"...Eastern Italian Alps from Mesolithic to Middle Bronze Age..."

[Manofthehour]

I saw this posted by J-Man earlier. 
Could someone list the haplogroups? Some info on the autosomal would be nice as well. Thanks. 
https://www.ebi.ac.uk/ena/browser/view/PRJEB70242

Dna data from this region and time period has been much anticipated.

[ChrisR]

PRJEB70242
New insights into the genetic history of prehistoric populations in Eastern Italian Alps from Mesolithic to Middle Bronze Age and highlights of the importance of this region as a crossroads of human movements in prehistory.

---

Secondary Study Accession:
ERP155181
Study Title:Paleogenomic data of Prehistoric Alps individuals
Center Name:European Academy Research;EURAC research
ENA-FIRST-PUBLIC: 2024-05-31; ENA-LAST-UPDATE: 2024-05-31
98 Items

interested and following mainly for EBA and MBA and hoping more LBA and IA samples will come.

Seems unusual that the samples are public before any preprint or paper?

[R.Rocca]

interested and following mainly for EBA and MBA and hoping more LBA and IA samples will come.

I am interested to see if they found typical Bell Beaker U152 & subclade L2 in the EBA, but also if the Balkan EBA mix of R-Z2013+J2b+I2a made it up to the Italian Alps and if so, during what period.

Seems unusual that the samples are public before any preprint or paper?

It's 50/50. Sometimes the data comes out first, sometimes the preprint.

[La Tene]

Just a wild guess

Mesolitic?

eastern_alps:3130,0.132035,0.113739,0.189692,0.185726,0.135102,0.054384,0.011281,0.042229,0.07731,-0.000364,-0.01429,-0.01169,0.017393,-0.001651,0.041802,0.054229,0.009779,0.006081,-0.006411,0.047148,0.087845,0.011747,-0.043999,-0.145563,0.008263

Neolitic? - plot near enough to Sardinia and bit further from (pre greek?) sicily. 

Sample Italy_North_BellBeaker_2:I2477__BC_2065__Cov_67.96%,0.125205,0.17264,0.032432,-0.057494,0.079092,-0.036814,0.00141,-0.000923,0.061766,0.083646,-0.001137,0.015436,-0.02334,-0.000413,-0.024158,-0.012331,-0.005215,-0.005321,0.007668,-0.02076,-0.002121,0.007419,-0.01405,-0.023979,-0.003353 

plots with them (Europe 1 PCA)

