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Thread: Paleogenomics of Upper Paleolithic to Neolithic European hunter-gatherers

  1. #1
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    Paleogenomics of Upper Paleolithic to Neolithic European hunter-gatherers

    Looks like the data is available shortly so maybe it needs a dedicated thread.

    Eurasia has been populated by modern humans for over 45,000 years and for the vast majority of their time they relied on a foraging lifestyle. Our knowledge of the genetic relatedness and structure of European hunter-gatherers is, however, still limited, because dedicated studies are challenged by the scarce availability and poor molecular preservation of human remains from that period. Here we analyze 356 ancient hunter-gatherer genomes including new genomic data of 116 individuals from 14 countries in western and central Eurasia, dating between 35,000 and 5,000 years ago (35-5 ka). We identify a new genetic ancestry profile in individuals associated with the Upper Paleolithic Gravettian from western Europe, which is distinct from contemporaneous groups related to this archeological culture in central and southern Europe. However, it resembles that of preceding individuals associated with the Aurignacian and survives during the Last Glacial Maximum (LGM, ~25-19 ka) in human populations from southwestern Europe, associated with the Solutrean and later Magdalenian, which re-expanded northward and northeastward after the LGM. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups during the LGM, alongside a north-to-south expansion of Epigravettian-associated populations. From at least 14 ka, a lineage related to this culture expands from the south across the rest of Europe largely replacing the Magdalenian-associated gene pool. After a period of limited admixture across the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, also characterized by marked differences in inherited phenotypic traits.

    https://www.ebi.ac.uk/ena/browser/view/PRJEB51862

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  3. #2
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    List of bams.

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    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693280/WCX002.A0101.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693281/WCX002.A0102.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693282/WCX002.A0103.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693283/WCX004.A0101.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693284/WCX004.A0102.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693285/WCX004.A0103.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693286/WOL001.A0101.bam

  4. The Following 10 Users Say Thank You to teepean47 For This Useful Post:

     Agamemnon (12-23-2022),  David Bush (01-18-2023),  Gentica277282 (12-23-2022),  J Man (12-23-2022),  Jack Johnson (01-06-2023),  JMcB (01-07-2023),  JRD (12-23-2022),  Riverman (12-26-2022),  siberoberingian (03-02-2023),  Strider99 (12-23-2022)

  5. #3
    Gold Class Member
    Posts
    619
    Sex
    Nationality
    Finnish
    Y-DNA (P)
    R1b-Z142
    mtDNA (M)
    H10g

    These look like mtDNA bams.

    Code:
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693299/AAT001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693300/AC16_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693301/AC16_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693302/ACR001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693303/AMI001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693304/AMI002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693305/BRM001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693306/CRN001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693307/CRN002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693308/CRW001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693309/DLV005_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693310/DLV006_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693311/DOB001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693312/DOG001_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693313/DOG001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693314/DOG002_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693315/DOG002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693316/DOG003_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693317/DOG003_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693318/DOG004_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693319/DOG004_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693320/DOG006_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693321/DOG007_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693322/DOG007_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693323/DOG009_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693324/DOG009_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693325/DOG010_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693326/DOG010_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693327/DON005_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693328/DON006_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693329/DRI001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693330/FRL006_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693331/FRM001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693332/GER002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693333/GER003_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693334/GFW001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693335/GFW002.003_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693336/GFW004_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693337/GFW005_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693338/GFW007_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693339/GFW008_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693340/GFW009_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693341/GOY001_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693342/GOY001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693343/GOY007_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693344/GOY007_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693345/GOY009_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693346/GOY009_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693347/GOY014_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693348/GOY014_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693349/IGR001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693350/JAZ001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693351/KRZ001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693352/KVH001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693353/KVH001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693354/KVH002_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693355/LMA001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693356/LPI002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693357/MAF001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693358/MAZ001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693359/MAZ003_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693360/MN2001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693361/MN2002_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693362/MN2003_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693363/MNN001.002_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693364/MNN003_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693365/MNN004_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693366/MNN005_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693367/MNN006_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693368/MNN007_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693369/MPR001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693370/MUR001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693371/MUR002_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693372/MUR005_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693373/MUR007_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693374/MUR017_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693375/MUR021_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693376/OKL001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693377/OKL002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693378/ORM001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693379/OST001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693380/OST002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693381/OST003_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693382/PA12_ds_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693383/PA12_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693384/PIN004_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693385/PRD001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693386/RIE002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693387/RIP001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693388/STO001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693389/TTK001_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693390/UOO004_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693391/UOO012_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693392/UOO015_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693393/UOO023_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693394/UOO025_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693395/UOO029_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693396/UOO033_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693397/UOO035.056_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693398/UOO037_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693399/UOO047_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693400/UOO049_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693401/UOO051_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693402/UOO052_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693403/UOO053_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693404/UOO059_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693405/VO1001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693406/VO1003_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693407/VO1004_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693408/VO1005_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693409/VO2001_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693410/VSL002_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693411/VSL002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693412/VSL003_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693413/VSL003_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693414/VSL004_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693415/WCX002_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693416/WCX002_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693417/WCX004_ds_halfUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693418/WCX004_ss_nonUDG.bam
    ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR106/ERR10693419/WOL001_ds_halfUDG.bam

