de G25 et nMonte, donc je soupçonne quelque chose du même tonneau que ce que j'ai tenté ici. Je ne comprends pas bien où il va.
    c'est un peu ce que je me disais aussi...

  12. #49
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    Ruderico: for info, I tried Iron_Gates HG in place of WHG in the qpAdm-runs that I published yesterday (as I seem to remember that the authors say that this group is the most closely related to AHG). Same results: unfeasible models only.
    Last edited by anglesqueville; 05-02-2019 at 04:50 PM.
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  13. The Following 2 Users Say Thank You to anglesqueville For This Useful Post:

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