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Thread: Filling Important Gaps in the Genomic History of Southwest Asia

  1. #11
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    Quote Originally Posted by pmokeefe View Post
    Haplogroups for The Genomic History of the Bronze Age Southern Levant here:
    https://www.cell.com/cms/10.1016/j.c...b12aa70d4/mmc2
    M J H20a 2334-2149 calBCE (3810±20 BP, PSUAMS-2167)
    M J K 1971-1782 calBCE (3560±20 BP, OS-139225)
    M J T2e 1950-1800 BCE
    F n/a (female) .. 1950-1800 BCE
    M J2a1b1 H+152 1527-1439 calBCE (3220±20 BP, OS-139223)
    M J H14a 1496-1302 calBCE (3135±30 BP, Poz-83433)
    M J1a2b H2a2a 1800-1650 BCE
    M J1a2b U2d 1800-1650 BCE
    M J2a J1d1a1 1623-1518 calBCE (3295±20 BP, PSUAMS-4852)
    M J1a2b U2e1b 1600-1500 BCE
    F n/a (female) U2e1b 1600-1500 BCE
    M n/a (<50000 autosomal SNPs) J1d 1600-1500 BCE
    M R U3b 1600-1500 BCE
    F n/a (female) U3b 1600-1500 BCE
    M E1b1b1b2a1 T2c1+146 1550-1450 BCE
    M E1b1b1b2a1a T2c1+146 1550-1450 BCE
    F n/a (female) N1b1a2 1900-1700 BCE
    M J1a2b N1b1 1900-1700 BCE
    M J1a2b T1a 1880-1700 calBCE (3470±20 BP, OS-139224)
    M n/a (<50000 autosomal SNPs) .. 1732-1451 calBCE (3300±55 BP, RTK-6767)
    M n/a (<50000 autosomal SNPs) .. 1700-1600 BCE
    M J1a2b T2b7a 1700-1500 BCE
    F n/a (female) T2 1688-1535 calBCE (3338±21 BP, RTK-7899)
    F n/a (female) U1a1a3 1650-1550 BCE
    M J .. 1638-1413 calBCE (3240±55 BP, RTK-6765)
    M J K1a18 1600-1500 BCE
    M n/a (<50000 autosomal SNPs) X 1600-1500 BCE
    F n/a (female) T1a 1600-1500 BCE
    F n/a (female) T2c1a 1600-1500 BCE
    F n/a (female) .. 1600-1500 BCE
    M R1b1a1a2 J2a2a2 1600-1500 BCE
    M J U3b 1600-1278 calBCE (3160±55 BP, RTK-6766)
    M T1a1a1b2 HV2a1 1550-1300 BCE
    M J1a2b H5'36 1509-1432 calBCE (3207±20 BP, RTK-7898)
    M J1 K1a 1107-923 calBCE (2845±25 BP, PSUAMS-2166)
    M T1a1a1b2b2b1a1a2 X2 1011-846 calBCE (2790±30 BP, Poz-83471)
    M J1a2b HV1b3 1800-1700 BCE
    M E1b1b1b2a1 R0a2 1800-1700 BCE
    F n/a (female) N1b1b 1450-1250 BCE
    M n/a (<50000 autosomal SNPs) n/a (<2x mtDNA coverage) 2500-2000 BCE
    F n/a (female) T1a 2500-2000 BCE
    M J T1a2 2500-2000 BCE
    F n/a (female) U1a1 2500-2000 BCE
    M n/a (<50000 autosomal SNPs) n/a (<2x mtDNA coverage) 2500-2000 BCE
    F n/a (female) n/a (<2x mtDNA coverage) 2500-2000 BCE
    M n/a (<50000 autosomal SNPs) .. 2500-2000 BCE
    M n/a (<50000 autosomal SNPs) H40a 2500-2000 BCE
    F n/a (female) J1c2i 2500-2000 BCE
    F n/a (female) .. 2500-2000 BCE
    M J .. 2500-2000 BCE
    M J2b N1b1a2 2500-2000 BCE
    F n/a (female) n/a (<2x mtDNA coverage) 2500-2000 BCE
    F n/a (female) U3a2a 1550-1150 BCE
    M J1a2b N1b1a 1550-1150 BCE
    M J1a2b N1b1a2 1412-1234 calBCE (3065±30 BP, PSUAMS-1992)
    F n/a (female) N1b1a 1409-1265 calBCE (3070±25 BP, PSUAMS-1991)
    M J1a2b U3b3 1550-1150 BCE
    M J1a2b U3b1a 1550-1150 BCE
    F n/a (female) H23 1550-1150 BCE
    F n/a (female) H1+152 1550-1150 BCE
    F n/a (female) U3a3 1550-1150 BCE
    F n/a (female) U3b3 1550-1150 BCE
    M J1a2b U3b 1550-1150 BCE
    F n/a (female) H 1550-1150 BCE
    M J1a2b T2c1a 1550-1150 BCE
    F n/a (female) T2c1a 1550-1150 BCE
    F n/a (female) U1a'c 1550-1150 BCE
    M J U4a 1550-1150 BCE
    F n/a (female) I5 1496-1396 calBCE (3155±20 BP, PSUAMS-3720)
    M J1a2b J1b2 1492-1303 calBCE (3130±25 BP, PSUAMS-1987)
    M J1a2b N2a1 1428-1293 calBCE (3100±25 BP, PSUAMS-1989)
    M J1a2b L0f2b 1424-1288 calBCE (3095±25 BP, PSUAMS-1990)
    M J1a2b T1a1 1384-1213 calBCE (3025±20 BP, PSUAMS-3719)

