Y-SNP calls for Mittnik (2018) The genetic prehistory of the Baltic Sea region

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  • August 5, 2020 at 3:20 pm #31326
    Carlos Quiles
    Keymaster

      Mittnik, A., Wang, C., Pfrengle, S. et al. The genetic prehistory of the Baltic Sea region. Nat Commun 9, 442 (2018).

      https://doi.org/10.1038/s41467-018-02825-9

      Abstract:

      While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from ~9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.

      Accession number: PRJEB23635

      Batch Y-chromosome SNP Calls with Yleaf v. 2.3 from FASTQ files, bwa-mem with hg38 reference, and parameters r=1, q=0, b=0.

      Google Drive.

      Haplogroup.info.

      The following is a list of automated Y-DNA haplogroup predictions obtained with Clean tree v2:

      WARNING: Please note that the haplogroup prediction algorithm works best with modern DNA, and its strict requirements make the prediction rather impractical for ancient DNA – in fact, males usually turn out to have not enough quality for a reliable prediction.

      If anything, positive haplogroup predictions (especially under R1b and I2) will normally turn out to be wrong because they are based on few reads, due to the sample being either a) female or b) low coverage.

      The usual process for checking out Y-chromosome haplogroups in ancient DNA samples is as follows:

      1. Select the male individual you want to check out for in the Ancient DNA Dataset.
      2. Look up its library ID (object-ID) at ENA Browser search form (top right) to obtain the accession number(s) for the available sample(s) corresponding to that individual.
      3. Look for files obtained with Yleaf for that accession number(s); more specifically, look for individual Derived and Ancestral SNPs in the ACCESSION_NUMBER.out or ACCESSION_NUMBER.out.csv documents.

      When in doubt about a specific sample, you can ask a question in this thread.