eastern_alps:3150,0.120652,0.178733,0.033941,-0.070737,0.074475,-0.037092,-0.000235,0.004154,0.045404,0.090025,0.00065,0.019633,-0.024083,0.001376,-0.027687,-0.009149,0.004042,0.007475,0.017346,-0.011255,-0.000125,0.010758,-0.007395,-0.011327,-0.004431
eastern_alps:3111,0.120652,0.180764,0.032432,-0.062985,0.074783,-0.032351,0.001645,0.012923,0.052154,0.078908,-0.002761,0.012739,-0.022894,0.003303,-0.028908,-0.014717,0.006389,0.004307,0.013324,-0.007629,0.002246,0.000742,-0.016145,-0.030727,0.000479
eastern_alps:3112,0.110408,0.179749,0.031301,-0.062985,0.075399,-0.035977,0.000235,-0.005307,0.052563,0.089296,-0.006658,0.010041,-0.02884,-0.002064,-0.020222,-0.023336,-0.00339,0.004307,0.00176,-0.013882,0.00549,0.001731,-0.007888,-0.011929,-0.000838
eastern_alps:3113,0.122929,0.174671,0.033187,-0.052003,0.077861,-0.034025,-0.00141,-0.004615,0.058698,0.088931,0.001786,0.018583,-0.019177,-0.003303,-0.030809,-0.013126,0.014994,0.003801,0.006411,-0.004127,0.004118,0.002473,-0.012941,-0.026871,-0.002515
eastern_alps:3115,0.129758,0.180764,0.031678,-0.072029,0.078476,-0.023148,0.002115,0.005077,0.051949,0.090389,0.007957,0.015886,-0.028692,-0.018304,-0.030809,0.003315,0.027641,0.005321,0.005279,-0.012631,0.006489,0.010881,-0.012941,-0.009881,-0.007544
eastern_alps:3116,0.1161,0.179749,0.030924,-0.055233,0.071398,-0.031236,0.001645,-0.003,0.055426,0.08638,-0.000487,0.006444,-0.022894,-0.00289,-0.024022,-0.004906,0.0103,-0.003674,0.006536,-0.004502,0.004617,0.001978,-0.015283,-0.024461,0.003113
eastern_alps:3118,0.135449,0.183811,0.033187,-0.062985,0.064935,-0.0251,-0.00564,-0.004154,0.06013,0.086927,-0.002598,0.008243,-0.029286,0.003991,-0.020765,-0.013126,-0.003781,0.005194,0.017346,-0.02051,-0.003494,0.003833,-0.010599,-0.019521,0.001078
eastern_alps:3119,0.129758,0.179749,0.038089,-0.060724,0.063089,-0.028168,-0.003055,0.003923,0.045609,0.08146,-0.001299,0.02203,-0.024678,-0.013762,-0.021037,0.000796,0.008475,-0.001014,0.012193,-0.016258,0.004492,0.011005,-0.010353,-0.015665,-0.001197
eastern_alps:3120,0.133173,0.175687,0.030924,-0.066861,0.081554,-0.027889,0.00094,0.003,0.048677,0.088931,0.005196,0.023829,-0.024232,-0.010322,-0.027823,0.004508,0.031423,0.005194,0.013952,-0.009004,-0.002745,0.008532,0.001479,-0.012291,-0.002634
eastern_alps:3122,0.127482,0.17264,0.032432,-0.05491,0.070167,-0.028168,0.001175,-0.005769,0.051131,0.0831,0.002761,0.010491,-0.028989,-0.002202,-0.022801,-0.012066,0.014473,0.004687,-0.002388,-0.008004,-0.00287,0.009769,-0.003697,-0.014098,0.002275
eastern_alps:3123,0.10927,0.18178,0.030924,-0.06137,0.068936,-0.034582,-0.00658,0.002538,0.057471,0.08474,0.007795,0.01079,-0.02557,-0.003578,-0.021444,0.001591,0.017341,0.003547,0.012696,-0.01063,0.001373,0.000866,-0.008011,-0.017954,0.001317
