Y-SNP calls for Saag (2019) The Arrival of Siberian Ancestry Connecting the East

Home Miscellanea Population Genomics Y-SNP calls for Saag (2019) The Arrival of Siberian Ancestry Connecting the East

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      Carlos Quiles
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      Saag, L., Laneman, M., Varul, L., Malve, M., Valk, H., Razzak, M. A., … & Scheib, C. L. (2019). The arrival of Siberian ancestry connecting the eastern Baltic to Uralic speakers further East. Current Biology, 29(10), 1701-1711. https://doi.org/10.1016/j.cub.2019.04.026

      Abstract:

      In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200–400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC–50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC–450 AD) (IngIA) and 7 Middle Age Estonian (1200–1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1, 2, 3, 4, 5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic.

      Accession number: PRJEB31893

      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.

      ERR3262727 NA NA 1928291 7446 0.0 0.0 1.0 0.0
      ERR3262716 NA NA 31543 17 0 0 0 0
      ERR3262740 NA NA 2251 2 0 0 0 0
      ERR3262749 NA NA 10818 42 0 0 0 0
      ERR3262723 NA NA 745076 2813 0.0 0.0 1.0 1.0
      ERR3262734 NA NA 1210 3 0 0 0 0
      ERR3262728 NA NA 3497245 13420 0.0 0.0 1.0 1.0
      ERR3262767 NA NA 16237 10 0 0 0 0
      ERR3262718 R1a1a1b1a3a1a5~ R-BY30624 1855649 7028 1.0 1.0 1.0 1.0
      ERR3262756 R1a1a1b1a2b~ R-CTS3607*(xFGC19250,FGC13675,Y9082,FGC39341,FGC21216,JN84,FGC37077,YP4854,YP6345,FGC19273,YP6062,YP314,S3369,YP5917,Y16502,YP6012,YP310,FGC15017,YP1150) 2498057 9907 1.0 1.0 1.0 1.0
      ERR3262726 NA NA 484193 49 0 0 0 0
      ERR3262745 NA NA 25383 5 0 0 0 0
      ERR3262737 NA NA 22600 79 0 0 0 0
      ERR3262717 NA NA 2649554 10052 0.0 0.0 1.0 1.0
      ERR3262736 NA NA 22623 80 0 0 0 0
      ERR3262715 NA NA 6040 8 0 0 0 0
      ERR3262763 NA NA 2702387 10832 0.0 0.0 1.0 1.0
      ERR3262759 NA NA 1901919 7581 0.0 0.0 1.0 1.0
      ERR3262766 NA NA 18573 58 0 0 0 0
      ERR3262744 NA NA 656254 100 0 0 0 0
      ERR3262735 R1a1a1b1a2b3a~ R-S3358*(xYP1450,YP5306,FGC19247,Y17525,FGC13675,YP586,FGC21228,FGC17210,YP6344,Y16016,FGC19283,Y19886,FGC10155,YP5923,FGC4539,FGC15017) 2057506 7940 1.0 1.0 1.0 1.0
      ERR3262762 R1a~ R-F2948/etc*(xCTS2132,Y19506) 2511467 10101 1.0 1.0 1.0 1.0
      ERR3262719 NA NA 5346472 20265 0.0 0.0 1.0 1.0
      ERR3262755 NA NA 57907 238 0 0 0 0
      ERR3262754 NA NA 45020 189 0 0 0 0
      ERR3262714 NA NA 10364 33 0 0 0 0
      ERR3262738 NA NA 103155 381 0.0 1.0 1.0 0.0
