Y-SNP calls for Olalde (2019): The genomic history of the Iberian Peninsula over

Tagged: aquitano, Bell Beaker, Bronce, Bronze Age, campaniforme, Celtiberian, celtiberico, Cogotas, haplogroups, Humanejos, Iberian, Lusitanian, Neolítico, Olalde, R-DF27, R-L23, R-M269, R-P312, R-U152, R1b, Tartessos, Y-DNA

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August 8, 2020 at 9:37 am #31360

Carlos Quiles

Keymaster

Olalde, I., Mallick, S., Patterson, N., Rohland, N., Villalba-Mouco, V., Silva, M., … & Soares, P. (2019). The genomic history of the Iberian Peninsula over the past 8000 years. Science, 363(6432), 1230-1234.

https://doi.org/10.1126/science.aav4040

Abstract:

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

Accession number: PRJEB30874

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:

Select the male individual you want to check out for in the Ancient DNA Dataset.

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.

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.

ERR3078460 NA NA 29502 16 0 0 0 0
ERR3078298 NA NA 602697 538 0 0 0 0
ERR3078483 NA NA 344930 942 0 0 0 0
ERR3078384 NA NA 28342 28 0 0 0 0
ERR3078378 NA NA 161380 209 0.0 1.0 1.0 0.0
ERR3078320 NA NA 161594 402 0 0 0 0
ERR3078268 NA NA 4881417 19439 0 0 0 0
ERR3078417 NA NA 69134 84 0 0 0 0
ERR3078495 R1b1a1b R-CTS1415^^/etc*(xCTS7650) 289003 238 1.0 1.0 1.0 1.0
ERR3078436 R1b1a1b1 R-L23*(xS263,FGC419,L1231,L356,S653,MC20,L1334,Z17836,A6464,FGC18027,FGC5637,L1308,CTS8704,BY638,FGC33060,L130,FGC58892,FGC37092) 671148 756 1.0 1.0 1.0 1.0
ERR3078398 NA NA 974682 932 0 0 0 0
ERR3078396 R1b1a1b1a1a R-PF6543*(xM405,L326,A8055) 1037273 5192 1.0 1.0 1.0 1.0
ERR3078371 R1b1a1b R-CTS8052/etc*(xS22641,FGC419,PF742.2,L356,FGC5596,L743,BY404,FGC5637,CTS8704,FGC11355,AM01878) 325021 365 1.0 1.0 1.0 1.0
ERR3078508 R1b1a1b R-CTS2466/etc*(xL493,BY63580,S1743,CTS1789,DF23,ZS347,S1115,L226,Y16226,ZS5732^^,S10807,FGC43481,L130,FGC11334,FGC23381,CTS7556) 62633 336 1.0 1.0 1.0 1.0
ERR3078463 J2a J-F2078/etc*(xCTS11251,PF5044) 492401 3461 1.0 1.0 1.0 1.0
ERR3078343 NA NA 2226654 11640 0 0 0 0
ERR3078377 R1b1a1b1a1a2 R-P312*(xL1231,L356,L192.1,Z2248,DF19,ZZ38) 1500038 9379 1.0 1.0 1.0 1.0
ERR3078513 NA NA 393450 389 0 0 0 0