  6. The Following 8 Users Say Thank You to teepean47 For This Useful Post:

     David Bush (01-18-2023),  Gentica277282 (12-23-2022),  J Man (12-23-2022),  Jack Johnson (01-06-2023),  JMcB (12-23-2022),  JRD (12-23-2022),  siberoberingian (03-02-2023),  W‚ldpykjong (12-25-2022)

  7. #4
    Gold Class Member
    Posts
    619
    Sex
    Nationality
    Finnish
    Y-DNA (P)
    R1b-Z142
    mtDNA (M)
    H10g

    Y-DNA haplogroups. Yleaf with two reads.

    I am uploading Y-DNA bams to Google drive:

    https://drive.google.com/drive/folde...usp=share_link

    Females removed:

    https://anthrogenica.com/showthread....l=1#post898835
    Last edited by teepean47; 12-23-2022 at 08:14 PM.

  8. The Following 27 Users Say Thank You to teepean47 For This Useful Post:

     Agamemnon (12-23-2022),  Arlus (12-23-2022),  Bygdedweller (12-23-2022),  David Bush (01-18-2023),  ffffffffff00 (12-23-2022),  Fried (12-31-2022),  G-Man (12-23-2022),  J Man (12-23-2022),  J1 DYS388=13 (12-23-2022),  Jack Johnson (01-08-2023),  JMcB (12-23-2022),  JRD (12-23-2022),  Kale (12-23-2022),  Kelso (12-23-2022),  Megalophias (12-23-2022),  MethCat (12-25-2022),  Orentil (12-23-2022),  peloponnesian (12-23-2022),  PLogan (12-23-2022),  pmokeefe (03-12-2023),  RCO (12-23-2022),  Rufus191 (Yesterday),  siberoberingian (03-02-2023),  Strider99 (12-23-2022),  Surtakey (01-16-2023),  VladimirTaraskin (12-23-2022),  W‚ldpykjong (12-25-2022)

  9. #5
    Gold Class Member
    Posts
    619
    Sex
    Nationality
    Finnish
    Y-DNA (P)
    R1b-Z142
    mtDNA (M)
    H10g