eastern_alps:3125,0.121791,0.185842,0.042238,-0.065569,0.07109,-0.026774,-0.004465,0.004154,0.050108,0.080913,-0.001949,0.015436,-0.031665,-0.005643,-0.023751,-0.02201,0.001956,0.006588,0.008296,-0.011631,-0.003494,-0.001113,-0.006409,-0.013014,-0.006945
eastern_alps:3126,0.119514,0.18178,0.033564,-0.053295,0.07663,-0.022311,-0.00235,-0.000923,0.050517,0.085104,-0.005359,0.01169,-0.027056,-0.000826,-0.013436,-0.000265,0.024382,-0.001394,0.015209,-0.001626,0.010232,0.002473,-0.011092,-0.022774,-0.00012
eastern_alps:3131,0.119514,0.171624,0.038089,-0.061047,0.074168,-0.027331,0.00282,0.004154,0.044995,0.083282,0.006496,0.014237,-0.027502,-0.00867,-0.019951,-0.005701,0.008084,-0.000887,0.011061,-0.010255,0.003369,0.008903,-0.005793,-0.009399,-0.005269
eastern_alps:3133,0.129758,0.171624,0.036204,-0.059432,0.066782,-0.026495,0.00423,0.003,0.039473,0.081095,-0.000487,0.013638,-0.032111,-0.002615,-0.023208,0.006232,0.025295,-0.00266,-0.007668,-0.004877,0.002371,0.002844,-0.004807,-0.014219,0.000239
eastern_alps:3135,0.126344,0.175687,0.030924,-0.064923,0.073552,-0.024821,-0.001175,0.001154,0.055221,0.078908,0.003248,0.013788,-0.032111,-0.005367,-0.031759,0.009414,0.027511,0.004307,0.008799,-0.015257,0.001747,0.003833,-0.007272,-0.020123,0.002754
eastern_alps:3138,0.117238,0.169593,0.03017,-0.073644,0.065551,-0.035419,-0.005405,-0.000231,0.050926,0.090389,0.001949,0.01124,-0.02334,-0.007707,-0.024701,-0.003315,0.016168,0.008615,0.010307,-0.008004,0.010232,0.011129,-0.014173,-0.013255,-0.004431
eastern_alps:3139,0.1161,0.177718,0.028284,-0.066215,0.060011,-0.039324,-0.005875,0.000231,0.046836,0.080548,-0.001624,0.018583,-0.026016,-0.005367,-0.026194,-0.011138,0.004172,0.004814,0.009804,-0.008504,0.00025,0.002349,-0.002342,-0.01928,-0.002754
eastern_alps:3140,0.119514,0.177718,0.030547,-0.062339,0.064627,-0.037371,-0.004465,-0.005077,0.056449,0.08474,0,0.008393,-0.02215,-0.00867,-0.022394,-0.015248,-0.010431,0.005321,0.011439,-0.015382,0.007861,-0.002844,-0.008011,-0.024702,-0.006945
eastern_alps:3141,0.125205,0.17264,0.031301,-0.066538,0.075399,-0.037092,-0.002585,-0.006923,0.054403,0.096038,-0.004384,0.019333,-0.036125,-0.010046,-0.010315,-0.017104,0.00352,0.007981,0.003771,-0.019759,-0.002371,0.00136,-0.010353,-0.020003,0.003832
eastern_alps:3142,0.120652,0.175687,0.033941,-0.069122,0.076322,-0.03263,-0.008225,0.000231,0.056244,0.092029,-0.002111,0.014087,-0.020218,-0.004679,-0.020629,-0.009812,0.017993,-0.004814,0.012947,-0.01088,0,0.005441,-0.006409,-0.01205,-0.002515
eastern_alps:3144,0.121791,0.176702,0.039975,-0.062339,0.072013,-0.025379,-0.00047,0.000462,0.048268,0.083646,-0.003735,0.016785,-0.030178,-0.004817,-0.018187,-0.002519,0.014603,-0.000507,0.006788,-0.005753,-0.00287,0.004946,-0.002835,-0.013737,0.005389