ERR3078531 R1b1a1b1a1a R-L151*(xM405,S450,DF17,CTS8289,L628,F1343,CTS11567,L356,L21,DF99,Y18211,ZZ38,A8061,FGC37095) 764423 3524 1.0 1.0 1.0 1.0
ERR3078523 R1b1a1b1a1 R-L52*(xFGC36479,Z262,CTS278,FGC12405,FGC22940,S471,Z2248,ZZ38) 199539 542 1.0 1.0 1.0 1.0
ERR3078482 R1b1 R-CTS7585*(xYSC0000054,Z160,Y7369,S1746,L1231,L356,S6154,ZS1494,S279,A1334,CTS8704,BY15360,Y24710) 781133 571 1.0 1.0 1.0 1.0
ERR3078313 NA NA 57154 79 0 0 0 0
ERR3078303 NA NA 6112005 24867 0 0 0 0
ERR3078395 NA NA 1113652 5880 0.0 0.0 1.0 1.0
ERR3078434 R1b1a1b1a1a2 R-P312*(xDF17,S359,DF84,L409,FGC5512) 126741 578 1.0 1.0 1.0 1.0
ERR3078289 I1 I-CTS136/etc*(xY4782,Y30876,FGC22082,Y19673,FGC9461,A11339,A1603,BY2580,FGC22161,A12058,S243) 124036 515 1.0 1.0 1.0 1.0
ERR3078285 NA NA 23607 53 0 0 0 0
ERR3078519 R1b1a1b R-CTS11468/etc*(xAM01882,S20039,S383,S22641,FGC12018,FGC12403,FGC31485,FGC22513,Z260,Z2248,ZZ38,A8056,GG466) 194314 948 1.0 1.0 1.0 1.0
ERR3078305 NA NA 1085947 5357 0 0 0 0
ERR3078475 R1b1a1b1a1a2 R-P312*(xL1231,L356,Z260,Z2245,L1199,S233,DF99,Y18210,ZZ38) 2652416 15783 1.0 1.0 1.0 1.0
ERR3078447 NA NA 47515 39 0 0 0 0
ERR3078390 NA NA 21413 15 0 0 0 0
ERR3078509 E1b1b1 E-CTS6834/etc*(xCTS9471,Z36182,MZ73,BY9765,PF2576,MZ100,FGC18888^,M123,FGC18708) 309851 1655 1.0 1.0 1.0 1.0
ERR3078451 NA NA 61694 210 0.0 1.0 1.0 0.0
ERR3078490 NA NA 59157 151 0 0 0 0
ERR3078394 NA NA 443358 404 0 0 0 0
ERR3078542 R1b1a1b1a1 R-P310*(xZ375,L48,FGC20667,S15526,A2148,L1231,L356,BY170,A7304,FGC9798,BY554,BY183,BY404,FGC11809,Z16519,A802,ZS4590,A2288,FGC18026,Z16433,L554,S868,CTS9738,BY248,ZS5732^^,A67,S6168,Y23532,FGC33069,BY19857,FGC33378,CTS12966,ZZ38) 243744 1315 1.0 1.0 1.0 1.0
ERR3078399 R1b1a1b1a1 R-CTS7650*(xZ4715,FGC13260,S378,S1743,S22641,L1231,L192.1) 561505 642 1.0 1.0 1.0 1.0
ERR3078335 NA NA 44153 61 0.0 0.0 1.0 1
ERR3078449 R1b1a1b1a1a2c1 R-L21*(xBY204,Y16283) 21473 99 1.0 1.0 1.0 1.0
ERR3078473 R1b1a1b1a1a2 R-P312*(xL1231,L409,CTS7958,PF6584,F1493.2,L1358,BY247,DF99,ZZ38) 699828 4347 1.0 1.0 1.0 1.0
ERR3078327 NA NA 2106570 10150 0.0 0.0 1.0 1.0
ERR3078510 NA NA 31895 137 0 0 0 0
ERR3078302 NA NA 103076 215 0 0 0 0
