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Thread: Defining Y-SNP variation among the Flemish population (Western Europe) by full genome

  1. #1
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    Suebi Kingdom Portugal 1143 Portugal 1485 Portugal Order of Christ Brazilian Empire Brazil

    Defining Y-SNP variation among the Flemish population (Western Europe) by full genome

    Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing

    Maarten H.D.Larmuseau, Gilles P.P.L.Otten, Ronny Decorte, Philip Van Damme, MatthieuMoissede

    Highlights:
    Population-wide data of forensic relevant Y-SNPs are lacking.
    A representative sample of 270 full Y chromosomes from Flemish males is collected.
    Based on the full Y chromosomes, the Y-SNP variation in Flanders is characterised.
    Y-SNP variation is covered according to the latest minimal reference Y-tree.
    Recommendations for future population samples for Y-SNPs are discussed.

    Abstract
    Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the ‘jungle’ of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the ‘Minimal Reference Y-tree’, was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study.

    Keywords
    Next-generation sequencing, Full Y chromosome, Y-SNPs, AMY-tree, Belgium


    Haplogroup Sub-haplogroup Minimal Reference Y-tree N


    A A1-M31 1
    E1b1b E-V65 1
    E1b1b E-V13 7
    E1b1b E-M34*(xM84) 1
    G G-Z738*(xCTS4803) 2
    G G-CTS4803 4
    G G-PF3359 2
    I1 I-M253*(xZ131,DF29) 2
    I1 I-L22*(xP109,Z74) 5
    I1 I-P109 2
    I1 I-Z74*(L813) 1
    I1 I-Z59*(xZ60,Z2040) 5
    I1 I-Z60*(xZ2539,Z140) 1
    I1 I-Z2539 4
    I1 I-Z140 4
    I1 I-Z138 4
    I1 I-Z63*(xL1237) 3
    I1 I-L1237 1
    I2 I-CTS595*(xM26,L1286) 1
    I2 I-M26 2
    I2 I-L1286 1
    I2 I-L38 2
    I2 I-M284 2
    I2 I-L1229 4
    I2 I-L701 1
    I2 I-L801*(xCTS1977,CTS6433) 3
    I2 I-CTS1977 4
    I2 I-CTS6433*(xZ78) 2
    I2 I-Z78 1
    J1 J-FGC6064 1
    J1 J-PF7264 1
    J1 J-FGC11 1
    J2a J-Z438 5
    J2a J-Z6065 2
    J2a J-Z500*(xM92) 1
    J2a J-M92 1
    J2a J-L227 1
    J2a J-Z7671 1
    J2b J-L283 4
    Q Q-L245 1
    R1a R-Z283*(xM458,Z91,Z284) 1
    R1a R-Z92 1
    R1a R-CTS3402*(xL365) 1
    R1a R-L448 1
    R1a R-Z2122*(xM582) 1
    R1a R-M582 1
    R1a R-Z2125 2
    R1b R-L389*(xP297) 1
    R1b R-M269*(xL23) 1
    R1b R-Z2103 3
    R1b R-M412*(xL11) 1
    R1b R-L11*(xU106,P312) 6
    R1b R-U106*(xZ8057,Z18,Z381,FGC396) 2
    R1b R-Z18 5
    R1b R-Z156 21
    R1b R-Z301*(xU198,L48) 3
    R1b R-U198 2
    R1b R-L48*(xL47,Z9) 3
    R1b R-L47 5
    R1b R-Z9*(xZ30,Z331) 1
    R1b R-Z30 12
    R1b R-Z331 7
    R1b R-FGC396 1
    R1b R-P312*(xL238,DF19,DF99,DF27,U152,M529) 1
    R1b R-DF19 10
    R1b R-DF99 1
    R1b R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) 6
    R1b R-Z225 1
    R1b R-Z2552 1
    R1b R-Z2557 1
    R1b R-Z34609 3
    R1b R-Z209*(xZ216,CTS4065) 4
    R1b R-Z216*(xZ214) 1
    R1b R-CTS4065 1
    R1b R-Z198*(xZ262) 1
    R1b R-Z262 3
    R1b R-U152*(xL2,Z36,Z56,Z192) 4
    R1b R-L2*(xZ367,Z49) 7
    R1b R-Z34 1
    R1b R-Z49*(xZ142) 5
    R1b R-Z142 3
    R1b R-Z36 2
    R1b R-Z56*(xS47,Z144) 1
    R1b R-S47 3
    R1b R-Z144 1
    R1b R-Z192 3
    R1b R-M529*(xDF63,DF13) 2
    R1b R-DF63 1
    R1b R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) 11
    R1b R-DF21*(xP314,Z246,S3058) 1
    R1b R-DF41 2
    R1b R-DF49*(xDF23) 2
    R1b R-L513 3
    R1b R-Z251 3
    R1b R-Z2534 3
    L L-M357*(xM2398) 1
    T T-Z709 1
    T T-L131 2