eastern_alps:3145,0.129758,0.174671,0.046386,-0.05814,0.074475,-0.039324,-0.004465,0.001846,0.054199,0.086744,0.001299,0.014987,-0.032111,-0.014726,-0.015744,0.000133,0.025686,0.005068,0.004022,-0.00075,-0.001497,-0.000247,-0.001725,-0.014821,-0.002634
eastern_alps:3146,0.112685,0.17264,0.036204,-0.054587,0.066782,-0.030678,-0.007755,-0.001385,0.046631,0.07909,0,0.015736,-0.023191,0,-0.020222,-0.016574,0.000782,0.000507,0.005656,0.000625,0.002496,0.002226,-0.012448,-0.023015,-0.005868
eastern_alps:3147,0.120652,0.174671,0.027153,-0.055233,0.072321,-0.038766,-0.00752,0.008077,0.052972,0.08638,-0.00406,0.013788,-0.02661,-0.010735,-0.030944,0.002917,0.03064,0.007348,0.007165,-0.003126,0.001872,0.002349,-0.01898,-0.021931,-0.008502
eastern_alps:3149,0.118376,0.183811,0.026021,-0.069768,0.067397,-0.03012,-0.00517,-0.009692,0.048268,0.086198,0.006983,0.009741,-0.030327,-0.007156,-0.021444,-0.005967,0.015125,-0.001647,0.002137,-0.015382,0.00836,0.000618,-0.008997,-0.02169,-0.003952
eastern_alps:3153,0.126344,0.176702,0.038466,-0.07106,0.076014,-0.038766,0.002115,0.000231,0.050108,0.088385,-0.00406,0.015736,-0.034638,-0.012386,-0.028501,0.001193,0.024773,0.004181,0.007919,-0.009254,-0.001747,-0.003339,-0.009983,-0.013857,-0.001676
eastern_alps:3154,0.127482,0.174671,0.037712,-0.065569,0.075706,-0.030678,-0.005405,-0.002077,0.055017,0.094581,-0.003735,0.01169,-0.031516,-0.007294,-0.023615,0.001458,0.024643,0.00228,0.005782,-0.018134,-0.005615,0.001731,-0.007888,-0.012652,0.004311
eastern_alps:3155,0.120652,0.173656,0.036581,-0.062016,0.07663,-0.024263,0.00094,0.005769,0.056244,0.086744,0.006008,0.015137,-0.030029,0.000413,-0.019679,-0.005038,0.011474,0.003801,0.008673,-0.010005,-0.006613,0.004946,-0.009737,-0.020846,0.005868
eastern_alps:3156,0.118376,0.184826,0.030547,-0.073967,0.075091,-0.036256,-0.009165,0.005307,0.05563,0.095856,-0.00682,0.010491,-0.029286,0.000138,-0.011808,-0.012994,-0.01369,0.002027,0.012067,-0.016758,0.001747,0.004204,-0.010353,-0.018075,-0.003592
eastern_alps:ROMT2A,0.125205,0.177718,0.040729,-0.052649,0.075399,-0.031236,-0.00564,0.003461,0.05604,0.085833,-0.005359,0.017534,-0.030178,-0.01679,-0.027008,0.008486,0.024773,0.003041,0.010182,-0.012381,0.008984,0.004699,-0.00986,-0.014821,-0.002515
eastern_alps:ROMT12EB,0.126344,0.182795,0.046386,-0.059432,0.077553,-0.03263,-0.00799,0.003,0.055221,0.086744,0.001786,0.019633,-0.025272,0.005092,-0.023615,-0.01538,0.004563,0.000507,0.008547,-0.015257,0.002246,0.004946,-0.015529,-0.031691,0.00012
eastern_alps:SOLT59,0.118376,0.167562,0.024513,-0.063954,0.070167,-0.033188,0.00047,0.004154,0.041723,0.079455,0.000162,0.014987,-0.029732,0.001101,-0.027958,-0.003978,0.010431,0.005574,0.01169,-0.007879,0.004991,0.010758,-0.008381,-0.027594,-0.004191

