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-   -   Nat Geo 2.0 Next Gen Y-DNA haplogroup prediction seems wrong (http://forums.familytreedna.com/showthread.php?t=39171)

ddxue 2nd February 2016 12:02 AM

Nat Geo 2.0 Next Gen Y-DNA haplogroup prediction seems wrong
 
My Y-DNA haplogroup came out as J-CTS2906, which seems to be also known as J2-M92 or J2a1b1. The problem is... I'm Han Chinese from Eastern China and I couldn't find any studies that found J2 in Han Chinese (or J1 for that matter). My autosomal breakdown on gedmatch using the various admixture tools is ~70-90% East Asian and ~10-30% Siberian. The gedmatch oracle consistently lists Northern Han Chinese and various Tibeto-Burman speaking minorities as the populations with the shortest genetic distance from me.

The FTDNA transfer results are a mess. It only lists SNP's I tested positive for, not the ones I tested negative for. I used the ISOGG tree chrome extension to view them and there are positive matches in many haplogroups. On a quick glance it seems I have the most in haplogroup I1 and J2 (isn't I1 Scandinavian?). Here are my FTDNA Y-DNA SNP transfer results:

Quote:

A531+, A91+, BY1142+, BY1357+, BY136_FGC19909_Z18229+, BY1551+, BY1586+, BY1734+, BY20+, BY2243+, BY2391+, BY2462+, BY2510+, BY65_Z18181+, BY763+, BY876+, CTS10031+, CTS10147+, CTS10188+, CTS10229+, CTS103+, CTS10300+, CTS10428+, CTS10433+, CTS10442+, CTS10448+, CTS10534+, CTS10552+, CTS10572+, CTS10615+, CTS10648+, CTS1066+, CTS10720+, CTS10723+, CTS10745+, CTS10761+, CTS10821+, CTS1083+, CTS10847+, CTS10923+, CTS11012+, CTS11041+, CTS11071+, CTS11088+, CTS11126+, CTS11148+, CTS11149+, CTS11190+, CTS11261+, CTS11354+, CTS114+, CTS1141+, CTS11436+, CTS11441+, CTS1148+, CTS11503+, CTS11522+, CTS11530+, CTS11544+, CTS1164+, CTS11651+, CTS1171+, CTS11710+, CTS11726+, CTS11731+, CTS11759+, CTS11816+, CTS11907+, CTS11949+, CTS11970+, CTS12023+, CTS12058+, CTS1216+, CTS12449+, CTS12450+, CTS12472+, CTS12578+, CTS12652+, CTS1276+, CTS12856+, CTS12879+, CTS12931+, CTS12933+, CTS12934+, CTS12948+, CTS12976+, CTS1340+, CTS1353+, CTS1413+, CTS1436+, CTS1633+, CTS1710+, CTS1758+, CTS1806+, CTS1831+, CTS1854+, CTS191+, CTS2+, CTS202+, CTS2067+, CTS210+, CTS2105+, CTS2134+, CTS2230+, CTS2275+, CTS2284+, CTS2289+, CTS2413+, CTS244+, CTS2488+, CTS2491+, CTS2515+, CTS2550+, CTS2670+, CTS2709+, CTS278+, CTS280+, CTS2800+, CTS2848+, CTS2906+, CTS2947+, CTS305+, CTS316+, CTS3202+, CTS3221+, CTS3268+, CTS3366+, CTS3403+, CTS3430+, CTS3466+, CTS347+, CTS3519+, CTS352+, CTS3536+, CTS3543+, CTS3654+, CTS3658+, CTS3663+, CTS3700+, CTS3802+, CTS3837+, CTS3868+, CTS3902+, CTS3996+, CTS4053+, CTS4086+, CTS4089+, CTS4094+, CTS4137+, CTS4178+, CTS4209+, CTS4235+, CTS4326+, CTS4406+, CTS4443+, CTS4463+, CTS4608+, CTS4643+, CTS4715+, CTS4781+, CTS4784+, CTS4793+, CTS4853+, CTS4984+, CTS5052+, CTS5152+, CTS5156+, CTS5254+, CTS5304+, CTS5334+, CTS5359+, CTS5370+, CTS5383+, CTS5410+, CTS5522+, CTS