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  3. #12
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    Really quickly, as a first impression from the Southern Levant paper: They model Ashkenazi Jews as nearly 60% Middle Eastern (Megiddo_MLBA+Iran_Chl). We've discussed this topic before and a predominant opinion here is that it's probably markedly lower than that, closer to 40-30%.

    One major issue I'm seeing with the analysis here (which was done with an ADMIXTURE derived method and not something formal stat based?? Correct me if I'm wrong) is that the Tuscan control group comes out as 30-40% Middle Eastern. Do we really accept that? The authors should have seen right there that the analysis is very questionable because other published models for central Italians are nowhere close to that. My guess is they're lumping too many components together and their Middle East component is absorbing Aegean ancestry.

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  5. #13
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    Nice developments in methods:

    As an alternative, we developed a methodology we call LINADMIX, which relies on the output of ADMIXTURE (Alexander et al., 2009) and uses constrained least-squares to estimate the contribution of given source populations to a target population (see STAR Methods).
    Lol @ this, this is basically nMonte but with ADMIXTURE output as the coordinates, hahahaha...

    As a complementary approach, we developed a tool we call pseudo-haplotype ChromoPainter (PHCP), which is an adaptation of the haplotype-based method ChromoPainter (Lawson et al., 2012) to ancient genomes (see STAR Methods; Methods S1F). We first established that these methods provide meaningful estimates of ancestry in the context of this study by using them to re-compute the ancestry proportions that we were able to model with qpAdm. Both LINADMIX and PHCP (Table S3; Figure S3; Methods S1F) produce qualitatively similar estimates as qpAdm (Table S2).
    Very nice
    Quoted from this Forum:

    "Which superman haplogroup is the toughest - R1a or R1b? And which SNP mutation spoke Indo-European first? There's only one way for us to find out ... fight!"

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  7. #14
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    Suebi Kingdom Portugal 1143 Portugal 1485 Portugal Order of Christ Brazilian Empire Brazil
    Supplemental Information for Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus

    Table S9
    Assignment of Y Chromosome and Mitochondrial Haplogroups, Related to STAR Methods Sex determination and uniparental haplotypes.