    Total 270


    http://www.sciencedirect.com/science...7249731730220X
    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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  3. #2
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    J2a1 Z6065>Y7708>M47
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    H1j

    United States of America Lebanon Germany United Kingdom Belgium Switzerland
    I got all excited that DF19 was one of the largest P312 subclades for once, and then I realized they broke up the other ones.
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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     Webb (11-01-2017)

  5. #3
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    We can get more SNPs in the Supplementary data

    Sample Sub-haplogroup Minimal Reference Y-tree Sub-haplogroup AMY-tree version 2.2 Called Y-SNPs


    MMML001 E-M34*(xM84) E1b1b1c1* [E-M34*] 11738
    MMML002 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 10042
    MMML003 I-Z59*(xZ60,Z2040) I1a2a* [I-Z59*] 11148
    MMML004 R-L11*(xU106,P312) R1b1a2a1c1 [R-DF100] 9894
    MMML005 J-Z6065 J2a1* [J-L26*] 11029
    MMML006 J-Z438 J2a1a1c3 [J-Z387] 12022
    MMML007 R-CTS3402*(xL365) R1a1a1a2a1b1a* [R-CTS3402*] 10106
    MMML008 I-Z59*(xZ60,Z2040) I1a2a* [I-Z59*] 11283
    MMML009 G-PF3359 G2a3* [G-L190*] 11074
    MMML010 J-FGC6064 J1b1* [J-L620*] 10987
    MMML011 R-Z36 R1b1a2a1b2c [R-Z36] 9722
    MMML012 I-CTS1977 I2a2a1b2a* [I-L801*] 11002
    MMML013 R-Z301*(xU198,L48) R1b1a2a1a2b* [R-Z301*] 9750
    MMML014 R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) R1b1a2a1b1* [R-DF27*] 9542
    MMML015 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9735
    MMML016 R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) R1b1a2a1b1* [R-DF27*] 9498
    MMML017 E-V13 E1b1b1a2c [E-AMM1902] 11980
    MMML018 G-CTS4803 G2a3b2b [G-Z726] 11394
    MMML019 R-M529*(xDF63,DF13) R1b1a2a1b3* [R-M529*] 10100
    MMML020 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9575
    MMML021 R-Z142 R1b1a2a1b2b2 [R-Z49] 9219
    MMML022 R-Z142 R1b1a2a1b2b2 [R-Z49] 10034
    MMML023 I-L22*(xP109,Z74) I1a1c* [I-L22*] 11041
    MMML024 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 9740
    MMML025 R-Z30 R1b1a2a1a2b2b1a1* [R-Z8*] 10260
    MMML026 E-V13 E1b1b1a2c [E-AMM1902] 11759
    MMML027 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9327
    MMML028 E-V13 E1b1b1a2c [E-AMM1902] 11676
    MMML029 I-Z78 I2a2a1b2a2a [I-Z78] 11184
    MMML030 R-Z301*(xU198,L48) R1b1a2a1a2b3 [R-L259] 9765
    MMML031 R-Z49*(xZ142) R1b1a2a1b2b2 [R-Z49] 9917