5649+, CTS5690+, CTS58+, CTS5828+, CTS585+, CTS5860+, CTS5874+, CTS5933+, CTS5939+, CTS597+, CTS5998+, CTS6062+, CTS6063+, CTS6090+, CTS6117+, CTS6135+, CTS6265+, CTS6266+, CTS6285+, CTS6352+, CTS636+, CTS6365+, CTS6378+, CTS6394+, CTS6403+, CTS6438+, CTS6447+, CTS6449+, CTS6468+, CTS6481+, CTS6492+, CTS6506+, CTS656+, CTS6613+, CTS6631+, CTS6677+, CTS6704+, CTS6848+, CTS6865+, CTS687+, CTS6916+, CTS6918+, CTS6967+, CTS7022+, CTS7101+, CTS7120+, CTS7147+, CTS7167+, CTS7186+, CTS7193+, CTS7227+, CTS7266+, CTS7275+, CTS7285+, CTS7299+, CTS730+, CTS7317+, CTS7335+, CTS736+, CTS7451+, CTS7598+, CTS7601+, CTS7611+, CTS7626+, CTS7642+, CTS7803+, CTS7810+, CTS7925+, CTS7929+, CTS7942+, CTS8027+, CTS8126+, CTS8203+, CTS8216+, CTS8300+, CTS8301+, CTS8440+, CTS8492+, CTS8506+, CTS8521+, CTS860+, CTS8645+, CTS8723+, CTS8815+, CTS8889+, CTS9056+, CTS914+, CTS9154+, CTS9240+, CTS9322+, CTS9325+, CTS9335+, CTS9387+, CTS9471+, CTS9518+, CTS9525+, CTS9539+, CTS9558+, CTS9677+, CTS97+, CTS9716+, CTS9757+, CTS9894+, CTS9900+, CTS9925+, CTS9975+, CTS9976+, DF109_FGC4101_S660_Y2845+, F1007+, F1012+, F1013+, F1024+, F1030+, F1055+, F1096+, F1108+, F1127+, F1159+, F1191+, F1207+, F1217+, F1221+, F1241+, F1291+, F1302+, F1307+, F1329+, F1367+, F1382+, F1405+, F1412+, F142+, F1420+, F1442+, F1474+, F1476+, F1490+, F1539+, F1540+, F1564+, F1567+, F1574+, F1594+, F1597+, F1677+, F1703+, F1704+, F1712+, F1714+, F1727+, F1753+, F1767+, F1796+, F1804+, F1813+, F1848+, F1874+, F188+, F1899+, F1905+, F1924+, F1946+, F1956+, F2018+, F202+, F2028+, F2048+, F2067+, F2132+, F2142+, F2149+, F2155+, F2165+, F2208+, F2211+, F2224+, F2236+, F2282+, F2304+, F2327+, F2332+, F2343+, F2370+, F2371+, F2379+, F240+, F2402+, F2434+, F2480+, F2512+, F2516+, F2546+, F2558+, F2587+, F2600+, F2620+, F2654+, F2673+, F2688+, F2710+, F2718+, F2724+, F2742+, F2753+, F2761+, F2767+, F2792+, F2808+, F2837+, F2840+, F2850+, F2869+, F287+, F2873+, F2924+, F2947+, F2960+, F2961+, F2985+, F299+, F2990+, F2992+, F3032+, F3043+, F3048+, F3056+, F3057+, F3082+, F3108+, F3111+, F3122+, F3136+, F3143+, F3195_PF1806+, F3270+, F3311+, F3324+, F3335+, F3368_PF3566+, F3395+, F3402_PF3567+, F3422+, F3444+, F3451+, F3491+, F3518+, F3556+, F3582+, F3595+, F3625+, F3632+, F3643+, F3670+, F3692+, F3697+, F371+, F3735+, F3739+, F3744+, F3789+, F3806+, F386+, F3869+, F3892+, F3907+, F3949+, F3956+, F3994+, F3998+, F4003+, F4010+, F4111+, F4176+, F4188_PF3539+, F4244+, F4251+, F4257+, F4282+, F4338+, F492+, F526+, F557+, F565+, F61+, F646+, F716+, F719+, F736+, F741+, F743+, F767+, F771+, F819+, F836+, F837+, F845+, F862+, F896+, F910+, F995+, FGC11678+, FGC11897_YP327+, FGC16179_Y6682_Z4084+, FGC16192_Y4462_Z16217+, FGC16362_Z18162+, FGC16466_Z16739+, FGC16683_Y5619+, FGC1721_Y5322+, FGC20866_ZS2566+, FGC20874_ZS2572+, FGC24646+, FGC28639_YP556+, FGC29572+, FGC3718_Y6369+, FGC6948_Y2703+, IMS-JST029149+, K257+, K386+, L104+, L1093+, L1186+, L1247+, L132+, L1324+, L167+, L183+