Perhaps not Bell beakers, but maybe in the Bell Beaker era? On PCA still close the hypothetical Neolithic samples above but bit more north (steppe?) shifted. However other samples (see below) that plot close to or with them are approximately dated late MBA (around 1300 BC)

Samples Italy_MBA:I18132_I18133__BC_1300__Cov_unknown,0.127482,0.165531,0.038466,-0.047158,0.053856,-0.028447,-0.011751,0.000692,0.040496,0.077815,0.001137,0.014987,-0.020069,-0.005092,-0.015879,-0.010077,0.000913,0.003801,0.005908,-0.013381,-0.000374,0.001113,-0.007395,-0.01205,0.000838 

& 

Italy_MBA:I18130_I18131__BC_1300__Cov_unknown,0.119514,0.161469,0.039598,-0.045866,0.068628,-0.021753,0.002115,0.000923,0.043973,0.079819,0.004384,0.017984,-0.02334,-0.004679,-0.014386,-0.014983,-0.008345,0.005574,0.008673,-0.014632,0.007736,0.003091,-0.006162,-0.010122,-0.0097

overlap or plot extremely close  (Europe 1 PCA)

eastern_alps:3132,0.117238,0.169593,0.026021,-0.040375,0.053856,-0.012829,-0.005405,-0.001154,0.046018,0.069614,0.000974,0.009591,-0.015163,-0.00055,-0.021715,-0.006099,0.012126,0.004181,0.00176,0.000875,-0.006863,0.000989,-0.004067,-0.004338,-0.005628
eastern_alps:3117,0.124067,0.168578,0.038843,-0.046835,0.064627,-0.019522,-0.005875,-0.002538,0.035178,0.071437,0.002111,0.013638,-0.028097,-0.011147,-0.013436,-0.013922,0.004172,0.006208,0.009553,-0.008379,-0.002371,0.006059,-0.010969,-0.016267,0.00455
eastern_alps:3161,0.126344,0.171624,0.036204,-0.035853,0.057549,-0.024821,-0.004465,0.003923,0.0452,0.069432,0.003897,0.012439,-0.028394,0.000688,-0.013436,-0.013789,0.002738,0.007855,0.011061,-0.008129,0.003494,0.008408,-0.011092,-0.019521,-0.004431
eastern_alps:3152,0.127482,0.174671,0.033187,-0.05491,0.061858,-0.022311,-0.01034,0.000231,0.03436,0.070161,-0.000812,0.016186,-0.027651,-0.011285,-0.025515,-0.001458,0.029597,0.007221,0.000377,0.002126,-0.004617,0.003833,-0.008751,-0.012652,-0.001796
eastern_alps:3159,0.120652,0.166547,0.039221,-0.052649,0.063089,-0.018965,0,-0.003692,0.040905,0.069067,-0.004222,0.009891,-0.030921,-0.010184,-0.019272,-0.005171,0.011343,0.000253,0.008547,-0.007003,-0.002246,0.005564,-0.011585,-0.011327,0.003952
eastern_alps:3143,0.127482,0.170609,0.041106,-0.055233,0.059088,-0.023706,-0.003995,-0.002077,0.042745,0.069432,-0.003897,0.01109,-0.028692,-0.003441,-0.017101,-0.010342,-0.003651,-0.00038,0.006034,-0.016758,0.001622,0.002968,-0.00419,-0.015906,-0.001676
eastern_alps:3148,0.12862,0.164516,0.042615,-0.041667,0.062165,-0.024821,-0.004935,-0.004846,0.045813,0.069067,0.000812,0.014237,-0.031665,-0.007844,-0.013165,-0.014983,0.002999,0.004307,0.005908,-0.014507,-0.002246,0.011005,-0.011092,-0.016629,-0.004071
eastern_alps:3121,0.120652,0.171624,0.038466,-0.050388,0.069244,-0.026774,-0.002585,0.001154,0.041927,0.073077,0.002273,0.013338,-0.030773,-0.000413,-0.017236,-0.016971,-0.010952,-0.000253,0.008296,-0.015883,-0.000624,0.008408,-0.014543,-0.013134,-0.001317

Plot close to some IA italic samples (like 3151), so maybe EBA-MBA? I'm guessing closer to west coast italian samples  (Europe 1 PCA)

eastern_alps:3151,0.129758,0.152329,0.045254,-0.014212,0.052933,-0.017012,0.000705,0.006692,0.02986,0.052666,-0.001137,0.008992,-0.024083,-0.010459,-0.006922,-0.009546,0.001434,-0.008868,0.006159,-0.003502,-0.001996,-0.000742,-0.008627,-0.007471,-0.006107
2eastern_alps:3124,0.120652,0.155376,0.050534,-0.024548,0.049548,-0.01506,-0.00376,0.005077,0.027406,0.058316,-0.000974,0.016935,-0.027948,-0.014038,-0.009229,0.005569,0.0236,0.006208,-0.000754,-0.004627,-0.002995,0.010881,-0.003451,-0.011327,-0.002275

Closer to the previous group, but in between  (Europe 1 PCA)

1eastern_alps:3134,0.117238,0.164516,0.037335,-0.038114,0.053241,-0.027889,-0.00517,-0.005538,0.026588,0.05868,-0.002436,0.01124,-0.024975,-0.004404,-0.015472,-0.016971,-0.002608,0.00152,0.010056,-0.014007,0.000125,0.002226,-0.007765,-0.003133,-0.001916

Looks like a full blown Celt! (so most probably EBA-MBA). Overlaps with Lech EBA and Baden Wurttemberg Hallstatt  (Europe 1 PCA)

eastern_alps:3057,0.121791,0.142174,0.050534,0.022287,0.040931,0.007809,-0.00235,-0.006231,0.017794,0.014579,0.000812,0.01154,-0.015461,-0.013212,0.005022,0.002121,0.007302,0.003674,-0.004525,-0.008254,0.006988,0.005935,-0.001109,-0.006989,-0.000838

[AimSmall]

eastern_alps_avg(n=33),0.12234248,0.1772253,0.034089515,-0.062838182,0.072265242,-0.031472364,-0.0026277273,0.00083918182,0.051657727,0.086114818,-0.00010333333,0.014405424,-0.027596879,-0.0052880303,-0.023072424,-0.0059826061,0.012738182,0.0030059394,0.008456,-0.010262455,0.0018830909,0.0040842424,-0.0090045758,-0.018129515,-0.0015240303

Code:

Distance to:    eastern_alps_avg(n=33)
0.01984013    Hungary_C_Balaton_Lasinja:I1907__BC_4233__Cov_72.60%
0.02099717    Italy_Sicily_MN:I4065__BC_4865__Cov_77.64%
0.02233406    Switzerland_EBA_1:TU908_SX21__BC_2377__Cov_50.19%
0.02241845    Italy_South_C.SG:R4.SG__BC_2891__Cov_97.21%
0.02244915    Switzerland_EBA_1:TU910_SX22__BC_2999__Cov_47.09%
0.02305948    Italy_C.SG:R1014_oEEF.SG__BC_5124__Cov_49.54%
0.02360029    Italy_Sicily_MN:I4063__BC_4882__Cov_90.22%
0.02360962    France_MN:OBN004__BC_4578__Cov_43.35%
0.02425125    France_Alsace_Lingolsheim_MN:TU916_SX30__BC_4712__Cov_38.32%
0.02468847    Czechia_N_oWHG:I7950__BC_3448__Cov_71.10%
0.02521591    Romania_Urziceni_C:I14161__BC_4150__Cov_66.33%
0.02587824    France_MN:OBN007__BC_4427__Cov_47.03%
0.02610992    Italy_South_Tyrol_ECA:3058__BC_2860__Cov_45.18%
0.02644849    Italy_Sardinia_SantImbenia_RomanImperial.SG:R11835.SG__BC_788__Cov_62.73%
0.02659430    Czechia_Eneolithic:I7272__BC_3467__Cov_65.81%
0.02691619    Italy_BA_Grotta_Nisco:NEO823__BC_2715__Cov_unknown
0.02720850    Malta_Xaghra_LN:Xaghra9__BC_2465__Cov_83.70%
0.02725637    Italy_North_Remedello_C.SG:RISE489_noUDG.SG__BC_2752__Cov_42.67%
0.02743937    France_MN:FLR002__BC_4022__Cov_44.67%
0.02780032    Romania_C_Bodrogkeresztur:I7136__BC_4124__Cov_78.07%
0.02786772    Italy_Sardinia_LBA:I10364__BC_975__Cov_56.61%
0.02851801    France_MN:FLR007__BC_4376__Cov_63.13%
0.02856583    Hungary_LateC_Protoboleraz:I2791__BC_3573__Cov_70.95%
0.02860401    Italy_South_C.SG:R5.SG__BC_2882__Cov_80.74%
0.02871618    Romania_Iclod_LN:rom046__BC_4628__Cov_23.63%

Target: eastern_alps_avg(n=33)
Distance: 0.0791% / 0.00079052 | ADC: 0.25x RC
11.8 Italy_South_Tyrol_ECA
11.8 Malta_Xaghra_LN
11.4 Czechia_Eneolithic
8.8 Switzerland_EBA_1
8.4 Hungary_LateC_Baden
8.0 France_MN
5.6 Switzerland_LN
5.2 Italy_LaSassa_CA.SG
5.0 Italy_North_Remedello_C.SG
5.0 Italy_Sicily_MN
5.0 Poland_BKG.SG
4.6 Italy_BA_Grotta_Nisco
3.0 Poland_LBK_Late_N
2.6 Italy_Sardinia_IA_Punic_2
1.6 France_Alsace_Lingolsheim_MN
1.4 Hungary_C_Balaton_Lasinja
0.8 Romania_C_Bodrogkeresztur

[Albruic]

My great Aunt (Half Venetian half Emilian)

Distance to: Albruic_GreatAunt
0.04305165 eastern_alps:3057
0.05486179 eastern_alps:3151
0.06645166 2eastern_alps:3124
0.07337653 1eastern_alps:3134
0.08361367 eastern_alps:3132
0.08913989 eastern_alps:3161
0.09076084 eastern_alps:3117
0.09215681 eastern_alps:3148
0.09265410 eastern_alps:3159
0.09591378 eastern_alps:3143
0.10005623 eastern_alps:3152
0.10180409 eastern_alps:3121
0.10919978 eastern_alps:3146
0.10977408 eastern_alps:3133
0.11189766 eastern_alps:3122
0.11229889 eastern_alps:3131
0.11279759 eastern_alps:3119
0.11454678 eastern_alps:3144
0.11560683 eastern_alps:SOLT59
0.11703179 eastern_alps:3139
0.11731006 eastern_alps:3126
0.11952967 eastern_alps:3116
0.11997877 eastern_alps_avg(n=33)
0.12144258 eastern_alps:3125
0.12162148 eastern_alps:3155


Target: Albruic_GreatAunt
Distance: 3.1073% / 0.03107258
69.2 eastern_alps:3057
24.2 1eastern_alps:3134
6.6 eastern_alps:3132

[R.Rocca]

I've been trying to download the BAMs and process them in YLeaf, but they all look to be unaligned. I used WGS Extractor and the same thing. Anyone having the same issues?

