Y-SNP calls for Haak (2015): Massive migration from the steppe was a source for

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  • August 20, 2020 at 4:29 pm #31466
    Carlos Quiles
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      Haak, W., Lazaridis, I., Patterson, N. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

      https://doi.org/10.1038/nature14317

      Abstract:

      We generated genome-wide data from 69 Europeans who lived between 8,000–3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies1,2,3,4,5,6,7,8 and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000–5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000–7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian6. By ∼6,000–5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin9 of at least some of the Indo-European languages of Europe.

      Accession number: PRJEB8448

      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.

      ERR769645 NA NA 145822 97 0 0 0 0
ERR769636 NA NA 46119 27 0 0 0 0
ERR769603 NA NA 929774 2227 0.0 1.0 1.0 0.0
ERR769648 NA NA 79036 152 0 0 0 0
ERR769616 NA NA 87410 68 0 0 0 0
ERR769604 T1a T-M70 187607 377 1.0 1.0 1.0 1.0
ERR769617 NA NA 1434568 1355 0 0 0 0
ERR769585 NA NA 23900 23 0 0 0 0
ERR769591 NA NA 1837991 5568 0.0 1.0 1.0 0.0
ERR769702 NA NA 21136 5 0 0 0 0
ERR769615 NA NA 1203259 3620 0 0 0 0
ERR769724 NA NA 1940 2 0 0 0 0
ERR769639 NA NA 116070 135 0 0 0 0
ERR769637 NA NA 827114 1510 0.0 0.0 1.0 1.0
ERR769599 NA NA 1794431 965 0 0 0 0
ERR769740 NA NA 2646 1 0 0 0 0
ERR769631 NA NA 4574 7 0 0 0 0
ERR769628 NA NA 53192 28 0.0 0.0 1.0 1
ERR769730 NA NA 683 2 0 0 0 0
ERR769607 R1b1b R-PF6376*(xPF6331,V35,Y8440) 863236 2816 1.0 1.0 1.0 1.0
ERR769626 R1b1a1b1b R-CTS1078*(xL277.1) 383761 1216 1.0 1.0 1.0 1.0
ERR769736 NA NA 2996 1 0 0 0 0
ERR769622 R1b1a1b1b R-Z2105*(xL277.1,CTS7822) 565350 1668 1.0 1.0 1.0 1.0
ERR769638 NA NA 1067238 560 0 0 0 0
ERR769699 NA NA 2212 1 0 0 0 0
ERR769697 NA NA 38783 38 0 0 0 0
ERR769723 NA NA 11283 6 0 0 0 0
ERR769706 NA NA 917 1 0 0 0 0
ERR769651 NA NA 109627 197 0 0 0 0
ERR769649 R1a1a1b1a2 R-S204*(xS205,L784,CTS3402,YP1150) 1584452 4724 1.0 1.0 1.0 1.0
ERR769620 R1b1a1b1b R-CTS1078*(xL277.1) 214239 1111 1.0 1.0 1.0 1.0
ERR769701 NA NA 3543 2 0 0 0 0
ERR769647 NA NA 352420 283 0 0 0 0
ERR769598 G2a2a G-PF3147/etc*(xFGC6662,L91,Z45971,Z36525) 235093 775 1.0 1.0 1.0 1.0
ERR769613 NA NA 9202708 21509 0 0 0 0