, L187+, L213+, L245+, L253+, L254+, L294+, L325+, L387+, L440+, L442+, L453+, L459+, L464_1+, L484+, L492+, L496+, L498+, L503+, L533+, L542+, L551+, L552+, L556+, L557+, L625+, L636+, L665+, L72+, L782+, L784+, L817+, L840+, L99+, M102+, M116+, M129+, M139+, M171+, M251+, M262+, M275+, M288+, M367+, M39+, M94+, M9574+, M9588+, MC14+, N4+, NGC5+, P102+, P108+, P117+, P118+, P129+, P135+, P136+, P141+, P145+, P148+, P151+, P159+, P160+, P166+, P181+, P194+, P202+, P268+, P269+, P289+, P305+, P40+, P52+, P59+, P77+, P80+, P84+, P91+, PAGES00010+, PAGES00048+, PAGES00081+, PAGES00101+, PAGES00105+, PF1015+, PF1026+, PF1031+, PF1085+, PF1097+, PF1141+, PF1147+, PF1152+, PF1164+, PF1169+, PF121+, PF1226+, PF1232+, PF1252+, PF1269+, PF1270+, PF1279+, PF1283+, PF133+, PF1368+, PF147+, PF156+, PF1562+, PF1577+, PF1587+, PF22+, PF228+, PF2334+, PF2436+, PF2438+, PF2466+, PF2481+, PF2495+, PF2579+, PF2593+, PF2611+, PF2624+, PF2635+, PF2643+, PF2745+, PF276+, PF288+, PF293+, PF302+, PF3051+, PF3086+, PF3107+, PF3188+, PF3220+, PF3248+, PF328+, PF3298+, PF331+, PF3320+, PF3561+, PF3823+, PF3890+, PF3964+, PF3986+, PF40+, PF4105+, PF4193+, PF4246+, PF4533+, PF4573+, PF4576+, PF4589+, PF4592+, PF4647+, PF4653+, PF4720+, PF4876+, PF4879+, PF4888+, PF4957+, PF5014+, PF5104+, PF5122+, PF5123+, PF5125+, PF5147+, PF5169+, PF535+, PF5381+, PF5436+, PF5517+, PF5735+, PF5744+, PF5784+, PF5787+, PF5792+, PF5815+, PF5819+, PF601+, PF6063+, PF625+, PF6275+, PF6286+, PF6300+, PF6314+, PF6369+, PF644+, PF6673+, PF668+, PF671+, PF679+, PF6864+, PF6865+, PF6914+, PF698+, PF700+, PF7067+, PF7328+, PF7341+, PF7374+, PF7434+, PF747+, PF7527+, PF7552+, PF7557+, PF791+, PF794+, PF806+, PF829+, PF888+, PF907+, PF926+, PF93+, PF946+, PF95+, PF966+, PF968+, PF971+, PF997+, PK1+, PR805+, rs35407486+, rs9785743+, rs9786774+, S3207+, s5153+, S7123+, SK1247_Y4915+, SK1410_Y5528_Z20169+, V174+, V183_F1743+, V186+, V187+, V199+, V205+, V21+, V216+, V221+, V227+, V232_F1029+, V250+, V29+, V32+, V59+, V78+, V79+, V8+, V90+, V94+, Y1038+, Y1049+, Y1083+, Y1113+, Y1122+, Y2799_Z7648+, Y32+, Y4482_Z12144+, Y4486_Z4016+, Y4488_Z4051+, Y4493_Z4133+, Y4496_Z7169+, Y4864_Z16422+, Y5272+, Y5305_Z16500+, Y5759_Z16420+, Y6181+, Y6674_Z3968+, Y6691+, Y6694_Z4141+, Y763+, YP321+, YSC0000081+, YSC0000150+, YSC0000216+, YSC0000292+, YSC0001071+, Z11180+, Z1149+, Z12163+, Z12214+, Z130+, Z133+, Z138+, Z1435+, Z1455+, Z1456+, Z1459+, Z1476+, Z148+, Z1483+, Z1504+, Z1518+, Z1589+, Z1593+, Z1616+, Z18133+, Z18140+, Z1817+, Z18186+, Z1835+, Z187+, Z189+, Z1975+, Z2069+, Z2082+, Z2094+, Z213+, Z2396+, Z269+, Z270+, Z274+, Z284+, Z2970+, Z2976+, Z2983+, Z30+, Z306+, Z315+, Z319+, Z347+, Z350+, Z3723+, Z39+, Z3965+, Z3999+, Z4059+, Z4073+, Z4083+, Z4090+, Z4091+, Z4095+, Z4145+, Z4151+, Z477+, Z515+, Z531+, Z544+, Z60+, Z625+, Z638+, Z72+, Z75+, Z767+, Z966+, ZS1727+, ZS251+
Is there any way to get to the bottom of this without paying for additional Y-DNA testing?