ERR3078401 R1b1a1b R-PF6482/etc*(xFGC14883,S265,Z350,S379,FGC427,Z272,CTS11567,FGC22500,L744,BY39391,FGC13017,S470,Z20657,ZS347,A5,M2775,A7662,ZS4590,A8431,FGC17449,BY4055,Y23535,A11730,BY634,A6496,L238,CTS7556,GG729,Y31469,FGC31947) 234102 1009 1.0 1.0 1.0 1.0
ERR3078477 NA NA 2166914 13581 0.0 0.0 1.0 1.0
ERR3078516 NA NA 102794 108 0 0 0 0
ERR3078330 NA NA 57394 119 0.0 1.0 1.0 0.0
ERR3078393 R1b1a1b1a1a R-L151/etc*(xM405,L221,A8058) 519371 3555 1.0 1.0 1.0 1.0
ERR3078486 NA NA 158184 613 0.0 1.0 1.0 0.0
ERR3078348 NA NA 20184 47 0 0 0 0
ERR3078471 NA NA 52251 78 0 0 0 0
ERR3078368 NA NA 890808 1035 0.0 0.0 1.0 1.0
ERR3078308 NA NA 2387658 11809 0.0 0.0 1.0 1.0
ERR3078470 E1b1b1a1b1 E-CTS9086/etc*(xCTS5045,Z37809,A9483,SK888,Z36778) 166762 1441 1.0 1.0 1.0 1.0
ERR3078387 R1b1a1b1a1 R-P311*(xS263,FGC396,S26140,Z212,S359,L2,CTS7958,PF6584,FGC5512,BY2586,ZZ38) 281256 1716 1.0 1.0 1.0 1.0
ERR3078469 NA NA 289954 1377 0 0 0 0
ERR3078281 NA NA 12970 17 0 0 0 0
ERR3078340 NA NA 492743 509 0.0 1.0 1.0 0.0
ERR3078456 R1b1a R-L388*(xBY15598,AMM490.2,L493,BY94690,S511,S1746,Z272,S251,CTS11567,L356,L526,FGC37085,M12149,PF7566,GG746,Y31469,PH4238,CTS5330) 284934 1431 1.0 1.0 1.0 1.0
ERR3078433 NA NA 19058 23 0 0 0 0
ERR3078356 NA NA 116399 344 0.0 1.0 1.0 0.0
ERR3078448 NA NA 19423 74 0 0 0 0
ERR3078492 R1b1a1b1a1a R-L151*(xS263,A2148,L1245,L408,FGC5511,L719,ZZ38) 304284 1403 1.0 1.0 1.0 1.0
ERR3078511 J2a~ J-F1183/etc*(xCTS11251,PF5008) 1644087 7970 1.0 1.0 1.0 1.0
ERR3078474 NA NA 178582 177 0 0 0 0
ERR3078279 NA NA 202763 777 0.0 1.0 1.0 0.0
ERR3078405 NA NA 1872135 11801 0.0 0.0 1.0 1.0
ERR3078520 NA NA 7739 8 0 0 0 0
ERR3078265 R1b1a1b1a1 R-CTS7650*(xFGC30616,Y10790,Y7369,FGC419,PF7598,L564,FGC37092) 322127 455 1.0 1.0 1.0 1.0
ERR3078506 NA NA 17320 125 0 0 0 0
ERR3078488 NA NA 40720 85 0 0 0 0
ERR3078487 NA NA 204641 186 0.0 0.0 1.0 0.0
ERR3078461 R1b1a1b1a1a R-L151*(xM405,Z272,S457,L881,CTS11567,L594,BY247,ZZ38,A8056) 337825 1662 1.0 1.0 1.0 1.0
ERR3078369 NA NA 251421 320 0 0 0 0
ERR3078306 NA NA 1771960 9099 0 0 0 0
ERR3078283 NA NA 150650 547 0.0 0.0 1.0 0.0
ERR3078361 I2a1b I-P217*(xCTS9139,S10898,FGC29570) 236338 667 1.0 1.0 1.0 1.0
ERR3078407 R1b1a1b1a1a R-L151*(xAM01882,S493,S25234,L782,M467,L46,Z160,Z348,FGC427,S12025,S1217,Z264,L881,F1343,CTS6519.1,L2,CTS7193.2,BY247,Y18211,ZZ38,FGC37083) 489625 2778 1.0 1.0 1.0 1.0