      SRR6354817 NA NA 1520008 14710 0.0 0.0 1.0 1.0
SRR6354818 R1a1~ R-F1157/etc*(xL168,YP1322) 491220 5605 1.0 1.0 1.0 1.0
SRR6354816 NA NA 15962 9 0 0 0 0
SRR6354773 R1a1 R-Page65.2*(xYP5531,Z2035,YP1130,Y64231,FGC19054,Y34275,Y27214,YP1214,YP4529,Y16017,PF7525,YP574,BY30713,YP5522,A11104,BY30795,FGC46023,CTS1211,FGC11883,YP3904,YP721,YP5879,FGC64143,YP5970,AM01870,YP1068,YP1301) 690395 6749 1.0 1.0 1.0 1.0
SRR6354792 NA NA 52349 657 0 0 0 0
SRR6354791 R1a1a1b1a3a4~ R-YP1370 132735 1620 1.0 1.0 1.0 1.0
SRR6354770 NA NA 7281 82 0 0 0 0
SRR6354799 NA NA 61436 56 0 0 0 0
SRR6354807 NA NA 11694 9 0 0 0 0
SRR6354758 R1a~ R-F1769/etc*(xPF7542,YP4216) 585160 6427 1.0 1.0 1.0 1.0
SRR6354831 NA NA 122985 203 0 0 0 0
SRR6354771 NA NA 17834 11 0 0 0 0
SRR6354811 NA NA 87481 62 0 0 0 0
SRR6354783 NA NA 1002506 10268 0.0 0.0 1.0 1.0
SRR6354772 NA NA 73497 37 0 0 0 0
SRR6354793 Q1 Q-CTS5301*(xF1755,CTS11357,Z35845,P8.2,Z35892,Z19389,BZ3494,BZ2061,Y18739,FGC8423,BY1520,BZ2620,Y2824,YP911,YP922,L329,Y15811,F5015,Y17797,BZ1042) 99535 943 1.0 1.0 1.0 1.0
SRR6354819 R1a1~ R-CTS5437*(xAM01870) 15694 69 1.0 1.0 1.0 1.0
SRR6354820 NA NA 8937 34 0 0 0 0
SRR6354789 R1a1a1~ R-M649*(xYP4527,FGC32020,AMM272,Y130583,YP4356,FGC13709,PH4687,FGC74362,YP1156,BY30775,FGC11913,FGC55626,YP4343,Y11819,F19106,CTS6835,YP1179,Y31833,YP5957,Y34246,Y940,YP4921,YP1543,Y37900,FGC30891,YP1507) 84089 989 1.0 1.0 1.0 1.0
SRR6354822 R1a1a1b~ R-F3044*(xPF6161,YP5524,BY30793,FGC45975,CTS3402,YP5314,FGC11897,YP4957,YP4728,Y13508,FGC55633,Y24743,YP5292,PH5012,S23533,YP4964,YP4248,BY30798,YP4885,YP5689,YP5539,Y29967,YP6058,YP993,YP1258,CTS6835,YP622,FGC28668,Y16257,YP3898,YP721,Y17491,YP5957,AM01870) 417992 4781 1.0 1.0 1.0 1.0
SRR6354797 J1 J-CTS7412*(xZS9839,L92.1,L93,FGC7631,ZS6599,FGC6088,CTS1460,ZS3189,PH1443,Z27617) 471810 1072 1.0 1.0 1.0 1.0
SRR6354825 Q1b Q-CTS2385/etc*(xY11653,Z19488,Z35514,Z35744,FGC8482,Y7343,YP4037,Y6836) 59393 568 1.0 1.0 1.0 1.0
SRR6354821 NA NA 960377 9988 0.0 0.0 1.0 1.0
SRR6354833 NA NA 27238 146 0 0 0 0
SRR6354769 NA NA 5670 46 0.0 1.0 1.0 0.0
SRR6354760 NA NA 55103 223 0.0 0.0 1.0 1.0
SRR6354814 R1a1a1b~ R-CTS9754*(xPF6202,BY30795,FGC45975,FGC19244,Y3842,L448,M699,Y940,YP4922,Y19762,CTS7114,FGC113,YP5959) 108882 1289 1.0 1.0 1.0 1.0
SRR6354761 NA NA 1422 11 0 0 0 0
SRR6354813 R1a1a1b~ R-CTS9754*(xPF6202,BY30795,FGC45975,FGC19244,YP6408,Y5647,L448,S345,YP3911,M699,FGC7398,Y940,YP4922,Y19762,S23592,CTS7114,FGC113,YP5959,YP626,CTS11926) 151077 1699 1.0 1.0 1.0 1.0
SRR6354778 NA NA 1111361 11222 0.0 0.0 1.0 1.0
SRR6354828 I2a1a2~ I-Z2587*(xBY2063,Y13339,F3145) 187857 2193 1.0 1.0 1.0 1.0
SRR6354786 NA NA 10393472 52991 0.0 0.0 1.0 1.0
SRR6354764 NA NA 1995 19 0 0 0 0
SRR6354795 NA NA 6129 32 0 0 0 0
