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

[Pribislav]

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

Could you post the list so we can know which samples are male?

[Villanovan]

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?

Yes.

18 G2 (all G-L497)
1 J2 (J-PF5032)
1 R1b (downstream R-L2)
1 I2

[Villanovan]

Could you post the list so we can know which samples are male?

The Gs (with impressive diversity under G-L497):
ROM301, ROM305, ROM308, ROM309
STE01, STE03, STE04, STE05
NOG201, NOG301,NOG302
VEL102, VEL701  
BER01
COR01
MEZ02
PAL01
SOL03

The J:
ISE01

The R1b:
SIU01

The I:
MAD01

There's this dissertation that includes several Trentini samples from Eneolithic to Bronze Age, always G-M201, including two related to Polada Culture (RomIIIT12b/RomIII120b and RomIV58). On Romagnano:
"The grave goods and the date clearly indicate affinity to the Polada A culture."
https://openscience.ub.uni-mainz.de/bits...003475.pdf
Bronze Age samples are from Nogarole, Romagnano III (Polada A), Romagnano IV (Polada A) and Paludei di Volano. PdVT3 and RomIIIT12b/RomIII120b are BA samples confirmed for G-M201, while RomIV58, also from BA, is a probable G-M201 according to the dissertation (it hasn't met authentication requirements though):
"Haplotype G was still present in the Bronze Age, as documented by one confirmed sequence each from Paludei di Volano and Romagnano III (as well as another probable G2a from Romagnano IV)".
RomIIIT12b/RomIII120b was likely negative for the subclade of Otzi, G2a2a1a2-L91.
Unfortunately, only specific PCR-based SNPs were done, so no shotgun sequencing (WGS).

Perhaps ROM309 (ROMT12EB) is this RomIIIT12b/RomIII120b from the dissertation (?). If so, it'd be related to Polada.

[ArmandoR1b]

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 ...)

I had looked at a few files over the past few weeks and this was one of them.

I show him to be derived for CTS3226/Z741 and Z1817 in haplogroup G-M201>L89>L156>P15>L1259>L30>L141>P303>L140>PF3346>Z3065>PF3345>L497>CTS9737>Z1817

https://discover.familytreedna.com/y-dna/G-Z1817/story

He is also derived for upstream SNP Z3035 in hg G-M201>L89>L156>P15>L1259>L30>L141>P303>L140>PF3346>Z3065>PF3345>L497>CTS9737

There is an ancestral read for Z736 in hg G-M201>L89>L156>P15>L1259>L30>L141>P303>L140>PF3346>Z3065>PF3345>L497 but 3 downstream derived calls causes that ancestral read to be checked. It's probably due to C>T deamination.

Due to how much time it took to process the files I gave up. I am waiting for the study to be published so I know what to expect for the files I analyze.

[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?

Yes.

18 G2 (all G-L497)
1 J2 (J-PF5032)
1 R1b (downstream R-L2)
1 I2

Very interesting thank you...Looking forward to seeing which time period and site the J2a-PF5032 sample comes from.

[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 ...)

I had looked at a few files over the past few weeks and this was one of them.

I show him to be derived for CTS3226/Z741 and Z1817 in haplogroup G-M201>L89>L156>P15>L1259>L30>L141>P303>L140>PF3346>Z3065>PF3345>L497>CTS9737>Z1817

https://discover.familytreedna.com/y-dna/G-Z1817/story

He is also derived for upstream SNP Z3035 in hg G-M201>L89>L156>P15>L1259>L30>L141>P303>L140>PF3346>Z3065>PF3345>L497>CTS9737

There is an ancestral read for Z736 in hg G-M201>L89>L156>P15>L1259>L30>L141>P303>L140>PF3346>Z3065>PF3345>L497 but 3 downstream derived calls causes that ancestral read to be checked. It's probably due to C>T deamination.

Due to how much time it took to process the files I gave up. I am waiting for the study to be published so I know what to expect for the files I analyze.

Yeah, I added those in following post. We've found virtually the same then (see below).

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.

[Villanovan]

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

Do you have by any chance coordinates for 3157 and 3162?

[Hodo Scariti]

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

Many thanks for info. Are the R1b samples all L2?

[Riverman]

Is there a list of all available haplogroups, no matter how basal, already?

[Pribislav]

MAD01; Italy_Mesolithic; I2-Z161>Z189>S21760* (xPH4495)

ISE01; Italy_Neolithic; J2a2-PF5008>L581>Z37823>PF5000 (xY29677,PF5016)

ROM309; Italy_LCA/EBA; G2a2b-L497>Z1815>Y7538>Z1816* (xZ1823,Y8903,FGC809)

STE04; Italy_MBA; G2a2b-L497>Z1815>Y7538>Z1816>FGC809>FGC807>Z40896>FT71628>Z31846>Y96077 (xZ44688,FT239213)

[ArmandoR1b]

What is the archaeological context of 3057? Are there c14 dates?

L2: 4 derived reads: R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2
Y3960: 14 derived reads: R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2>DF110>Y3964

No calls between those two

https://discover.familytreedna.com/y-dna...64/classic

[Villanovan]

We should have splits under G-L497.

Curiously, no G-Z726 (upstream G-CTS4803 and G-Z16775) among the G-L497 samples from this paper. G-Z726 (and especially G-CTS4803) would be the most frequent under G-L497, and also the most frequent among G-L497 ancient samples related to Hallstatt + La Tène...

[ArmandoR1b]

Yeah, I added those in following post. We've found virtually the same then (see below).

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.

What to you think if we all agree to abandon the ISOGG longhand name and start using the ancestral path from FTDNA that Pribislav and some others had started using? ISOGG hasn't updated since 2020 and FTDNA continually identifies SNPs that can help with tree placement.

[R.Rocca]

What is the archaeological context of 3057? Are there c14 dates?

L2: 4 derived reads: R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2
Y3960: 14 derived reads: R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2>DF110>Y3964

No calls between those two

https://discover.familytreedna.com/y-dna...64/classic

In the larger BAM, he has 23 derived reads at Y3960 and two at Y3962. He seems pretty solidly R-Y3960*(xR-FTA30946,R-Y46692).

[ArmandoR1b]

What is the archaeological context of 3057? Are there c14 dates?

L2: 4 derived reads: R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2
Y3960: 14 derived reads: R-M207>M173>M343>L754>L761>L389>P297>M269>L23>L51>P310>L151>P312>Z46516>ZZ11>U152>L2>DF110>Y3964

No calls between those two

https://discover.familytreedna.com/y-dna...64/classic

In the larger BAM, he has 23 derived reads at Y3960 and two at Y3962. He seems pretty solidly R-Y3960*(xR-FTA30946,R-Y46692).

I abstain calling anything * anymore. FTA30946 is far downstream of MF100284 and FTA30946 has a formation date of 1550 BCE per https://discover.familytreedna.com/y-dna...0946/story YFull shows similar. No idea when that was changed but YFull has an archive of each tree update.

At FTDNA the 3 current subclades of Y3964 are R-A1722, R-MF100284, & R-BY73356 https://discover.familytreedna.com/y-dna/R-Y3964/story

I've recently updated my database due to changes in the phylogeny of the tree. I won't always be up to date but the latest change I made is better than what I had.

edit: the program I used somehow removed some of the reads for Y3960. I checked with a different program and now I see more reads. No big deal. The important part is that I see reads that others see either way.
edit2: I also see Y3962/DF100 with 2 reads. I need to add that to the database though.