    One read

    Code:
    Sample_name	Hg	Hg_marker	Total_reads	Valid_markers
    AAT001	R-Y29948	Y30209	45670	5646
    ACR001	NA		1633	451
    ACR001	NA		4441	1181
    AMI001	R-FT129056	Y179192	31119	5068
    AMI002	R-Y134945	Y41522	3697	791
    BRM001	I-M423	AM01285;L178.1;etc.	12978	3780
    BR_Y	I1	CTS1393	3718	1648
    CIO001	I-FGC29230	FGC29238	1973	607
    CIO001	NA		4115	1200
    CRCsnp_Y	I-Y3259	L1316;CTS7391	12602	5272
    CRN001	I-S21825*(xY4213)	Y4216;Y5139;etc.	180433	36517
    CRN002	I-S21825*(xY4213)	Y4222;Y4200;etc.	192238	38266
    CRW001	NA		20373	3756
    DLV005	IJ*(xJ)	PF3535;Y1887;etc.	104796	23541
    DLV006	C-F3393*(xF1370)	Z1426;K35	110245	21916
    DOB001	I-M423	M423;S2654;etc.	211127	42439
    DOG001	I-Y151541	Y151541	13210	6652
    DOG001	I-Y3259*(xY6098)	PF3858;PF3861;etc.	31038	10639
    DOG002	I-Y3104*(xL621)	CTS11030;S7721	9956	5112
    DOG002	I-Y3104*(xL621,L161)	Z2585;CTS11030;etc.	19480	7276
    DOG003	NA		4236	586
    DOG003	NA		6023	724
    DOG003	NA		771	86
    DOG004	I-S21825*(xY21979)	Y4200	12244	3046
    DOG004	NA		1113	329
    DOG006	E-PH784	Y30737	6093	1362
    DOG006	NA		7767	1375
    DOG007	I-S6635	PF6915;S6648	8962	4732
    DOG007	I-S6635	S6648;PF3918	60379	18190
    DOG009	IJ*(xJ)	FGC1583	9477	2384
    DOG009	NA		23234	8670
    DOG010	G-Z6148	Y38041	43966	15665
    DOG010	G-Z6148	Z6894	10046	3658
    DON005	R-Y262427	Y262427	6455	1787
    DON006	I-Y4213	Y4235	6105	1421
    DRI001	I-M423	AM01285;YP207;etc.	106683	26394
    FRL006	C-F3393*(xF1370)	CTS6773	115821	24951
    FRM001	NA		2795	491
    GA165c_Y	NA		2644	327
    GA166c_Y	NA		2	3
    GA221snp_Y	NA		335	66
    GA222snp_Y	NA		167	40
    GA223snp_Y	NA		551	147
    GA235snp_Y	NA		469	57
    GA236snp_Y	NA		1080	146
    GA237snp_Y	NA		2311	374
    GA238snp_Y	NA		150	45
    GA239snp_Y	NA		459	156
    GA240snp_Y	NA		169	64
    GA250snp_Y	R-S6285	YP4644	6080	1167
    GA251snp_Y	NA		2413	1022
    GA252snp_Y	A1b	V3785	11788	2310
    GA253snp_Y	NA		1851	264
    GA259snp_Y	NA		2173	1176
    GA260snp_Y	I*(xI1,I2)	PF3663;PF3736;etc.	4646	3045
    GA263snp_Y	NA		1975	240
    GA64snp_Y	NA		141	85
    GA79c_Y	I-P37*(xM423)	Z2619	9716	3429
    GA81snp_Y	NA		5356	1706
    GA82c_Y	I-P37*(xM423)	CTS1007;CTS7700;etc.	16255	7531
    GA89c_Y	NA		4162	717
    GA90c_Y	I-P37*(xM423)	Z2610	5621	1683
    GA94snp_Y	NA		495	240
    GER002	A1b	L1013	5356	1768
    GER002	B-V1108	Y42726	6623	1090
    GER002	NA		3809	1600
    GER003	C*(xM217)	F3395;Y2798;etc.	8514	3433
    GER003	C-V20*(xV86)	Y12148	6594	2586
    GER003	C-V20*(xV86)	Z28851	11792	3854
    GFW001	I-S2555*(xY10720)	Y11317;Y13081;etc.	42064	14528
    GFW002	I-M423	S2654;M423;etc.	84374	26899
    GFW003	I-M423	Z2601;AM01285;etc.	55010	19800
    GFW004	R-BY54624	Y159343	9880	1776
    GFW005	I-BY33169*(xM838)	Y28229;Y227125	164561	37797
    GFW007	R-Y179346	Y179708	21548	3812
    GFW008	IJ*(xJ)	FGC1583;FGC1571;etc.	19147	4260
    GFW009	I*(xI1)	CTS646;CTS7831;etc.	4642	1715
    GOY001	NA		1593	549
    GOY001	R-L754	PF6261	11392	4246
    GOY001	R-P297*(xY13200,M269)	CTS9018	6352	1850
    GOY007	NA		10616	3334
    GOY007	NA		14960	4960
    GOY007	NA		3073	700
    GOY009	NA		2951	725
    GOY009	R-Y23226	Y23228	9600	2130
    GOY014	NA		1830	495
    GOY014	NA		203	70
    GOY014	P-P226	PF5964	2486	721
    IGR001	Q-L56*(xL53)	S324;M1071;etc.	80030	17877
    JAZ001	R-S18307	Y89660	14365	2523
    KRZ001	NA		499	106
    KRZ001	NA		587	111
    KVH001	P-P226*(xQ)	M1215	4835	1464