    MMML032 R-Z18 R1b1a2a1a1* [R-Z18*] 10044
    MMML033 J-Z438 J2a1a1c3 [J-Z387] 10647
    MMML034 I-CTS6433*(xZ78) I2a2a1b2a2* [I-CTS6433*] 10809
    MMML035 R-Z2125 R1a1a1a2b1b1 [R-Z2123] 10054
    MMML036 R-DF41 R1b1a2a1b3a2 [R-DF41] 9667
    MMML037 R-S47 R1b1a2a1b2d2a [R-S47] 9477
    MMML038 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9715
    MMML039 I-Z138 I1a2b [I-Z138] 10822
    MMML040 G-Z738*(xCTS4803) G2a3b2a1 [G-L42] 11216
    MMML041 I-L801*(xCTS1977,CTS6433) I2a2a1b2a* [I-L801*] 11233
    MMML042 R-Z209*(xZ216,CTS4065) R1b1a2a1b1a1a* [R-Z209*] 9875
    MMML043 L-M357*(xM2398) L1d* [L-M357*] 11007
    MMML044 R-Z156 R1b1a2a1a2a* [R-Z156*] 10056
    MMML045 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9730
    MMML046 R-Z49*(xZ142) R1b1a2a1b2b2 [R-Z49] 10538
    MMML047 I-L1229 I2a2a1a* [I-L1229*] 11054
    MMML048 I-Z63*(xL1237) I1a3* [I-Z63*] 10866
    MMML049 R-Z18 R1b1a2a1a1a [R-L257] 9699
    MMML050 T-L131 T1b* [T-L131*] 11414
    MMML051 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9884
    MMML052 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9759
    MMML053 R-DF21*(xP314,Z246,S3058) R1b1a2a1b3a1* [R-DF21*] 11094
    MMML054 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9774
    MMML055 I-M253*(xZ131,DF29) I1c [I-AMM438] 11061
    MMML056 R-Z30 R1b1a2a1a2b2b* [R-Z9*] 9649
    MMML057 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9601
    MMML058 R-S47 R1b1a2a1b2d2a [R-S47] 9549
    MMML059 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 9783
    MMML060 R-Z9*(xZ30,Z331) R1b1a2a1a2b2b* [R-Z9*] 9699
    MMML061 J-FGC11 J1b1b3a1* [J-L858*] 13285
    MMML062 E-V13 E1b1b1a2c [E-AMM1902] 11718
    MMML063 I-L22*(xP109,Z74) I1a1c* [I-L22*] 11160
    MMML064 R-Z144 R1b1a2a1b2d1 [R-Z144] 9671
    MMML065 I-L22*(xP109,Z74) I1a1c* [I-L22*] 10372
    MMML066 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9556
    MMML067 R-Z30 R1b1a2a1a2b2b1a* [R-Z7*] 9413
    MMML068 R-S47 R1b1a2a1b2d2a [R-S47] 9958
    MMML069 R-Z251 R1b1a2a1b3a7 [R-Z251] 9718
    MMML070 I-M26 I2a1a1* [I-M26*] 11019
    MMML071 E-V65 E1b1b1a1b [E-V65] 11375
    MMML072 I-Z59*(xZ60,Z2040) I1a2a* [I-Z59*] 11182
    MMML073 R-Z251 R1b1a2a1b3a7 [R-Z251] 9767
    MMML074 R-L11*(xU106,P312) R1b1a2a1* [R-S127*] 9706
    MMML075 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9538
    MMML076 R-Z216*(xZ214) R1b1a2a1b1a1a1* [R-Z216*] 9610
    MMML077 R-Z2125 R1a1a1a2b1b1 [R-Z2123] 10402
    MMML078 I-Z140 I1a2a1b1 [I-AMM442] 10807
    MMML079 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9544
    MMML080 R-U152*(xL2,Z36,Z56,Z192) R1b1a2a1b2* [R-U152*] 10069