    Individual ID Y-Haplogroup Terminal SNP Haplogroup
    ALA001 J1a2a1a2d2b2b2~ CTS11741/PF4847 X2
    ALA002 J1a2a1a2d2b2b2~ CTS11741/PF4847 N1a3a2
    ALA004 J2a1a1a2b2a1b~ PF4843/Z2324 X2e2a
    ALA008 H2 P96 H6a1b
    ALA009 J1c3
    ALA011 J2a1a1a2b2a PF5126/Z1847 X2d
    ALA013 H47
    ALA014 J2b1 M205 H14b
    ALA015 T1a1a CTS11451 K1a
    ALA016 I2
    ALA017 U1a1d
    ALA018 J1a2a1a2d2b2b2~ CTS11741/PF4847 HV1b3b
    ALA019 H2a3
    ALA020 H6a
    ALA023 N1b1a
    ALA024 U3b
    ALA025 H
    ALA026 J1a2a1a2d2b2b2~ CTS11741/PF4847 T1a
    ALA028 K1a17
    ALA029 T2
    ALA030 H5a1j
    ALA034 H13a2b2
    ALA035 J1a2a1a2d2b2b2~ CTS11741/PF4847 H20a
    ALA037 W3b
    ALA038 J1b3b1
    ALA039 K1a+150
    ALA084 L2 L595
    ALA095 J2b2~ CTS6812/Z2454 HV
    ALX002 G1 M342 K1a12a1a
    ART001 J2a1a1a2b2a1 PF5132 H14b3
    ART004 G M201/PF2957 H
    ART005 J1c
    ART009 K1a28
    ART010 U8b1a1
    ART011 J2a1a1a2b2a PF5126/Z1847 T2c1
    ART012 N1a1a1a
    ART014 G2a2b1 M406/PF3285 X2i+@225
    ART015 E1b1b1b2a1a1~ CTS4483/L795 U1a1d
    ART017 J2a1a1a2b2a PF5126/Z1847 T2c1+146
    ART018 J1a2b1~ Z1842 H14a+146
    ART019 J2a1a1a2b2a1 PF5132 K1a3
    ART020 J2a1a F4326/L27/PF5111/S396 J1c16
    ART022 J2a1a1a2b2a PF5126/Z1847 J1c
    ART023 J2a1a F4326/L27/PF5111/S396 U3b1
    ART024 G2a2b1 M406/PF3285 X2i+@225
    ART026 K1a8b
    ART027 J2a1a1a2b1b M319 T1
    ART032 H2 P96 N1b1a2
    ART038 R1b1a2 V1636 K1a17a
    ART039 I5a
    ART042 H2 P96 T1b
    CBT001 T2b
    CBT002 K1a3
    CBT003
    CBT004 HV1
    CBT005 G2a2b1 M406/PF3285 K1a
    CBT010 K1a
    CBT011 K1a
    CBT013 G2a2b1a FGC5089/Y2729 HV1
    CBT014 G2a2b1a FGC5089/Y2729 H5
    CBT015 G2a2b1a FGC5089/Y2729 U3a2
    CBT016 K1a3
    CBT017 K1a3
    CBT018 X2
    ETM001 J1a2a1a2 P58/Page8/PF4698
    ETM004
    ETM005 J1a2a1a2 P58/Page8/PF4698
    ETM006 U3b3
    ETM010 E1b1b1b2a1a1~ CTS4483/L795 J1b1b1
    ETM012 J1a2a1a2d2b~ CTS5266/PF4870/Z2321 T2c1+146
    ETM014 U3b2a1
    ETM016 U8b1a2b
    ETM018 G2a P287/PF3140 J1b1b1
    ETM023 H14a
    ETM026 T1a1 L162/Page21 K1a4
    IKI002 J1c16
    IKI009 J2a1
    IKI012
    IKI016 I5
    IKI017
    IKI024 J2a1 PF4610 U1b1
    IKI030
    IKI034 K1a17
    IKI036 J2b1c
    IKI037 G2a2b1 M406/PF3285
    IKI038 X1'2'3
    KRD001 H2 P96
    KRD002 G2a2 CTS4367/L1259/M3308/PF2970
    KRD003 J1a2a~ AM01306/CTS1797/PF4689/Z2356
    KRD004
    KRD005 CT -NA- low coverage
    KRD006
    MTT001 U7
    POT002 H13a2b
    TIT021 J2b M12
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  9. #15
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    Albanian
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    E-CTS1273*

    Albania Kosovo Montenegro
    Quote Originally Posted by RCO View Post
    Supplemental Information for Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus

    Table S9
    Assignment of Y Chromosome and Mitochondrial Haplogroups, Related to STAR Methods Sex determination and uniparental haplotypes.