    KVH001	R-PH155*(xY258456)	SK2056	3698	1154
    KVH002	R-L51	Y410	17043	2941
    LMA001	NA		11146	3561
    LPI002	I-Y19077	Y19546	16639	6418
    LPI002	I-Y21293	A8286	8518	3087
    LPI002	I1*(xL121)	Z2844;V1423;etc.	16291	6851
    LRO001	NA		14909	848
    MA158snp_Y	A1*(xA1a)	Y9694;Y10177	3542	1290
    MA159snp_Y	R-Z645	V4100	1818	833
    MA160snp_Y	NA		302	90
    MA161snp_Y	NA		656	376
    MA169snp_Y	NA		4063	784
    MA170snp_Y	NA		441	145
    MAF001	I-M423	AM01271;FGC7084;etc.	19313	5235
    MAZ001	NA		17424	5865
    MAZ001	P-P226*(xQ)	P230;M1257;etc.	20961	6321
    MAZ003	C-V20*(xV86)	Z28801	22722	8385
    MAZ003	C-V20*(xV86)	Z28838;V20	23466	8074
    MN2001	R-YP1272	YP1300	19693	7853
    MN2002	R-M459*(xM735)	V2035;L120;etc.	126157	22502
    MN2003	R-P297*(xM269)	L502;CTS9018;etc.	60278	18249
    MNN001	NA		9290	1822
    MNN002	R-FT12510	Y171702	17089	2830
    MNN003	NA		3928	1211
    MNN004	R-M198*(xYP1051,M417)	CTS1619;Y206;etc.	5452	2305
    MNN005	R-Y17760	Y17780	54519	6580
    MNN006	R-M269	L150;S4969;etc.	20202	3267
    MNN007	NA		3122	682
    MPR001	R-Y23200	Y23201	40296	5309
    MUR001	Q-Y570*(xF746)	F1261	15967	4837
    MUR002	NA		4410	896
    MUR005	Q-F746*(xM120,YP1500)	F1755;Y648;etc.	23609	8627
    MUR007	P-P226*(xR)	CTS7194;PF5898;etc.	21608	7413
    MUR017	Q-Y570*(xF746)	Y570;F2753	12064	4582
    MUR021	Q-F746*(xM120,YP1500)	Y602;F818;etc.	19907	6257
    OKL001	R-BY101743	Y167882	16776	3126
    OKL002	I-M423	Z2595;AM01291;etc.	118976	27965
    ORM001	R-L23*(xZ2103)	S141	10134	1990
    OST001	R-Y20367	Y20369	1556	349
    OST003	I-L121	Z2762	62688	17469
    PIN004	NA		5010	192
    PIN004	NA		5173	182
    PIN004	NA		5310	177
    PRD001	I-P37*(xM423)	Z2619;PF4058	41123	9887
    RIE002	J-L817*(xZS7789)	S4950	4211	1077
    RIE002	J-P58	P58	4753	1355
    RIE002	NA		2168	605
    RIP001	I-M223*(xY3259)	CTS2312;CTS11545;etc.	119600	23780
    STO001	R-FGC19760	FGC19765	67723	8080
    TTK001	Q-Y6802*(xY45075)	YP6168	36968	9039
    UOO004	R-P297*(xM269)	PF6459	7245	1681
    UOO012	R-YP4141*(xYP5018,YP4132)	YP4227;YP4182	36523	10552
    UOO015	NA		4582	925
    UOO023	NA		8086	1538
    UOO023	R-Y16483	Y16741	15061	2506
    UOO025	R-L23	S141	8358	1573
    UOO029	NA		4490	1012
    UOO033	Q-M930*(xM3,L804)	M861;M885	94093	27524
    UOO035	Q-F1096*(xM25)	Y9312	16766	3961
    UOO037	NA		13698	2294
    UOO047	NA		14943	2391
    UOO049	IJ*(xI)	FGC1566;P123;etc.	15284	5564
    UOO051	R1a*(xYP4141,M459)	PF6153	8547	1822
    UOO052	Q-Y570	F1748	56110	11813
    UOO053	Q-Y570	F1261;F1202	40327	9122
    UOO056	Q-F746*(xM120,YP1500)	F790;Y649;etc.	27275	7158
    UOO059	NA		18662	5573
    VO1001	I-S2555	Y10708	22447	4591
    VO1003	I-L460*(xP37)	L460	53510	13353
    VO1004	I-L701*(xP78)	Y4892	36798	8572
    VO1005	NA		12254	3322
    VO2001	R-PF6287*(xY7777,BY17643)	PF6330;PF6299	87111	18250
    VSL002	I-S21825*(xY21979)	S15308	18985	5817
    VSL002	I-Y4213*(xY4192,FT344596)	Y4269	39377	10959
    VSL003	I-P37*(xM423)	AM00519	10785	2548
    VSL003	NA		7450	1954
    VSL004	R-PF6287*(xY7777,BY17643)	PF6304;PF6287;etc.	21901	7420
    WCX002	NA		1525	332
    WCX002	NA		5077	1006
    WCX002	R1b*(xPH155)	CTS2134	5995	1519
    WCX004	NA		1032	175
    WCX004	R-L23	S141	4799	1126
    WCX004	R-Y18894	Y145808	3350	719
    WOL001	I-M423	AM01291;Z2577	13232	4337
    XXX001	NA		18524	3879
    XXX001	R-FGC17907	Y300410	19919	3685
    XXX001	R-FT50902	Y175034	31101	4735
    XXX001	R-Z17121	Y219256	85729	8831

