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Old 2nd February 2016, 12:02 AM
ddxue ddxue is offline
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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+, 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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+, 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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+, 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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?
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  #2  
Old 2nd February 2016, 02:55 AM
Parameswara Parameswara is offline
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Smile

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.
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  #3  
Old 2nd February 2016, 02:59 AM
Parameswara Parameswara is offline
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Smile Haplogroup J

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  #4  
Old 2nd February 2016, 03:07 AM
Parameswara Parameswara is offline
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Smile Henan J2

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  #5  
Old 2nd February 2016, 06:48 AM
Kavellion Kavellion is offline
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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.
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  #6  
Old 2nd February 2016, 08:27 AM
Armando Armando is offline
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Quote:
Originally Posted by ddxue View Post
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.
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  #7  
Old 2nd February 2016, 02:29 PM
ddxue ddxue is offline
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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/

Last edited by ddxue; 2nd February 2016 at 02:42 PM.
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  #8  
Old 2nd February 2016, 05:27 PM
dna dna is offline
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@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

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Feel the bleeding edge of scientific research
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  #9  
Old 2nd February 2016, 09:09 PM
Armando Armando is offline
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Quote:
Originally Posted by dna View Post
@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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  #10  
Old 2nd February 2016, 10:52 PM
ddxue ddxue is offline
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After much help from Ray Banks, the administrator of the haplogroup C ISOGG tree, I'm sure I'm not haplogroup J. From the haplogroup J google doc, I searched every SNP that defines J-M304 (the top-level mutation). Many SNP's were not tested and were not in the csv file with my raw SNP results. However, many were in the file and I quickly came across many SNP's that I did not have the mutation for. Therefore there is no way I can be haplogroup J.

Then I looked at the haplogroup C google doc and looked up the SNP's that define C-M130. Nat Geo tested 13 of the SNP's that define C-M130 and I test positive for the mutation on 12 of them. I'm unclear as to why I do not have the F1367 C->G mutation since Ray told me if I am haplogroup C I should have ALL of the M130 mutations that were tested for.

Right now I'm operating the assumption I'm haplogroup C. It looks like I'm in C2/C-M217. I'm currently trying to figure out what specific subclade I belong to (if it's even possible with the level of testing Nat Geo did).
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