    MMML081 I-Z138 I1a2b [I-Z138] 10514
    MMML082 R-DF19 R1b1a2a1b5a [R-AMM1887] 9838
    MMML083 I-L701 I2a2a1b1* [I-L701*] 11045
    MMML084 T-L131 T1b* [T-L131*] 11124
    MMML085 R-DF49*(xDF23) R1b1a2a1b3a3* [R-DF49*] 9809
    MMML086 R-Z30 R1b1a2a1a2b2b1a* [R-Z7*] 9492
    MMML087 I-L1229 I2a2a1a* [I-L1229*] 11365
    MMML088 I-L1237 I1a3a [I-L1237] 10849
    MMML089 R-Z30 R1b1a2a1a2b2b1a1a* [R-Z1*] 9509
    MMML090 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 9577
    MMML091 R-Z225 R1b1a2a1b1* [R-DF27*] 9406
    MMML092 R-U152*(xL2,Z36,Z56,Z192) R1b1a2a1b2* [R-U152*] 9808
    MMML093 R-DF19 R1b1a2a1b5a [R-AMM1887] 9830
    MMML094 R-Z283*(xM458,Z91,Z284) R1a1a1a2a* [R-Z283*] 10534
    MMML095 I-L1229 I2a2a1a* [I-L1229*] 10988
    MMML096 R-M412*(xL11) R1b1a2a* [R-L23* ] 9819
    MMML097 I-Z60*(xZ2539,Z140) I1a2a1* [I-Z60*] 10671
    MMML098 R-L448 R1a1a1a2a1c1 [R-L448] 10423
    MMML099 R-Z30 R1b1a2a1a2b2b1a1a* [R-Z1*] 9503
    MMML100 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 10022
    MMML101 R-L47 R1b1a2a1a2b2a1a* [R-L46*] 9707
    MMML102 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9793
    MMML103 R-Z192 R1b1a2a1b2e [R-Z192] 9720
    MMML104 G-CTS4803 G2a3b2b [G-Z726] 11012
    MMML105 I-Z59*(xZ60,Z2040) I1a2a* [I-Z59*] 11171
    MMML106 R-L48*(xL47,Z9) R1b1a2a1a2b2* [R-L48*] 9694
    MMML107 R-Z2552 R1b1a2a1b1* [R-DF27*] 10378
    MMML108 R-Z156 R1b1a2a1a2a* [R-Z156*] 9710
    MMML109 R-Z30 R1b1a2a1a2b2b1* [R-Z2*] 9836
    MMML110 R-L389*(xP297) R1b1* [R-L389*] 10379
    MMML111 J-L283 J2b2d [J-L283*] 11065
    MMML112 I-L22*(xP109,Z74) I1a1c* [I-L22*] 11351
    MMML113 R-DF99 R1b1a2a1b6 [R-DF99] 10393
    MMML114 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9376
    MMML115 R-Z92 R1a1a1a2a1b2 [R-Z92] 10102
    MMML116 Q-L245 Q1b1a [Q-L245] 10340
    MMML117 R-Z301*(xU198,L48) R1b1a2a1a2b* [R-Z301*] 9636
    MMML118 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 9727
    MMML119 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 10272
    MMML120 R-Z18 R1b1a2a1a1* [R-Z18*] 9653
    MMML121 I-L801*(xCTS1977,CTS6433) I2a2a1b2a* [I-L801*] 11163
    MMML122 R-Z49*(xZ142) R1b1a2a1b2b2 [R-Z49] 9869
    MMML123 R-Z209*(xZ216,CTS4065) R1b1a2a1b1a1a* [R-Z209*] 9694
    MMML124 R-L47 R1b1a2a1a2b2a1a* [R-L46*] 9808
    MMML125 I-CTS6433*(xZ78) I2a2a1b2a2* [I-CTS6433*] 11267
    MMML126 I-P109 I1a1c1 [I-P109] 10936
    MMML127 R-L513 R1b1a2a1b3a5b [R-Z249] 9929
    MMML128 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9146
    MMML129 R-Z192 R1b1a2a1b2e [R-Z192] 9721
    MMML130 R-Z49*(xZ142) R1b1a2a1b2b2 [R-Z49] 9574