    Individual ID Y-Haplogroup Terminal SNP Haplogroup
    ALA001 J1a2a1a2d2b2b2~ CTS11741/PF4847 X2
    ALA002 J1a2a1a2d2b2b2~ CTS11741/PF4847 N1a3a2
    ALA004 J2a1a1a2b2a1b~ PF4843/Z2324 X2e2a
    ALA008 H2 P96 H6a1b
    ALA009 J1c3
    ALA011 J2a1a1a2b2a PF5126/Z1847 X2d
    ALA013 H47
    ALA014 J2b1 M205 H14b
    ALA015 T1a1a CTS11451 K1a
    ALA016 I2
    ALA017 U1a1d
    ALA018 J1a2a1a2d2b2b2~ CTS11741/PF4847 HV1b3b
    ALA019 H2a3
    ALA020 H6a
    ALA023 N1b1a
    ALA024 U3b
    ALA025 H
    ALA026 J1a2a1a2d2b2b2~ CTS11741/PF4847 T1a
    ALA028 K1a17
    ALA029 T2
    ALA030 H5a1j
    ALA034 H13a2b2
    ALA035 J1a2a1a2d2b2b2~ CTS11741/PF4847 H20a
    ALA037 W3b
    ALA038 J1b3b1
    ALA039 K1a+150
    ALA084 L2 L595
    ALA095 J2b2~ CTS6812/Z2454 HV
    ALX002 G1 M342 K1a12a1a
    ART001 J2a1a1a2b2a1 PF5132 H14b3
    ART004 G M201/PF2957 H
    ART005 J1c
    ART009 K1a28
    ART010 U8b1a1
    ART011 J2a1a1a2b2a PF5126/Z1847 T2c1
    ART012 N1a1a1a
    ART014 G2a2b1 M406/PF3285 X2i+@225
    ART015 E1b1b1b2a1a1~ CTS4483/L795 U1a1d
    ART017 J2a1a1a2b2a PF5126/Z1847 T2c1+146
    ART018 J1a2b1~ Z1842 H14a+146
    ART019 J2a1a1a2b2a1 PF5132 K1a3
    ART020 J2a1a F4326/L27/PF5111/S396 J1c16
    ART022 J2a1a1a2b2a PF5126/Z1847 J1c
    ART023 J2a1a F4326/L27/PF5111/S396 U3b1
    ART024 G2a2b1 M406/PF3285 X2i+@225
    ART026 K1a8b
    ART027 J2a1a1a2b1b M319 T1
    ART032 H2 P96 N1b1a2
    ART038 R1b1a2 V1636 K1a17a
    ART039 I5a
    ART042 H2 P96 T1b
    CBT001 T2b
    CBT002 K1a3
    CBT003
    CBT004 HV1
    CBT005 G2a2b1 M406/PF3285 K1a
    CBT010 K1a
    CBT011 K1a
    CBT013 G2a2b1a FGC5089/Y2729 HV1
    CBT014 G2a2b1a FGC5089/Y2729 H5
    CBT015 G2a2b1a FGC5089/Y2729 U3a2
    CBT016 K1a3
    CBT017 K1a3
    CBT018 X2
    ETM001 J1a2a1a2 P58/Page8/PF4698
    ETM004
    ETM005 J1a2a1a2 P58/Page8/PF4698
    ETM006 U3b3
    ETM010 E1b1b1b2a1a1~ CTS4483/L795 J1b1b1
    ETM012 J1a2a1a2d2b~ CTS5266/PF4870/Z2321 T2c1+146
    ETM014 U3b2a1
    ETM016 U8b1a2b
    ETM018 G2a P287/PF3140 J1b1b1
    ETM023 H14a
    ETM026 T1a1 L162/Page21 K1a4
    IKI002 J1c16
    IKI009 J2a1
    IKI012
    IKI016 I5
    IKI017
    IKI024 J2a1 PF4610 U1b1
    IKI030
    IKI034 K1a17
    IKI036 J2b1c
    IKI037 G2a2b1 M406/PF3285
    IKI038 X1'2'3
    KRD001 H2 P96
    KRD002 G2a2 CTS4367/L1259/M3308/PF2970
    KRD003 J1a2a~ AM01306/CTS1797/PF4689/Z2356
    KRD004
    KRD005 CT -NA- low coverage
    KRD006
    MTT001 U7
    POT002 H13a2b
    TIT021 J2b M12
    Do you know where the J1 samples are from?

    Edit: Nevermind, I've found the supplementary information.
    Ydna: J1>P58>YSC234>ZS241

    Maternal Ydna: E-V13>CTS5856*

    Mtdna: T1a1l

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  11. #16
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    Not yet, trying to read the article
    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  13. #17
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    Awesome stuff!