ERR3078529 R1b1a1 R-CTS5577/etc*(xY14167,BY13053,AM01884,BY1053,JFS0008,L237,BY63580,S379,FGC427,Z205,L165,F3867.2,S180,S1468,PF6584,BY247,DF99,ZZ38,A8056,FGC37085,A15807) 250775 1077 1.0 1.0 1.0 1.0
ERR3078354 NA NA 97787 107 0 0 0 0
ERR3078476 NA NA 216496 991 0 0 0 0
ERR3078408 NA NA 90579 384 0 0 0 0
ERR3078527 NA NA 4534739 20064 0.0 0.0 1.0 1.0
ERR3078493 NA NA 24089 31 0 0 0 0
ERR3078496 R1b1a1b R-CTS12478*(xA564,S263,FGC419,L1231,L356,S6154,BY281,CTS6621,L1308,A121,BY16694) 534801 562 1.0 1.0 1.0 1.0
ERR3078420 NA NA 2241539 13148 0 0 0 0
ERR3078293 NA NA 41212 44 0 0 0 0
ERR3078350 NA NA 11739 13 0 0 0 0
ERR3078266 NA NA 39659 51 0 0 0 0
ERR3078462 NA NA 178406 144 0 0 0 0
ERR3078297 NA NA 17220 79 0 0 0 0
ERR3078533 R1b1a1b1a R-L51*(xM405,M228.1,A8068,FGC37095) 1581598 7527 1.0 1.0 1.0 1.0
ERR3078525 R1b1a1b R-CTS10834*(xS493,A7409,S516,CTS2509,M228.1,GG843.2,FGC31960) 168786 751 1.0 1.0 1.0 1.0
ERR3078459 R1b1a1b1a1a2a1b1a1~ R-Z264 193769 769 1.0 1.0 1.0 1.0
ERR3078342 NA NA 1380539 6646 0 0 0 0
ERR3078332 H2c1a~ H-Y21604 472550 2158 1.0 1.0 1.0 1.0
ERR3078517 NA NA 200013 226 0 0 0 0
ERR3078382 NA NA 1034625 6767 0.0 0.0 1.0 1.0
ERR3078455 R1b1a1b R-CTS8052*(xFGC14886,L237,S274,S23409,A9451,FGC19775,Y7370,S10817,FGC396,Z24515,PF7595,S359,PF4363,S471,ZZ38,CTS1843,PH2558) 215962 1184 1.0 1.0 1.0 1.0
ERR3078351 NA NA 149291 342 0.0 1.0 1.0 0.0
ERR3078383 NA NA 2089155 11214 0 0 0 0
ERR3078426 NA NA 296340 350 0 0 0 0
ERR3078344 NA NA 106334 108 0.0 0.0 1.0 1.0
ERR3078341 R1b1a1b1a1 R-CTS7650*(xA564,L884.2,S499,S22641,L1231,L356,L564) 581525 537 1.0 1.0 1.0 1.0
ERR3078414 NA NA 29831 33 0 0 0 0
ERR3078301 NA NA 47363 280 0 0 0 0
ERR3078526 R1b1 R-FGC35*(xY20761,CTS12478,BY21442,PF6368,Y7779) 1125040 1204 1.0 1.0 1.0 1.0
ERR3078286 NA NA 46319 46 0 0 0 0
ERR3078425 NA NA 618077 3646 0.0 0.0 1.0 1.0
ERR3078512 NA NA 1892914 9069 0.0 1.0 1.0 0.0
ERR3078485 NA NA 1675270 7665 0 0 0 0
ERR3078324 G2a2a1 G-PF3170*(xFGC58123,FGC6665,PF3240,Z6772,FGC2358,CTS2080.1,Z42566,Y60041.2,FGC34388,FGC35181) 631115 2467 1.0 1.0 1.0 1.0
ERR3078518 R1b1a1b1a1a2 R-P312*(xZ216,L617,FGC22513,PF6584,A9885,A2194,BY178,Y10794,Z16348,ZW09,A7662,Z16519,A1154,CTS7306,ZS5732^^,S3033,FGC15494,A14026,FGC11329,A121,BY592,DF99) 136697 737 1.0 1.0 1.0 1.0