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  11. #6
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    Pasting analysis from the news discussion thread here just to have it in the dedicated spot.
     
    Ok here's a cursory overview of the new samples and what I think they represent... (low coverage = unusable, poor coverage = don't use standalone, maybe ok grouped with similar samples)

    EHG from Russia and Baltics
    JAZ001, KAR001 (poor coverage), KVH001&002 (001 poor coverage), MN2001/2002/2003, MNN (3 good quality, 1 poor coverage, 3 low coverage), MUR001 (5 mediocre coverage, 1 poor coverage, 1 low coverage), UOO - tons of samples, VSL (2 decent samples, 1 poor coverage)

    WHG of the Bichon/Loschbour/Isles variety
    AAT001, ACR001 (low coverage), DOG (001&002 good coverage, 003-010 low coverage), FMR001 (poor coverage), KGH006, MAF001, MPR001, OKL001&002

    Miscellaneous European WHG
    AC16 - GrottaContinenza-like
    AMI001&002 - Central European WHG (Germany/Poland/Hungary)
    CRN001&002 - Iberian HG similar to Chan
    CRW001 - Looks quite close to Denmark HG
    DOB001 - Close match Germany_BadDurrenberg_HG
    DON005&006 - WHG of some kind, either early or Central European (low coverage)
    DRI001 - WHG (Denmark/Germany)
    GFW (5 good coverage samples out of 7) - WHG (Denmark/Germany)
    IGR001 - Ukrainian HG likely
    OST001-003 - Not quite sure, Balkan-WHG maybe?
    PRD001 - IronGates-like (poor coverage)
    STO001 - GrottaContinenza-like
    VO (3 decent samples, 2 poor coverage) - Ukrainian HG likely
    WCX - Denmark HG? (low coverage)
    WOL001 - Similar to Hungary-WHG (poor coverage)

    Magdelanians
    LMA001 (low coverage), MAZ003

    Previously published samples not given labels in this set
    - BER001 (EHG - poor coverage)
    - PES001: Arkhangelsk EHG
    - SRA62: Irish WHG
    - RIP001: higher coverage version of Tagliente

    Other not particularly revelatory samples
    BRM001 - Western EEF with high WHG (poor coverage)
    CIO001 - Cioclovina or something remarkably similar (low coverage)
    DLV005&006 - Vestonice, very closely related to the others if not duplicates.
    RIE002 - no idea (low coverage)
    LPI002 - Late Aurignacian? (low coverage)
    LRO001 - GoyetQ116_1 like (low coverage)
    PIN004 - Late Aurignacian? (low coverage)

    Now for the exciting stuff
    FRL006 - Looks like GoyetQ116_1 (complete with high Ust-Ishim & BachoKiro affinity) but more relevant to later Magdelanians. Good enough coverage, ~600k snps.
    GER002&003 - Similar to FRL006 (002 = low coverage, 003 = poor coverage)
    GOY (3 low coverage, 1 poor coverage) - Looks to be Gravettian period at Goyet site. Not particularly high affinity to anyone, likely mixed between late-GoyetQ116_1 types and Vestonice-like ancestry of a type more relevant to WHG.
    MAZ001 - Tough to make heads or tails of this, superficially looks like it could be a Dzudzuana but then again it's such poor coverage it could be a 3-toed sloth. Assuming MAZ003 the Magdelanian is from the same given the matching MAZ label, that either means MAZ001 is indeed a 3-toed sloth or he came from North Africa.
    ORM001 - GoyetQ116_1 like
    PA12 - Similar to Vestonice, but slightly higher affinity to BK1653 and WHG
    TTK001 - Extremely interesting. Very ANE, no discernable East-Asian, no discernable WHG. Lower paleo-Euro affinity than MA1/Yana, equal Native American affinity to MA1. Highest affinity is to Tarim_EMBA. Possible connection to Iran_N/CHG. Paleolithic Central Asian? Coverage is mediocre but not awful ~230k snps.