      ERR3262713 R1a1a1b1a2a R-S344/etc*(xVK09,YP689,BY30713,Y17284,S3375,Y17699) 649159 2471 1.0 1.0 1.0 1.0
      ERR3262747 R1a1a1b1a2b3a1a1a2a2~ R-YP5310 476744 1826 1.0 1.0 1.0 1.0
      ERR3262724 NA NA 2698091 10325 0.0 0.0 1.0 1.0
      ERR3262720 N1a1a~ N-CTS759*(xCTS5679,Y9280,Z35159,Y23758) 1781715 6746 1.0 1.0 1.0 1.0
      ERR3262768 R1a1a1~ R-CTS6423/etc*(xCTS7083,YP6477,PF6202,VK07,BY142958,BY30792,FGC45976,FGC19244,YP4829,YP5194,YP580,YP4531,FGC21225,YP4854,YP3987,Y12722,Y1399,Y35213,FGC40572,FGC74366,YP4337,Y40106,FGC15000,S221,YP3898,YP697,YP5881,YP5821,YP5957,AM00484,Y682,SUR86,Y19763,FGC10233,YP521,M12301,YP1546,YP1348,FGC10627,FGC113,YP5959,YP4767,YP624,FGC4547,FGC30901,YP5324,Y34302) 783356 2844 1.0 1.0 1.0 1.0
      ERR3262722 NA NA 93553 10 0 0 0 0
      ERR3262725 NA NA 3192735 12460 0.0 0.0 1.0 1.0
      ERR3262765 NA NA 3108491 11954 0.0 0.0 1.0 1.0
      ERR3262761 NA NA 135116 516 0 0 0 0
      ERR3262748 NA NA 554339 158 0 0 0 0
      ERR3262758 R1a1a1b~ R-CTS5508*(xFGC32020,BY32068,YP263,FGC20517,YP443,YP4651,FGC66342,BY30715,YP1135,FGC72554,YP514,A11460,S205,V3092,YP1145,S24902,S221,YP3912,YP713,Y17491,YP4758,AM00479,Z2125,Y38022,CTS7114,FGC10642,FGC123,Y37916,YP644,CTS2887,Y34292,Y24740) 1848828 7235 1.0 1.0 1.0 1.0
      ERR3262739 NA NA 2719673 10923 0.0 0.0 1.0 1.0
      ERR3262764 R1b1a1b1a1a2b1c1c R-FGC22963 173325 584 1.0 1.0 1.0 1.0
      ERR3262750 R1b1a1a1a R-Y14191 284026 1016 1.0 1.0 1.0 1.0
      ERR3262733 NA NA 3708036 14534 0.0 0.0 1.0 1.0
      ERR3262741 NA NA 21959 93 0 0 0 0
      ERR3262729 NA NA 5113 24 0 0 0 0
      ERR3262757 NA NA 151972 594 0.0 1.0 1.0 0.0
      ERR3262732 NA NA 23650 2 0 0 0 0
      ERR3262753 NA NA 283363 1027 0.0 1.0 1.0 0.0
      ERR3262721 N1a1a1a1a1a1a1b2~ N-Y4707*(xY5745,Y21046) 920653 3546 1.0 1.0 1.0 1.0
      ERR3262746 NA NA 140083 53 0 0 0 0
      ERR3262731 NA NA 145773 506 0.0 1.0 1.0 0.0
      ERR3262751 NA NA 18308 64 0 0 0 0
      ERR3262742 NA NA 15167 49 0 0 0 0
      ERR3262760 NA NA 228429 809 0 0 0 0
      ERR3262730 R1a1a1b1 R-PF6217*(xFGC32023,BY32078,AMM260,CTS456,CTS3402,YP1156,S5148,YP1121,YP4963,YP609,FGC54673,YP5863,YP6446,YP407,FGC28653,YP1372,YP3898,YP5888,YP5821,YP5965) 1883551 7251 1.0 1.0 1.0 1.0
      ERR3262752 R1a1a1b~ R-CTS9754*(xPF6161,Y5572,BY30708,YP5523,Y1401,YP4365,FGC4499,YP1150,Z286,YP3913,YP5881,YP5821,YP4758,M787,Y2392,FGC57581,Y34245,Y878,YP6251,Y34232,BY3873,YP5558,Y2423,Y34208,Z2123,YP1127,FGC48776,Y29558,Y12480,S15709,CTS3412,FGC126,PH4192,YP615,FGC4547,Y37,Z664,YP1507,Y35117,Y32226) 2110405 8364 1.0 1.0 1.0 1.0
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