    MMML131 I-CTS1977 I2a2a1b2a* [I-L801*] 11168
    MMML132 I-L1229 I2a2a1a* [I-L1229*] 11382
    MMML133 R-Z262 R1b1a2a1b1a2a1 [R-Z262] 9607
    MMML134 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9696
    MMML135 I-L1286 I2a1a2 [I-L1286] 10805
    MMML136 R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) R1b1a2a1b1* [R-DF27*] 9634
    MMML137 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9488
    MMML138 R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) R1b1a2a1b1* [R-DF27*] 9906
    MMML139 A1-M31 A1* [A-M31*] 13832
    MMML140 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 10192
    MMML141 R-Z36 R1b1a2a1b2c [R-Z36] 9901
    MMML142 I-Z74*(L813) I1a1c4* [I-Z74*] 11354
    MMML143 R-Z192 R1b1a2a1b2e [R-Z192] 9671
    MMML144 I-M284 I2a2a1* [I-CTS616*] 11256
    MMML145 R-L513 R1b1a2a1b3a5b [R-Z249] 9720
    MMML146 R-Z30 R1b1a2a1a2b2b1* [R-Z2*] 10226
    MMML147 J-Z7671 J2a1b2* [J-M67*] 11097
    MMML148 R-DF19 R1b1a2a1b5a [R-AMM1887] 9487
    MMML149 R-Z251 R1b1a2a1b3a7 [R-Z251] 9671
    MMML150 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9841
    MMML151 R-L513 R1b1a2a1b3a5b [R-Z249] 10079
    MMML152 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9645
    MMML153 R-DF19 R1b1a2a1b5a [R-AMM1887] 9375
    MMML154 R-Z30 R1b1a2a1a2b2b1a* [R-Z7*] 9992
    MMML155 R-P312*(xL238,DF19,DF99,DF27,U152,M529) R1b1a2a1b* [R-P312*] 9639
    MMML156 R-Z2557 R1b1a2a1b1* [R-DF27*] 9748
    MMML157 T-Z709 T1a1a [T-P77] 11245
    MMML158 I-Z2539 I1a2a1a [I-Z2539] 11000
    MMML159 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 9561
    MMML160 I-Z138 I1a2b [I-Z138] 10847
    MMML161 G-CTS4803 G2a3b2b [G-Z726] 11272
    MMML162 R-DF19 R1b1a2a1b5a [R-AMM1887] 10567
    MMML163 R-U198 R1b1a2a1a2b1* [R-U198*] 9756
    MMML164 I-M284 I2a2a1* [I-CTS616*] 11381
    MMML165 R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) R1b1a2a1b1* [R-DF27*] 9853
    MMML166 I-L22*(xP109,Z74) I1a1c* [I-L22*] 10719
    MMML167 J-L227 J2a1b2b1 [J-L227] 10820
    MMML168 R-Z142 R1b1a2a1b2b2 [R-Z49] 9943
    MMML169 I-L801*(xCTS1977,CTS6433) I2a2a1b2a* [I-L801*] 11396
    MMML170 R-Z34609 R1b1a2a1b1* [R-DF27*] 9819
    MMML171 I-Z2539 I1a2a1a [I-Z2539] 10862
    MMML172 I-Z140 I1a2a1b* [I-Z140*] 11149
    MMML173 R-Z49*(xZ142) R1b1a2a1b2b2 [R-Z49] 9388
    MMML174 I-CTS595*(xM26,L1286) I2a1a* [I-CTS595*] 10861
    MMML175 J-Z6065 J2a1* [J-L26*] 11446
    MMML176 R-L2*(xZ367,Z49) R1b1a2a1b2b* [R-L2*] 9880
    MMML177 J-PF7264 J1b1c [J-PF7264] 11323
    MMML178 R-Z331 R1b1a2a1a2b2b* [R-Z9*] 9840
    MMML179 R-Z56*(xS47,Z144) R1b1a2a1b2d* [R-Z56*] 9760