ERR3078386 NA NA 57168 82 0 0 0 0
ERR3078317 NA NA 158063 479 0.0 1.0 1.0 0.0
ERR3078357 NA NA 95401 103 0 0 0 0
ERR3078472 I2a2b I-SK1271/etc*(xY16664,BY2808,Y111878,Y54604) 524133 3588 1.0 1.0 1.0 1.0
ERR3078450 NA NA 45156 49 0 0 0 0
ERR3078453 NA NA 54702 321 0 0 0 0
ERR3078484 NA NA 11226 26 0 0 0 0
ERR3078309 NA NA 3789467 17524 0 0 0 0
ERR3078284 NA NA 896391 867 0.0 0.0 1.0 1.0
ERR3078282 NA NA 69764 90 0 0 0 0
ERR3078466 NA NA 558346 524 0 0 0 0
ERR3078479 E1b1b1a E-CTS9236/etc*(xFGC2141,Y27268) 1600653 7999 1.0 1.0 1.0 1.0
ERR3078269 NA NA 3653333 14976 0 0 0 0
ERR3078347 NA NA 30379 46 0 0 0 0
ERR3078295 NA NA 280935 332 0 0 0 0
ERR3078505 NA NA 30073 38 0 0 0 0
ERR3078412 NA NA 70018 111 0 0 0 0
ERR3078514 NA NA 3237241 16724 0.0 0.0 1.0 1.0
ERR3078443 NA NA 84146 65 0 0 0 0
ERR3078319 NA NA 76251 373 0.0 1.0 1.0 0.0
ERR3078300 NA NA 119834 107 0.0 0.0 1.0 1.0
ERR3078270 NA NA 59471 77 0 0 0 0
ERR3078359 NA NA 187634 494 0.0 1.0 1.0 0.0
ERR3078524 NA NA 85912 313 0 0 0 0
ERR3078329 NA NA 65213 81 0 0 0 0
ERR3078465 NA NA 1778680 11355 0 0 0 0
ERR3078392 NA NA 204048 330 0.0 1.0 1.0 0.0
ERR3078334 NA NA 9058 14 0 0 0 0
ERR3078273 NA NA 326677 336 0 0 0 0
ERR3078478 NA NA 95878 79 0 0 0 0
ERR3078415 R1b1a1 R-L502/etc*(xA561,A1243,CTS8234,S357,Z222,L356,DF106,S798,FGC5782,L1403,FGC11317,L277.1,CTS7556) 115835 378 1.0 1.0 1.0 1.0
ERR3078671 NA NA 205 3 0 0 0 0
ERR3078521 NA NA 9715 5 0 0 0 0
ERR3078530 NA NA 39944 48 0 0 0 0
ERR3078388 NA NA 789306 5740 0.0 0.0 1.0 1.0
ERR3078360 NA NA 17752 59 0 0 0 0
ERR3078339 NA NA 1595226 6433 0.0 0.0 1.0 0.0
ERR3078522 NA NA 12991 8 0 0 0 0
ERR3078468 NA NA 40834 82 0 0 0 0
ERR3078452 R1b1a1b R-PF6508/etc*(xFGC14877,A680,CTS2509,FGC396,FGC15054,L356,L21,DF19,ZZ38,A8056,BY16690,GG746) 198136 1076 1.0 1.0 1.0 1.0
ERR3078272 NA NA 1553715 7919 0.0 0.0 1.0 1.0
ERR3078290 NA NA 381566 538 0.0 0.0 1.0 1.0
ERR3078280 NA NA 1997562 8906 0 0 0 0
ERR3078373 NA NA 116274 471 0 0 0 0
ERR3078294 NA NA 41360 55 0 0 0 0
ERR3078444 NA NA 41151 54 0 0 0 0
ERR3078467 NA NA 23577 29 0 0 0 0
ERR3078372 R1b1a1b1a1 R-PF6540*(xS265,Z348,S12025,Z212,Z204,L356,BY247,DF19,ZZ38) 189565 905 1.0 1.0 1.0 1.0
ERR3078494 NA NA 333784 297 0 0 0 0ERR3078458 NA NA 16903 20 0 0 0 0