[Trojet]

I've been trying to download the BAMs and process them in YLeaf, but they all look to be unaligned. I used WGS Extractor and the same thing. Anyone having the same issues?

Yep, I had the same issue with Iron Age Switzerland samples.

Aligning the FASTQ files first through Usegalaxy (or another way) will do it. However, it's a lengthy process and I don't currently have the time to do it. On top of that, they don't seem to have listed the gender of the samples for this particular study..

[R.Rocca]

I've been trying to download the BAMs and process them in YLeaf, but they all look to be unaligned. I used WGS Extractor and the same thing. Anyone having the same issues?

Yep, I had the same issue with Iron Age Switzerland samples.

Aligning the FASTQ files first through Usegalaxy (or another way) will do it. However, it's a lengthy process and I don't currently have the time to do it. On top of that, they don't seem to have listed the gender of the samples for this particular study..

Thanks for confirming. The only one I tried to align with WGS Extractor was going to take THREE HOURS!. I just don't have enough time to do that nor tie up my laptop for that long.

[Villanovan]

I left the first one running in one of my laptops. Time consuming, indeed. It'd have been much easier if they had provided mapped BAMs.
As I've downloaded the uBAM, I had to convert it back to FASTQ using Samtools, before aligning it.

ROMT12EB (ROM309)
I would say G2a2b2a1a1b-L497 (xZ30452, Y19940, Z40742, Z726 ...)

[asquecco]

I'm not an expert in this type of analysis but, to allign on the Galaxy server the FASTQ files of the first 10 genomes, I used this tutorial:
https://www.youtube.com/watch?v=8l2fAKgoLdg
After downloading the generated BAM files on my laptop, YLeaf gave me just 1 meaningful prediction (file hg_prediction.hg):
ERR12308209 J-PF5000*(xJ-PH1795,J-PF4995,J-Y83029,J-Y25795,J-FT65301,J-M340,J-Y29673)
By the way, YLeaf returned error for the genome #1.

[Villanovan]

I'm not an expert in this type of analysis but, to allign on the Galaxy server the FASTQ files of the first 10 genomes, I used this tutorial:
https://www.youtube.com/watch?v=8l2fAKgoLdg
After downloading the generated BAM files on my laptop, YLeaf gave me just 1 meaningful prediction (file hg_prediction.hg):
ERR12308209 J-PF5000*(xJ-PH1795,J-PF4995,J-Y83029,J-Y25795,J-FT65301,J-M340,J-Y29673)
By the way, YLeaf returned error for the genome #1.

I may try this one (ERR12308209) to compare the results with those you got.

I didn't use YLeaf etc. I used an approach a bit different.
- I've downloaded the uBAM (it may be a good idea using Free Download Manager);
- Converted it to FASTQ using Samtools in WSL (quick process);
- Splitted the FASTQ in WSL (quick process);
- Compressed the FASTQ in WSL (quick process);
- Aligned FASTQ using WGS Extract (slow process) - it could have been through Samtools (also slow process anyway), but in this case I would have had to allocate more RAM for WSL (otherwise the process is killed), so never mind;
- Splitted Y using Samtools (quick process);
- Indexed using Samtools (quick process);
- Extracted the SNPs using Samtools (quick process);
- Interpreted the results "natively" (based on ISOGG), with some few manual checks in IGV, just for validation, and ignoring single reads. This process was also fast.

I.e., downloading and especially aligning are the "bottlenecks". The BAMs for the samples in the Elite Celtic paper were mapped, which made the whole thing way easier.