    Quite surprising to see AAT001 as R-M269, looks like a good coverage, very typical WHG. The number of y-calls there seems low compared to it's coverage, maybe something to that...
    AAT001
    "Ireland_Killuragh_HG.SG" 40.05
    "Loschbour.DG" 27.05
    "Germany_Falkenstein_HG" 21.4
    "Germany_Bottendorf_HG" 10.8
    "Ethiopia_Mota_4500BP.SG" 0.7
    Columns:,Anatolia_Boncuklu_N.SG,Anatolia_Barcin_N. SG,Iran_TepeAbdulHosein_N.SG,Iran_Wezmeh_N.SG,CHG. SG,Taforalt,ElMiron,Spain_Chan_HG.SG,Bichon.SG,Ita ly_GrottaContinenza_HG.SG,RUS_Arkhangelsk_HG.SG,RU S_Samara_Sidelkino_HG.SG,Afanasievo_KarasukIII.SG, Yamnaya_Kazakhstan_Karagash.SG,Botai.SG,Andaman_10 0BP.SG,Jomon.SG,RUS_Primorsky_DevilsCave_N.SG,RUS_ Irkutsk_Shamanka_EN.SG,RUS_Irkutsk_AngaraRiver_LN. SG,RUS_Irkutsk_Sokhter_LN.SG,RUS_Yakutia_Kamenka2_ LN.SG,RUS_Krasnoyarsk_Nefteprovod_BA.SG,Peru_RioUn callane_1800BP.SG,Bahamas_SouthAndros_Ceramic.SG

    A lot of low coverage samples turning up weird calls, probably contamination.
    Some of the very good coverage samples have disproportionately low # of y-calls coupled with unexpected haplogroups (maybe female?)

    Also update to the OST site. Blatterhohle-like situation.
    OST2 = ~77% WHG (56% Denmark, 16% Germany, 6% Ireland), ~23% EEF.
    AMI = I was mistaken before, these look like the Iberian HG Canes.
    Last edited by Kale; 12-23-2022 at 05:46 PM.
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  13. #7
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  15. #8
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    The update added the X and Y snp block typical of 1240k dataset which was missing before.
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  17. #9
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    Quote Originally Posted by Kale View Post
    Pasting analysis from the news discussion thread here just to have it in the dedicated spot.
     
    Ok here's a cursory overview of the new samples and what I think they represent... (low coverage = unusable, poor coverage = don't use standalone, maybe ok grouped with similar samples)

    EHG from Russia and Baltics
    JAZ001, KAR001 (poor coverage), KVH001&002 (001 poor coverage), MN2001/2002/2003, MNN (3 good quality, 1 poor coverage, 3 low coverage), MUR001 (5 mediocre coverage, 1 poor coverage, 1 low coverage), UOO - tons of samples, VSL (2 decent samples, 1 poor coverage)

    WHG of the Bichon/Loschbour/Isles variety
    AAT001, ACR001 (low coverage), DOG (001&002 good coverage, 003-010 low coverage), FMR001 (poor coverage), KGH006, MAF001, MPR001, OKL001&002

    Miscellaneous European WHG
    AC16 - GrottaContinenza-like
    AMI001&002 - Central European WHG (Germany/Poland/Hungary)
    CRN001&002 - Iberian HG similar to Chan
    CRW001 - Looks quite close to Denmark HG
    DOB001 - Close match Germany_BadDurrenberg_HG
    DON005&006 - WHG of some kind, either early or Central European (low coverage)
    DRI001 - WHG (Denmark/Germany)
    GFW (5 good coverage samples out of 7) - WHG (Denmark/Germany)
    IGR001 - Ukrainian HG likely
    OST001-003 - Not quite sure, Balkan-WHG maybe?
    PRD001 - IronGates-like (poor coverage)
    STO001 - GrottaContinenza-like
    VO (3 decent samples, 2 poor coverage) - Ukrainian HG likely
    WCX - Denmark HG? (low coverage)
    WOL001 - Similar to Hungary-WHG (poor coverage)