    MMML180 R-U106*(xZ8057,Z18,Z381,FGC396) R1b1a2a1a* [R-U106*] 9609
    MMML181 R-Z262 R1b1a2a1b1a2a1 [R-Z262] 9607
    MMML182 R-Z34609 R1b1a2a1b1* [R-DF27*] 9759
    MMML183 R-Z198*(xZ262) R1b1a2a1b1a2a* [R-Z198*] 9639
    MMML184 R-M529*(xDF63,DF13) R1b1a2a1b3* [R-M529*] 9803
    MMML185 E-V13 E1b1b1a2c [E-AMM1902] 11800
    MMML186 R-U198 R1b1a2a1a2b1* [R-U198*] 9676
    MMML187 J-L283 J2b2d [J-L283*] 11000
    MMML188 R-Z30 R1b1a2a1a2b2b1* [R-Z2*] 9810
    MMML189 R-DF27*(xZ225,Z2552,Z2557,Z2560,Z31644,Z34609,Z195) R1b1a2a1b1* [R-DF27*] 10014
    MMML190 R-Z262 R1b1a2a1b1a2a1 [R-Z262] 9576
    MMML191 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9640
    MMML192 R-L48*(xL47,Z9) R1b1a2a1a2b2* [R-L48*] 9436
    MMML193 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9448
    MMML194 I-Z140 I1a2a1b1 [I-AMM442] 10851
    MMML195 R-Z30 R1b1a2a1a2b2b1a1b [R-Z11] 9928
    MMML196 R-Z2534 R1b1a2a1b3a8a [R-Z2534] 9537
    MMML197 I-Z63*(xL1237) I1a3* [I-Z63*] 11074
    MMML198 R-DF41 R1b1a2a1b3a2 [R-DF41] 9526
    MMML199 G-CTS4803 G2a3b2b [G-Z726] 10992
    MMML200 R-L47 R1b1a2a1a2b2a* [R-L47*] 9556
    MMML201 G-PF3359 G2a3* [G-L190*] 10876
    MMML202 R-Z30 R1b1a2a1a2b2b1a1a1 [R-Z6] 9179
    MMML203 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9948
    MMML204 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 10658
    MMML205 R-DF63 R1b1a2a1b3b [R-DF63] 9891
    MMML206 R-U106*(xZ8057,Z18,Z381,FGC396) R1b1a2a1a* [R-U106*] 10933
    MMML207 J-Z438 J2a1a1c3 [J-Z387] 10611
    MMML208 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9676
    MMML209 I-Z63*(xL1237) I1a3* [I-Z63*] 11039
    MMML210 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9807
    MMML211 R-L11*(xU106,P312) R1b1a2a1c1 [R-DF100] 9499
    MMML212 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9454
    MMML213 R-Z2103 R1b1a2a2c [R-AMM1800] 9602
    MMML214 R-M269*(xL23) R1b1a2* [R-M269*] 10660
    MMML215 I-Z2539 I1a2a1a [I-Z2539] 10704
    MMML216 J-M92 J2a1b2a1* [J-M92*] 10816
    MMML217 G-Z738*(xCTS4803) G2a3b2* [G-L497*] 10730
    MMML218 R-Z34609 R1b1a2a1b1* [R-DF27*] 9797
    MMML219 R-Z2103 R1b1a2a2a [R-AMM1783] 9878
    MMML220 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9710
    MMML221 R-L11*(xU106,P312) R1b1a2a1c1 [R-DF100] 9685
    MMML222 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 10090
    MMML223 R-FGC396 R1b1a2a1a* [R-U106*] 9633
    MMML224 I-Z140 I1a2a1b1 [I-AMM442] 10946
    MMML225 R-U152*(xL2,Z36,Z56,Z192) R1b1a2a1b2* [R-U152*] 9473
    MMML226 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9737
    MMML227 R-Z156 R1b1a2a1a2a1* [R-AM00485*] 9879