For what it's worth, I got the following for ROM309:
G  -> CTS995+ (2x C), M3258+ (3x C), P257+ (2x A), U12+ (2x C), CTS5317+ (2x C), M3600+ (3x A), CTS10824+ (2x T);
G2a -> M3401+ (2x T);
G2a2b -> CTS90+ (3x A), Z3260+ (2x T);
G2a2b2a -> PF3332+ (3x T);
G2a2b2a1a1b -> Z731+ (2x G).
And also several positives upstream G, of course.

The main negatives downstream G2a2b2a1a1b are for Z30452 (2x T), Y19940 (2x G), Z40742 (2x G) and Z726 (4x T).

[Villanovan]

I'm not an expert in this type of analysis but, to allign on the Galaxy server the FASTQ files of the first 10 genomes, I used this tutorial:
https://www.youtube.com/watch?v=8l2fAKgoLdg
After downloading the generated BAM files on my laptop, YLeaf gave me just 1 meaningful prediction (file hg_prediction.hg):
ERR12308209 J-PF5000*(xJ-PH1795,J-PF4995,J-Y83029,J-Y25795,J-FT65301,J-M340,J-Y29673)
By the way, YLeaf returned error for the genome #1.

I may try this one (ERR12308209) to compare the results with those you got.

I didn't use YLeaf etc. I used an approach a bit different.
- I've downloaded the uBAM (it may be a good idea using Free Download Manager);
- Converted it to FASTQ using Samtools in WSL (quick process);
- Splitted the FASTQ in WSL (quick process);
- Compressed the FASTQ in WSL (quick process);
- Aligned FASTQ using WGS Extract (slow process) - it could have been through Samtools (also slow process anyway), but in this case I would have had to allocate more RAM for WSL (otherwise the process is killed), so never mind;
- Splitted Y using Samtools (quick process);
- Indexed using Samtools (quick process);
- Extracted the SNPs using Samtools (quick process);
- Interpreted the results "natively" (based on ISOGG), with some few manual checks in IGV, just for validation, and ignoring single reads. This process was also fast.

I.e., downloading and especially aligning are the "bottlenecks". The BAMs for the samples in the Elite Celtic paper were mapped, which made the whole thing way easier.

For what it's worth, I got the following for ROM309:
G  -> CTS995+ (2x C), M3258+ (3x C), P257+ (2x A), U12+ (2x C), CTS5317+ (2x C), M3600+ (3x A), CTS10824+ (2x T);
G2a -> M3401+ (2x T);
G2a2b -> CTS90+ (3x A), Z3260+ (2x T);
G2a2b2a -> PF3332+ (3x T);
G2a2b2a1a1b -> Z731+ (2x G).
And also several positives upstream G, of course.

The main negatives downstream G2a2b2a1a1b are for Z30452 (2x T), Y19940 (2x G), Z40742 (2x G) and Z726 (4x T).

mpileup defaults caused some reads to be ignored. I re-ran with all possible alignments, and got the following for ROM309 now, in addition:
G2a2b2a1a1b -> Z731+ (2x G) , CTS1899 (2x C)
G2a2b2a1a1b1 -> Z3035+ (3x C)
G2a2b2a1a1b1a -> CTS3226+ (2x A), Z1817+ (2x G), CTS12895+ (2x A)

And 2 negatives for Z16776 (G2a2b2a1a1b1a1), an equivalent of Z1816, Z727 etc.

One more G-L497 sample:

STE04 (ERR12311755)
(...)
G2a2b2a1a1b -> Z3390+ (2x T)
G2a2b2a1a1b1 -> Z735+ (2x T); negative for Z3205 though (2x C)
G2a2b2a1a1b1a -> Z6901+ (2x T), CTS11352+ (2x G); negative for CTS11605 (4x C)

@asquecco
I obtained the same result as yourself for ERR12308209 (ISE01) using Yleaf in WSL (I could not run it with my sw because the file was too big).

[asquecco]

I aligned the first 60 genomes and then I ran Yleaf with minimum number of reads=2.
The main 3 groups predicted by the tool are: 50% HG=G, 35% HG=R1b, 7% HG=I

[J Man]

I aligned the first 60 genomes and then I ran Yleaf with minimum number of reads=2.
The main 3 groups predicted by the tool are: 50% HG=G, 35% HG=R1b, 7% HG=I

Any J2?