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



RCO
10-31-2017, 04:48 PM
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/article/pii/S187249731730220X

Dewsloth
10-31-2017, 06:10 PM
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. :lol:

RCO
10-31-2017, 06:30 PM
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

Edward J
10-31-2017, 07:33 PM
Cool to see some J-Z387 in there...

GoldenHind
11-01-2017, 12:04 AM
Is there any indication on the source of the 270 samples?

ArmandoR1b
11-01-2017, 03:16 AM
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.

Govan
11-01-2017, 03:24 AM
I think it would be really great to have this all collected into a %. Bedankt !

Dewsloth
11-01-2017, 03:22 PM
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 :\:doh::noidea::pout::rolleyes: "P312+" or "other P312" study data with no further explanation and long delayed publication.

GoldenHind
11-01-2017, 09:45 PM
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.

gotten
11-05-2017, 09:08 PM
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.


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.



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 (http://www.phylotree.org/Y/tree/index.htm), 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.

Pylsteen
11-05-2017, 09:22 PM
Just to make sure, I assume that this is about modern day Flanders and not about historic Flanders? I ask because there is also the Brabant project.

gotten
11-05-2017, 10:07 PM
Just to make sure, I assume that this is about modern day Flanders and not about historic Flanders? I ask because there is also the Brabant project.

Yes, present day Flanders.

The Brabant DNA project (which has evolved into the Benelux DNA project) is based on a 38 STR marker test and a SNP confirmation of the major subhaplogroup. The publication mentioned in this topic is based on full genome sequencing of an unrelated sample set.

MitchellSince1893
11-05-2017, 10:20 PM
Double post

ADW_1981
11-05-2017, 10:21 PM
R1b R-Z209*(xZ216,CTS4065) 4

Out of only 209 samples this is fairly high.

DillonResearcher
11-05-2017, 10:22 PM
Is there a chance that we will get the raw data on the Big Tree? Presumably this would show which subclades the seven R-L2*(xZ367,Z49) testers (for example) fall into?

MitchellSince1893
11-05-2017, 10:26 PM
If my math is right 30 out 270 are U152 or 11.1%

This compares favorably with the Brabant study. 43 out of 395 samples, (10.9%) in West Flanders, East Flanders, and Flemish Brabant were U152,

And 30 out of 261 (11.4%) were U152 in East and West Flanders in the Brabant study.

EDIT: DUH...there is already another thread titled "30 U152 in the study "Defining Y-SNP variation among the Flemish population"

gotten
11-05-2017, 10:27 PM
R1b R-Z209*(xZ216,CTS4065) 4

Out of only 209 samples this is fairly high.

One of those is A7066+ and two are S19290+

icebreaker
11-06-2017, 01:46 AM
MMML214 R-M269*(xL23) R1b1a2* [R-M269*] 10660

I think he's a cool guy B)

icebreaker
11-06-2017, 01:48 AM
Will they (or anyone else) upload these results to yfull?

ADW_1981
11-06-2017, 04:02 AM
One of those is A7066+ and two are S19290+

Do we know the 4th?

gotten
11-06-2017, 11:36 AM
Do we know the 4th?

Some branch of Z295 (xZ216, xS25783, S21184-)

icebreaker
11-06-2017, 12:42 PM
One of those is A7066+ and two are S19290+

Can you see which SNPs are tested for MMML214 ? I'd like to know if he's PF7562*.

gotten
11-06-2017, 02:24 PM
Can you see which SNPs are tested for MMML214 ? I'd like to know if he's PF7562*.

That one is actually PF7563*

Dewsloth
11-06-2017, 04:25 PM
I guess I can't see the supplementary data.

I was hoping to find out the DF19 subclade breakdown (nearly all DF19s are either Z302 or DF88; both subclades go back to Beaker times), and if it tested the DF88s, how many were also Z17112.

gotten
11-06-2017, 09:03 PM
I was hoping to find out the DF19 subclade breakdown (nearly all DF19s are either Z302 or DF88; both subclades go back to Beaker times), and if it tested the DF88s, how many were also Z17112.