    MMML228 R-Z2103 R1b1a2a2c [R-AMM1800] 9750
    MMML229 R-U152*(xL2,Z36,Z56,Z192) R1b1a2a1b2* [R-U152*] 9843
    MMML230 R-DF19 R1b1a2a1b5a [R-AMM1887] 9246
    MMML231 I-Z138 I1a2b [I-Z138] 11145
    MMML232 R-M582 R1a1a1a2b1a1a [R-M582] 10047
    MMML233 R-L47 R1b1a2a1a2b2a* [R-L47*] 9689
    MMML234 R-L11*(xU106,P312) R1b1a2a1c1 [R-DF100] 9829
    MMML235 I-P109 I1a1c1 [I-P109] 10633
    MMML236 R-L11*(xU106,P312) R1b1a2a1c1 [R-DF100] 9311
    MMML237 R-DF19 R1b1a2a1b5a [R-AMM1887] 9699
    MMML238 R-DF19 R1b1a2a1b5a [R-AMM1887] 10027
    MMML239 E-V13 E1b1b1a2c [E-AMM1902] 11888
    MMML240 J-Z438 J2a1a1c3 [J-Z387] 10840
    MMML241 E-V13 E1b1b1a2c [E-AMM1902] 11790
    MMML242 R-Z2534 R1b1a2a1b3a8a [R-Z2534] 9535
    MMML243 I-Z2539 I1a2a1a [I-Z2539] 10959
    MMML244 R-Z18 R1b1a2a1a1* [R-Z18*] 9880
    MMML245 I-CTS1977 I2a2a1b2a* [I-L801*] 10719
    MMML246 J-L283 J2b2d [J-L283*] 10300
    MMML247 R-DF19 R1b1a2a1b5a [R-AMM1887] 10004
    MMML248 I-L38 I2a2b [I-L38] 11329
    MMML249 R-L48*(xL47,Z9) R1b1a2a1a2b2* [R-L48*] 9397
    MMML250 I-CTS1977 I2a2a1b2a* [I-L801*] 11237
    MMML251 J-Z438 J2a1a1c3 [J-Z387] 10720
    MMML252 R-Z18 R1b1a2a1a1a [R-L257] 9207
    MMML253 I-Z59*(xZ60,Z2040) I1a2a* [I-Z59*] 10585
    MMML254 J-Z500*(xM92) J2a1b2a2 [J-PF7394] 10880
    MMML255 I-L38 I2a2b [I-L38] 11254
    MMML256 R-Z209*(xZ216,CTS4065) R1b1a2a1b1a1a* [R-Z209*] 10024
    MMML257 I-M26 I2a1a1* [I-M26*] 10869
    MMML258 R-Z34 R1b1a2a1b2b1b1 [R-Z35] 9545
    MMML259 R-DF49*(xDF23) R1b1a2a1b3a3* [R-DF49*] 9959
    MMML260 I-M253*(xZ131,DF29) I1c [I-AMM438] 10695
    MMML261 R-DF19 R1b1a2a1b5a [R-AMM1887] 9793
    MMML262 R-DF13*(xDF21,DF41,DF49,L513,L1335,Z251,Z253,Z255,Y3 550) R1b1a2a1b3a* [R-Z2542*] 9645
    MMML263 R-CTS4065 R1b1a2a1b1a1a* [R-Z209*] 9497
    MMML264 R-Z156 R1b1a2a1a2a1a [R-AMM486] 9350
    MMML265 R-L47 R1b1a2a1a2b2a* [R-L47*] 10680
    MMML266 R-Z2122*(xM582) R1a1a1a2b1a* [R-Z2122*] 10474
    MMML267 R-Z2534 R1b1a2a1b3a8a [R-Z2534] 9838
    MMML268 R-Z209*(xZ216,CTS4065) R1b1a2a1b1a1a* [R-Z209*] 9926
    MMML269 J-L283 J2b2d [J-L283*] 11192
    MMML270 R-Z156 R1b1a2a1a2a* [R-Z156*] 9973
    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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  7. #4
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    Cool to see some J-Z387 in there...
    Paternal Line: Rhineland Germany (J2-Z387) - Confirmed
    Maternal Grandfather - (Škofja Loka, Slovenia) - R1a1 - Y2613 - Confirmed
    Paternal G-Grandfather - Germany - R1b - U106 - Confirmed
    Maternal G-Grandfather - Briano, Caserta, Italy - Possible R1b - L51