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  15. #18
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    H1ao1

    Suebi Kingdom Portugal 1143 Portugal 1485 Portugal Order of Christ Brazilian Empire Brazil
    Alalakh
    Arslantepe
    Çamlıbel Tarlası
    Büyükkaya
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    J1 FGC5987 to FGC6175 (188 new SNPs)
    MDKAs before Colonial Brazil
    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  17. #19
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    R1b S21184, BY50830+
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    U4b1a2 - FGS
    Y-DNA (M)
    ?
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    I2

    Canada England Wales Netherlands France Cornwall
    Maybe not the best place to put it. The male haplogroups are not really what I was expecting

    A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

    ID Period Sex (genetic) Y Haplogroup MT Haplogroup
    SFI-56 Iron Age II female - U1a1a
    SFI-55 Iron Age II male J H2a
    SFI-43 Iron Age III female - T2c1+146
    SFI-50 Iron Age III female - U1a
    SFI-36 Iron Age III female - R0a1a
    SFI-42 Iron Age III male J1-M267 H2a
    SFI-45 Iron Age III male J-M304 T2a1b1
    SFI-34 Iron Age III male J1-M267 T1a2
    SFI-35 Iron Age III male I2a1b-M436 R0a1a
    SFI-39 Iron Age III male H2-P96 I1b
    SFI-44 Iron Age III male J1a2a1a2-P58 T2c1+146
    SFI-47 Iron Age III male G2a2a1a2-L91 W6
    SFI-20 Hellenistic female - H41
    SFI-5 Hellenistic male Q1b-M346 K1a5a
    SFI-12 Hellenistic male E1b1b1a1a2-V65 H14a
    SFI-24 Early Roman female - H8b
    SFI-33 Early Roman female - T1
    SFI-11 Early Roman male G2a2b-L30 N1b1
    SFI-15 Early Roman male G2a2b1a2-M3302 I1c1
    YDNA: R1b-BY50830 Stepney, London, UK George Wood b. 1782 English <-> Bavarian cluster
    maternal-gf YDNA: ?? Gurr, James ~1740, Smarden, Kent, England.
    maternal-gm YDNA: R1b-P311+ Beech, John Richard b. 1780, Lewes, England
    maternal-ggf YDNA R1b-U106 Thomas, Edward b 1854, Sittingbourne, Kent
    paternal-ggf YDNA: R1b-Z17901. Gould, John Somerset England 1800s.
    paternal-ggf YDNA: R1b-L48. Scott, William Hamilton Ireland(?) 1800s

    other:
    Welch: early 1800s E-M84 Kent, England.

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     lppt (05-30-2020),  Onur Dincer (05-28-2020),  Power77 (05-28-2020),  Prometheus (05-29-2020),  RCO (05-28-2020),  Ruderico (05-28-2020)

  19. #20
    Registered Users
    Posts
    786
    Sex
    Ethnicity
    Albanian
    Y-DNA (P)
    J-ZS241
    mtDNA (M)
    T1a1l
    Y-DNA (M)
    E-CTS1273*

    Albania Kosovo Montenegro
    Quote Originally Posted by RCO View Post
    Alalakh
    Arslantepe
    Çamlıbel Tarlası
    Büyükkaya
    Ebla
    İkiztepe
    Tell Kurdu
    TItriş-Höyük
    Polutepe
    Mentesh Tepe
    Alkhantepe
    The J1 samples from the ancient site of Alalakh in southern Turkey are almost entirely J-Z2317, with one other sample being J-Z2324. It's very interesting considering that the city was believed to have been founded by the Amorites during the Bronze Age.

    The J-Z1842 sample is from Arslantepe which is today located in the Malatya region of eastern Turkey. This may strengthen the belief that Z1842 clusters expanded from eastern Anatolia into the Caucasus sometime during the Bronze Age or a little earlier.

    The other J-P58 samples are from the ancient site of Ebla in western Syria. One of the samples has been identified as P58>Z2321 whilst the others were left as P58. Inscriptions from this site that date back to the Bronze Age have been discovered and linguists believe that the language spoken in the city was part of the Eastern Semitic branch, the language has been coined as Eblaite.

    The other J1 sample is from Tell Kurdu which is a part of the Amuq/Amik Valley and is J-L620. If I recall correctly, it's believed that this site had ties with the Ubaid culture.
    Ydna: J1>P58>YSC234>ZS241

    Maternal Ydna: E-V13>CTS5856*

    Mtdna: T1a1l

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