ERR3078381 NA NA 118409 147 0 0 0 0ERR3078376 NA NA 1930347 11086 0.0 0.0 1.0 1.0

ERR3078370 NA NA 3746027 18206 0 0 0 0
ERR3078435 R1b1a1b R-CTS7400*(xJFS0003,S267,L1231,DF106,CTS11722,FGC17449,S423,FGC37110,CTS9416) 86733 426 1.0 1.0 1.0 1.0
ERR3078491 R1b1a1 R-PF6463*(xM478,BY15593,L151,CTS9219) 162160 666 1.0 1.0 1.0 1.0
ERR3078276 NA NA 1931322 9834 0 0 0 0
ERR3078418 R1b1a1b1a1a1c2b2a1b1a1b2b R-Z25289.2 328876 1093 1.0 1.0 1.0 1.0
ERR3078379 NA NA 39517 40 0 0 0 0
ERR3078292 NA NA 496259 538 0 0 0 0
ERR3078374 NA NA 42825 58 0 0 0 0
ERR3078481 NA NA 2922924 13804 0.0 0.0 1.0 1.0
ERR3078416 NA NA 15040 13 0 0 0 0
ERR3078397 NA NA 1073259 1263 0 0 0 0
ERR3078291 NA NA 1711346 7027 0.0 0.0 1.0 1.0
ERR3078353 NA NA 84233 301 0 0 0 0
ERR3078454 NA NA 8294 14 0 0 0 0
ERR3078457 NA NA 132902 130 0 0 0 0
ERR3078480 NA NA 102963 101 0 0 0 0
ERR3078321 NA NA 209369 554 0 0 0 0
ERR3078400 R1b1a1 R-L502*(xY14054,FGC36479,CTS7958,FGC5541,Z29805) 264335 724 1.0 1.0 1.0 1.0
ERR3078358 NA NA 40186 49 0 0 0 0
ERR3078389 NA NA 1874038 10496 0.0 0.0 1.0 1.0
ERR3078402 R1b1a1b1a1a R-PF6543*(xAM01884,S379,FGC415,Z24515,L1231,S487,CTS8492,FGC5524,ZZ38) 206193 1049 1.0 1.0 1.0 1.0
ERR3078424 R1b1a1 R-PF6524/etc*(xY13872,L265) 478536 3005 1.0 1.0 1.0 1.0
ERR3078299 NA NA 2442985 11413 0.0 0.0 1.0 1.0
ERR3078352 NA NA 229078 759 0 0 0 0
ERR3078507 R1b1a1b1 R-L23*(xS263,L628,Z222,L356,FGC42652,S279,A6464,A212,DC26,FGC33060,L130,FGC58883,A7911,FGC37083) 441562 496 1.0 1.0 1.0 1.0
ERR3078274 R1b1a1b R-CTS1416^^/etc*(xZ160,Y7369,S1743,S22641,L1231,L356,BY281,L743,A1334,DC26,FGC5782,FGC43488,L1315) 544683 660 1.0 1.0 1.0 1.0
ERR3078464 T1 T-PF7465*(xCTS7225) 146983 598 1.0 1.0 1.0 1.0
ERR3078515 R1b1a1b R-L1348*(xM405,L1231,L526,Y31465) 145032 572 1.0 1.0 1.0 1.0
ERR3078322 NA NA 170998 205 0 0 0 0
ERR3078267 R1b1a1b R-CTS8591*(xS5627,L1231,L356,L192.1) 467433 576 1.0 1.0 1.0 1.0
ERR3078504 NA NA 1687972 8391 0 0 0 0

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