SRR6354829 R1a1a1~ R-F3551*(xCTS7288,FGC10015,YP254,BY35659,YP5948,AMM272,BY27806,YP1185,S344,V3092,YP1157,FGC11898,YP5476,YP1436,CTS10875,FGC36394,Y24742,S6355,PH5012,Y23595,YP5162,FGC25763,Y17231,YP5010,YP618,YP6100,Y30182,YP4811,Y36790,YP5865,YP6455,YP409,YP5631,Y19143,Y14506,Y24038,YP5886,YP5820,FGC64132,YP5970,Y28659,Y890,Y34178,FGC57581,S24826,Y34251,Y34257,Y34225,YP5549,Y2429,Y662,YP4976,Y19836,FGC10210,FGC22493,YP6326,FGC59424,S23592,Y38026,CTS7297,FGC18226,FGC10639,FGC139,F1019,YP4769,Y58,Y39,CTS2887,Y34292) 791721 4038 1.0 1.0 1.0 1.0
SRR6354809 NA NA 26747 22 0 0 0 0
SRR6354774 R1b1a1a R-Y13208*(xY13207) 162819 1924 1.0 1.0 1.0 1.0
SRR6354798 NA NA 14014 10 0 0 0 0
SRR6354830 R1a1a1b1a3a2a1 R-S201 1386737 7640 1.0 1.0 1.0 1.0
SRR6354790 R1a1a1b2a2a1 R-Z2123*(xY19829) 55663 733 1.0 1.0 1.0 1.0
SRR6354806 R1a~ R-CTS5273/etc*(xPF7542,YP4216) 302361 3346 1.0 1.0 1.0 1.0
SRR6354779 R1a1a1b~ R-F3044/etc*(xPF6161,Y5572,BY30708,A11104,FGC45975,V3092,YP1150,S443,Y31833,YP5822,Y32945,AM01870) 606953 6780 1.0 1.0 1.0 1.0
SRR6354776 NA NA 20445 220 0 0 0 0
SRR6354824 NA NA 1868884 17443 0 0 0 0
SRR6354832 NA NA 2307 3 0 0 0 0
SRR6354837 I2a1a2~ I-AM01272/etc*(xAMM053,S10302) 400059 4689 1.0 1.0 1.0 1.0
SRR6354784 NA NA 2553 5 0 0 0 0
SRR6354815 NA NA 55019 55 0 0 0 0
SRR6354794 NA NA 124 2 0 0 0 0
SRR6354803 NA NA 3617 20 0 0 0 0
SRR6354835 NA NA 32495 150 0 0 0 0
SRR6354812 NA NA 19887 5 0 0 0 0
SRR6354826 NA NA 2511005 21881 0.0 0.0 1.0 1.0
SRR6354801 R1a~ R-F886*(xYP5948,YP6190,FGC72557,Y130583,Y24897,FGC19250,YP280,YP4964,Y32869,YP4472,Y11819,YP1257,Y16257,YP3911,SK2014,AM00479,FGC22471,FGC59402,YP1546,YP1358,S18885,F1345) 44400 524 1.0 1.0 1.0 1.0
SRR6354762 R1a1a1b~ R-F3044*(xBY30754,FGC45989,FGC19233,YP6408,BY27380,FGC55626,Y11819,YP6463,FGC28664,AM01870) 54873 633 1.0 1.0 1.0 1.0
SRR6354808 NA NA 33700 10 0 0 0 0
SRR6354788 NA NA 295704 3354 0.0 0.0 1.0 1.0
SRR6354787 NA NA 6397320 33620 0.0 0.0 1.0 1.0
SRR6354836 NA NA 13416 26 0 0 0 0
SRR6354781 NA NA 3004 9 0 0 0 0
SRR6354800 NA NA 3217 7 0 0 0 0
SRR6354782 NA NA 4992 5 0 0 0 0
SRR6354785 NA NA 182673 2028 0.0 0.0 1.0 1.0
SRR6354834 NA NA 33308 155 0 0 0 0
SRR6354796 NA NA 6646 38 0.0 0.0 1.0 0.0
SRR6354810 NA NA 22637 11 0 0 0 0
SRR6354767 NA NA 9043 85 0 0 0 0
SRR6354777 NA NA 514787 5722 0.0 0.0 1.0 1.0
SRR6354759 R1b1 R-FGC41*(xY13207,PF6497,BY15334,PF6333) 138397 1598 1.0 1.0 1.0 1.0
SRR6354804 NA NA 19410 149 0 0 0 0
SRR6354763 NA NA 39504 437 0.0 1.0 1.0 0.0
SRR6354780 R1a1a R-M515*(xS2846,AM01874,S344,V3092,YP1148,S24902,S443,Y17491,Y32945,F992,YP1060) 2088396 18964 1.0 1.0 1.0 1.0
SRR6354823 I2a1a1b1a~ I-Y4194*(xY4231) 834195 9025 1.0 1.0 1.0 1.0
SRR6354827 NA NA 25254 12 0 0 0 0
SRR6354805 R1a1a1b1a2b4~ R-YP1156 29527 377 1.0 1.0 1.0 1.0
SRR6354775 R1b1a1 R-CTS9018/etc*(xY13207,BY15594,L749) 173238 2086 1.0 1.0 1.0 1.0
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