  8. #5
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    Is there any indication on the source of the 270 samples?

  9. #6
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    Only 22 out of 270 are DF27 (8.14%). The new data confirms old data that DF27 in Europe, outside of Iberia and France, is less than 15%.

    YFull has 23 kits from Belgium and only 2 are DF27 (8.69%). The low number of kits made the percentage unreliable but the study confirms the rate.

    That also makes it look like the 11 out of 57 (9.43%) in the Netherlands has a chance of being really close to the actual rate.

    I'm looking forward to a lot more studies, like this one, throughout Europe that do full Y-chromosome testing so we can see how well the rates compare to Busby et al. and YFull and so on and so the under tested regions can be properly represented.

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  11. #7
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    I think it would be really great to have this all collected into a %. Bedankt !

  12. #8
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    J2a1 Z6065>Y7708>M47
    mtDNA (P)
    H1j

    United States of America Lebanon Germany United Kingdom Belgium Switzerland

    I just wanted to point out how nice it is to have a study where the P312 results are actually broken out.

    So much better than seeing a pile of "P312+" or "other P312" study data with no further explanation and long delayed publication.
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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  14. #9
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    Unless I just missed it, I didn't see any P312>L238 in the results. This is in accord with its absence in the Dutch study I referred to above, where no L238 was found among 500 male samples there either. For those unfamiliar with L238, it is primarily found in Scandinavia, where it appears to be plentiful.

  15. #10
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    Quote Originally Posted by RCO View Post
    We can get more SNPs in the Supplementary data
    For anybody interested; the supplementary information also contains the variant calls for each sample and is free to use for studies.

    Quote Originally Posted by GoldenHind View Post
    Is there any indication on the source of the 270 samples?
    From the paper:
    Peripheral blood of 270 Flemish males was collected for wholegenome
    sequencing. The main aim of the sampling was to obtain a
    control WGS sample of the Flemish population within the international
    MinE-project that aims to understand the genetic basic of amytrophic
    lateral sclerosis (ALS). The selected candidates have no known kinship
    in paternal line to each other and they all have different patrilineal
    surnames. All four grandparents of each participant were born in
    Flanders. Based on the birth place of the paternal grandfather, the DNA
    donors were distributed equally among Flanders.
    Quote Originally Posted by Dewsloth View Post
    I just wanted to point out how nice it is to have a study where the P312 results are actually broken out.
    It is great to hear this. The tree that is used is the minimal Y tree, which is a concise tree with SNPs that are stable and selected to occur at levels of more than 2% in populations (down to regions of 100 km). Definitely not a complete tree, but it gives a great overview of the most common branches, it is not easily uprooted and it should be possible to very reliably assign samples to its branches.

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