    Magdelanians
    LMA001 (low coverage), MAZ003

    Previously published samples not given labels in this set
    - BER001 (EHG - poor coverage)
    - PES001: Arkhangelsk EHG
    - SRA62: Irish WHG
    - RIP001: higher coverage version of Tagliente

    Other not particularly revelatory samples
    BRM001 - Western EEF with high WHG (poor coverage)
    CIO001 - Cioclovina or something remarkably similar (low coverage)
    DLV005&006 - Vestonice, very closely related to the others if not duplicates.
    RIE002 - no idea (low coverage)
    LPI002 - Late Aurignacian? (low coverage)
    LRO001 - GoyetQ116_1 like (low coverage)
    PIN004 - Late Aurignacian? (low coverage)

    Now for the exciting stuff
    FRL006 - Looks like GoyetQ116_1 (complete with high Ust-Ishim & BachoKiro affinity) but more relevant to later Magdelanians. Good enough coverage, ~600k snps.
    GER002&003 - Similar to FRL006 (002 = low coverage, 003 = poor coverage)
    GOY (3 low coverage, 1 poor coverage) - Looks to be Gravettian period at Goyet site. Not particularly high affinity to anyone, likely mixed between late-GoyetQ116_1 types and Vestonice-like ancestry of a type more relevant to WHG.
    MAZ001 - Tough to make heads or tails of this, superficially looks like it could be a Dzudzuana but then again it's such poor coverage it could be a 3-toed sloth. Assuming MAZ003 the Magdelanian is from the same given the matching MAZ label, that either means MAZ001 is indeed a 3-toed sloth or he came from North Africa.
    ORM001 - GoyetQ116_1 like
    PA12 - Similar to Vestonice, but slightly higher affinity to BK1653 and WHG
    TTK001 - Extremely interesting. Very ANE, no discernable East-Asian, no discernable WHG. Lower paleo-Euro affinity than MA1/Yana, equal Native American affinity to MA1. Highest affinity is to Tarim_EMBA. Possible connection to Iran_N/CHG. Paleolithic Central Asian? Coverage is mediocre but not awful ~230k snps.


    Quite surprising to see AAT001 as R-M269, looks like a good coverage, very typical WHG. The number of y-calls there seems low compared to it's coverage, maybe something to that...
    AAT001
    "Ireland_Killuragh_HG.SG" 40.05
    "Loschbour.DG" 27.05
    "Germany_Falkenstein_HG" 21.4
    "Germany_Bottendorf_HG" 10.8
    "Ethiopia_Mota_4500BP.SG" 0.7
    Columns:,Anatolia_Boncuklu_N.SG,Anatolia_Barcin_N. SG,Iran_TepeAbdulHosein_N.SG,Iran_Wezmeh_N.SG,CHG. SG,Taforalt,ElMiron,Spain_Chan_HG.SG,Bichon.SG,Ita ly_GrottaContinenza_HG.SG,RUS_Arkhangelsk_HG.SG,RU S_Samara_Sidelkino_HG.SG,Afanasievo_KarasukIII.SG, Yamnaya_Kazakhstan_Karagash.SG,Botai.SG,Andaman_10 0BP.SG,Jomon.SG,RUS_Primorsky_DevilsCave_N.SG,RUS_ Irkutsk_Shamanka_EN.SG,RUS_Irkutsk_AngaraRiver_LN. SG,RUS_Irkutsk_Sokhter_LN.SG,RUS_Yakutia_Kamenka2_ LN.SG,RUS_Krasnoyarsk_Nefteprovod_BA.SG,Peru_RioUn callane_1800BP.SG,Bahamas_SouthAndros_Ceramic.SG

    A lot of low coverage samples turning up weird calls, probably contamination.
    Some of the very good coverage samples have disproportionately low # of y-calls coupled with unexpected haplogroups (maybe female?)

    Also update to the OST site. Blatterhohle-like situation.
    OST2 = ~77% WHG (56% Denmark, 16% Germany, 6% Ireland), ~23% EEF.
    AMI = I was mistaken before, these look like the Iberian HG Canes.

    An R1b M 269 among a full fledged WHG population? What is the date of the sample?

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  19. #10
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    Quote Originally Posted by etrusco View Post
    An R1b M 269 among a full fledged WHG population? What is the date of the sample?
    Woops, teepean and I both forgot to check the .ind file it appears. AAT001 = female.
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