Parameswara 2nd February 2016 02:55 AM

Y-DNA has nothing to do with autosomal. You could be 100% east asian with any Y-DNA haplogroup. If you have non-chinese patrilineal ancestor, within 8-10 generation his non-chinese autosomal could be diluted.

Parameswara 2nd February 2016 02:59 AM

Haplogroup J
 
https://scontent-sin1-1.xx.fbcdn.net...c1&oe=57361E62

Parameswara 2nd February 2016 03:07 AM

Henan J2
 
https://scontent-sin1-1.xx.fbcdn.net...64&oe=5744D0B8

Kavellion 2nd February 2016 06:48 AM

J2 most commonly associated as jewish or arab, middle eastern anyway. I would think that a result like this for someone who was in another population would be pretty neat for the tester. All sorts of people were going to China to trade in the past.

Armando 2nd February 2016 08:27 AM

Quote:

Originally Posted by ddxue (Post 422004)
My Y-DNA haplogroup came out as J-CTS2906, which seems to be also known as J2-M92 or J2a1b1. The problem is... I'm Han Chinese from Eastern China and I couldn't find any studies that found J2 in Han Chinese (or J1 for that matter). My autosomal breakdown on gedmatch using the various admixture tools is ~70-90% East Asian and ~10-30% Siberian. The gedmatch oracle consistently lists Northern Han Chinese and various Tibeto-Burman speaking minorities as the populations with the shortest genetic distance from me.