ERR769632 NA NA 33012 30 0 0 0 0
ERR769594 NA NA 42200 45 0 0 0 0
ERR769623 R1b1a1 R-FGC57/etc*(xL51) 365022 880 1.0 1.0 1.0 1.0
ERR769742 NA NA 298 1 0 0 0 0
ERR769596 NA NA 231842 231 0 0 0 0
ERR769618 NA NA 3649295 9515 0.0 0.0 1.0 1.0
ERR769602 NA NA 709177 429 0 0 0 0
ERR769593 NA NA 49113 32 0 0 0 0
ERR769734 NA NA 4334 2 0 0 0 0
ERR769627 NA NA 109945 54 0 0 0 0
ERR769644 NA NA 1349465 4034 0.0 0.0 1.0 0.0
ERR769650 I2a1b2a I-L39*(xBY14018,BY25378,Y130087,BY14038,Y68424,BY14066,FGC29631) 363535 1394 1.0 1.0 1.0 1.0
ERR769643 NA NA 50361 30 0 0 0 0
ERR769584 R1b1a1a R-Y13872*(xM478,BY15591) 442717 1431 1.0 1.0 1.0 1.0
ERR769588 NA NA 85598 75 0 0 0 0
ERR769592 NA NA 330800 764 0 0 0 0
ERR769605 G2a2a1 G-PF3155*(xFGC6619,L91,BY183727) 666724 1139 1.0 1.0 1.0 1.0
ERR769589 NA NA 299291 2134 0 0 0 0
ERR769621 R1b1a1b1b R-Z2105 479968 1628 1.0 1.0 1.0 1.0
ERR769625 R1b1a1b1 R-L23*(xL51,Z2105) 2441131 6599 1.0 1.0 1.0 1.0
ERR769595 NA NA 201247 188 0 0 0 0
ERR769722 NA NA 10011 5 0 0 0 0
ERR769611 NA NA 118220 57 0 0 0 0
ERR769609 NA NA 146995 152 0 0 0 0
ERR769641 NA NA 18240 11 0 0 0 0
ERR769586 I2a2 I-L597/etc*(xFGC18601,BY1265,ZS3688,Z45438,M4099) 548206 2440 1.0 1.0 1.0 1.0
ERR769583 R1a1 R-M459/etc*(xM198,Y12479) 1307341 4319 1.0 1.0 1.0 1.0
ERR769587 I2a1a2 I-M423/etc*(xL161.1,A13908) 217464 1662 1.0 1.0 1.0 1.0
ERR769646 NA NA 237219 123 0 0 0 0
ERR769747 NA NA 3659 3 0 0 0 0
ERR769713 NA NA 45804 35 0 0 0 0
ERR769635 NA NA 406651 126 0 0 0 0
ERR769614 NA NA 132520 618 0 0 0 0
ERR769608 NA NA 4913390 11603 0 0 0 0
ERR769633 NA NA 135732 44 0 0 0 0
ERR769601 NA NA 13475 12 0 0 0 0
ERR769642 NA NA 193549 108 0 0 0 0
ERR769600 G2a2a G-PF3181/etc*(xM286,PF3233,BY186480,Z45971,Z45677) 172171 663 1.0 1.0 1.0 1.0
ERR769726 NA NA 800 2 0 0 0 0ERR769711 NA NA 11772 5 0 0 0 0

ERR769606 NA NA 41353 23 0.0 0.0 1.0 0.0
ERR769629 NA NA 2100092 1406 0 0 0 0
ERR769619 NA NA 96380 81 0 0 0 0
ERR769590 I2 I-L68/etc*(xL460,L596,L417) 312236 1931 1.0 1.0 1.0 1.0
ERR769612 NA NA 145619 270 0 0 0 0
ERR769630 R1a1a1~ R-M637/etc*(xCTS7083,FGC10001,PF6158) 1749305 5050 1.0 1.0 1.0 1.0
ERR769634 NA NA 47250 23 0 0 0 0
ERR769624 NA NA 20818 30 0 0 0 0
ERR769732 NA NA 34420 14 0 0 0 0
ERR769698 NA NA 5530 1 0 0 0 0
ERR769610 NA NA 154405 374 0.0 1.0 1.0 0.0
ERR769597 NA NA 91724 17 0 0 0 0
ERR769741 NA NA 3888 2 0 0 0 0
ERR769640 NA NA 31394 34 0 0 0 0
ERR769673 NA NA 8717 9 0 0 0 0
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