All 10 DF19 samples are DF88 and even Z17110, 9 of those are Z17112. Quite an amazing result.
I think a few of these SNPs probably classify to be added to the minimal Y-tree. They probably didn't occur enough in 1kG to be added to the initial minimal Y-tree (seems there is only 1 sample with DF88 [actually Y3095 as the location of DF88 is not sampled] in 1kG).

rafc
11-06-2017, 09:38 PM
It is great to hear this. The tree that is used is the minimal Y tree (http://www.phylotree.org/Y/tree/index.htm), 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.

I see they use V68 as a marker on their tree. Yfull has thrown it out completely now (it was lowest rated SNP before), Isogg has replaced it by L539 for a while now, and testing it often leads to wrong results. It doesn't seem they follow up on such evolutions. I'm aware of the problems with V68 since I belong to that clade, maybe it's an exception and all other SNP's are stable ones.

Dewsloth
11-06-2017, 09:59 PM
All 10 DF19 samples are DF88 and even Z17110, 9 of those are Z17112. Quite an amazing result.
I think a few of these SNPs probably classify to be added to the minimal Y-tree. They probably didn't occur enough in 1kG to be added to the initial minimal Y-tree (seems there is only 1 sample with DF88 [actually Y3095 as the location of DF88 is not sampled] in 1kG).

THANK YOU!

Z17110 would put them as all S4281, too. They're estimated to have formed around 1600BC. The next branching is S4268 at about 1300BC.

Z17112 seems to have formed right around the BA Collapse (~1200BC), and whoever that guy was, his sons and grandsons really made the most of it. They're a major branching-out point with numerous* surviving descendant lines from Germany to Ireland, some also in Scandinavia and a couple in Poland and Czech Rep.

Scroll down for Z17112 branches: https://www.familytreedna.com/public/R-DF19?iframe=yresults

I really appreciate your help. :)



*This is all, of course, relative. The total number of DF19s are not large compared to the big P312 subclades. We're not even a rounding-error for L21. :lol:

gotten
11-06-2017, 10:01 PM
I see they use V68 as a marker on their tree. Yfull has thrown it out completely now (it was lowest rated SNP before), Isogg has replaced it by L539 for a while now, and testing it often leads to wrong results. It doesn't seem they follow up on such evolutions. I'm aware of the problems with V68 since I belong to that clade, maybe it's an exception and all other SNP's are stable ones.

Some SNPs are included for continuity so it is easier to compare with older studies, but I agree that V68 probably deserves a phylogenetically equivalent SNP at the same position in the tree. I can forward your comment to one of the authors of that paper and see what their view is.

PhyloGeographer
11-14-2017, 02:08 PM
Great that a Flemish DNA study exists! Have they published the complete list of SNPs of each kit somewhere - or this testing is to be done in the future based on the results of the minimal Y-tree test? I see 4 J-L283, but the level of testing for this branch isn't too helpful for phylogeography as this SNP formed 10,000 ybp. At present YFull shows several dozens of branches much more recent than that, many of which very stable, much more recent than the R1a/R1b clades, and known for years. I hope those kits undergo advanced testing and the public is made aware of the results.

tchekitchek
11-14-2017, 02:20 PM
I wish there would be the same for Wallonia, i'd be curious

gotten
11-14-2017, 03:46 PM
Have they published the complete list of SNPs of each kit somewhere - or this testing is to be done in the future based on the results of the minimal Y-tree test?

Yes, the supplementary info on the publisher's website contains variants for each sample, so you can study each sample in more detail. No further testing should be necessary.

jcmax68
08-07-2019, 02:15 PM
I take in the x in front of the SNP means its negative for that marker? I am Z367>L20. If am reading right there are no Z367? This is interesting as Flemish/Norman origin has been one of my working hypotheses. But this suggests that hypothesis is unsupported, at least by this data set?