The FTDNA transfer results are a mess. It only lists SNP's I tested positive for, not the ones I tested negative for. I used the ISOGG tree chrome extension to view them and there are positive matches in many haplogroups. On a quick glance it seems I have the most in haplogroup I1 and J2 (isn't I1 Scandinavian?). Here are my FTDNA Y-DNA SNP transfer results:



Is there any way to get to the bottom of this without paying for additional Y-DNA testing?

Geno 2.0 NextGen is a real mess which is why you are seeing a mess at FTDNA. You are in haplogroup C. You match on almost all of your SNPs with the person whose father tested positive for C-M217 at 23andme and also has the STR haplotype of C-M217 at FTDNA.

ddxue 2nd February 2016 02:29 PM

One of the project Haplogroup C administrators responded to me and gave me a document with SNP's I should check for. I test positive for a lot of the general C-M130 SNP's in that document. These were in the ISOGG 2016 tree for haplogroup C but weren't in the 2015 tree so they weren't highlighted for me (bug with Chrome extension maybe?).

I have positive SNP's in a few different subclades of C:

C1a1 - CTS7285
C1b1a2b - F736, F741
C2e1a - F3949
C2e1a1 - F3739
C2e1b1a - F3735, F3806
C2e2 - F845, CTS6704, CTS10923, CTS12931

Unfortunately, I also test positive for a lot of the general J-M304 SNP's (seems like the ISOGG 2016 tree for haplogroup J is the same as the 2015 tree). These are the subclades of haplogroup J I have positive SNP's in:

J1a2b3 - L817
J2a1b1a - L556
J2a1h2c - L254
J2b - M102

I also test positive for a lot of SNP's in haplogroup I. This is just a huge mess.

Haplogroup C: https://docs.google.com/document/d/1...Pna4uvBELWRwU/

Haplogroup J: https://docs.google.com/document/d/1...fxNWs_9_UNPlw/

dna 2nd February 2016 05:27 PM

@ddxue, it is not a mess.

It is just that the same SNP can occur at different branches. We knew that about some of them, but with Big Y (and other research) more such situations are being discovered.

Mr W

P.S.
Feel the bleeding edge of scientific research :)

Armando 2nd February 2016 09:06 PM

Quote:

Originally Posted by ddxue (Post 422024)
One of the project Haplogroup C administrators responded to me and gave me a document with SNP's I should check for. I test positive for a lot of the general C-M130 SNP's in that document. These were in the ISOGG 2016 tree for haplogroup C but weren't in the 2015 tree so they weren't highlighted for me (bug with Chrome extension maybe?).

I have positive SNP's in a few different subclades of C:

C1a1 - CTS7285
C1b1a2b - F736, F741
C2e1a - F3949
C2e1a1 - F3739
C2e1b1a - F3735, F3806
C2e2 - F845, CTS6704, CTS10923, CTS12931

Unfortunately, I also test positive for a lot of the general J-M304 SNP's (seems like the ISOGG 2016 tree for haplogroup J is the same as the 2015 tree). These are the subclades of haplogroup J I have positive SNP's in:

J1a2b3 - L817
J2a1b1a - L556
J2a1h2c - L254
J2b - M102

I also test positive for a lot of SNP's in haplogroup I. This is just a huge mess.

Haplogroup C: https://docs.google.com/document/d/1...Pna4uvBELWRwU/

Haplogroup J: https://docs.google.com/document/d/1...fxNWs_9_UNPlw/

This goes to show how bad of a job Geno 2.0 NextGen is doing for some people.

Armando 2nd February 2016 09:09 PM

Quote:

Originally Posted by dna (Post 422031)
@ddxue, it is not a mess.

It is just that the same SNP can occur at different branches. We knew that about some of them, but with Big Y (and other research) more such situations are being discovered.

Mr W

P.S.
Feel the bleeding edge of scientific research :)

It's a mess because Geno 2.0 NextGen put his terminal SNP as J-CTS2906. He is the 2nd haplogroup C person to have this problem. BigY testing doesn't put people in the wrong haplogroup.


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