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Erik_Maher
11-19-2013, 03:39 AM
Haplogroup O-M117 is relatively common in East and Southeast Asia, especially among Sino-Tibetan populations. The key identifying STR feature is 388=10.

The O-M117 SNP is estimated to be about 19,000 years old. (See paper, "Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes".) This became apparent to me in the wide genetic distance between two O-M117 members of my extended family, whose 111-marker results came in over the weekend:

f288248, surname Martel, M133+ (~ M117)
12 24 15 10 13-18 11 10 12 12 14 28 19 9-9 11 11 24 15 20 34 12-13-14-15 9 11 19-21 15 15 18 18 33-36 11 11
11 9 16-16 8 12 7 8 11 11 12 17-17 14 11 12 12 15 7 13 23 17 13 12 11 15 11 11 12 11
34 15 8 15 12 24 27 20 11 12 12 13 11 9 12 11 12 11 13 30 12 14 22 15 9 10 23 16 21 13 22 17 12 16 25 12 20 21 11 13 18 9 12 11

f288250, surname Enriquez, M133+ (~ M117)
12 24 14 10 14-20 11 10 11 12 14 29 17 9-9 12 11 23 15 20 31 12-13-14-15 9 10 19-21 15 15 17 18 30-36 13 11
11 11 15-15 8 11 7 8 11 11 12 17-17 14 11 12 12 17 7 14 24 17 13 12 11 15 11 11 12 11
32 15 8 15 11 25 27 20 12 12 12 13 11 9 11 11 12 11 12 30 12 13 22 16 9 11 23 16 20 15 22 18 12 15 26 12 20 19 11 13 16 9 13 11

You might not think they were in the same haplogroup at first glance. Both trace direct male line descent to Cambanay, Danao City, Cebu, Philippines.

I ordered Big Y for Mr. Enriquez, for the benefit of science, and my plan is to ask Mr. Martel, sometime next year (when I scrounge up the dinero), if he would grant permission to do full Y sequencing with Full Genomes, to compare against Mr. Enriquez' Big Y and to further advance the science. I'm curious if anyone else in haplogroup O-M117 has ordered any advanced testing, or plans to do so? I am eager to chip in financially, if anyone has the desire but lacks the requisite moolah.

I'm curious about the state of research into haplogroup O in general; this is possibly the 2nd, 3rd, or 4th largest haplogroup after R, considering that about 20% of the world's population is Chinese, with estimates that 50 to 65% of East and SE Asians belong to haplogroup O. The O tree on ISOGG currently looks "sleepy", similar to how the haplogroup R tree looked in, say, 2007, before anyone even knew about L21. I have high hopes for new discoveries in O in the next year.

- E.M.

rock
11-19-2013, 05:04 PM
recent paper "Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers" estimated M117 5.4 K years,they named Oα for core downstream SNPs of M117.I think 5.4k years is for Oα.and they find M117 samples not belong to Oα.F438 is approximately in Oα1,two M117 in O3 project is F438+.almost half of the M117 they tested are Oα*,they probably will sequence these Oα* for subgroup better define,though the process is very slow.
below is their draft O tree posted on a forum half a year ago.use their F SNP,actual name and position not disclosed.I think the next O tree version will contain all source of new SNPs:F,CTS,etc,there are many branches not overlap.
O-M175, P191, P188
.O1-F75
..O1a-M119
...O1a1
....O1a1a-P203/M307
.....O1a1a1
......O1a1a1a
.......O1a1a1a1
.....O1a1a2
....O1a1b-M50, M110
..O1b-M268, P31
...O1b1
....O1b1a-PK4
.....O1b1a1-M95
......O1b1a1a
.......O1b1a1a1-M88
........O1b1a1a1a
.........O1b1a1a1a1
..........O1b1a1a1a1a
......O1b1a1b
.....O1b1a2
......O1b1a2a
.......O1b1a2a1-N9
....O1b1b
.....O1b1b1
......O1b1b1a
.....O1b1b2
...O1b2-M176/SRY465
....O1b2a-47z
....O1b2b-L682
.O2-M122, P198
..O2a-M324, P200, P199, P197
...O2a1-KL1/L465, KL2/L467, L127
....O2a1a
.....O2a1a1
......O2a1a1a
.......O2a1a1a1-M121
......O2a1a1b
.......O2a1a1b1
.....O2a1a2
....O2a1b-002611, KL3
.....O2a1b1
......Oγ-F11, F425/Page69
.......Oγ1
........Oγ1a
.........Oγ1a1
..........Oγ1a1a
...........Oγ1a1a1
............Oγ1a1a1a
.......Oγ2
.......Oγ3
.......Oγ4
........Oγ4a
.......Oγ5
.....O2a1b2
......O2a1b2a-F238
.......O2a1b2a1
........O2a1b2a1a
......O2a1b2b
...O2a2-P201
....O2a2a-M188
.....O2a2a1
......O2a2a1a-M159
......O2a2a1b-M7
.......O2a2a1b1-M209
........O2a2a1b1a
.........O2a2a1b1a1-M113
.....O2a2a2
......O2a2a2a
....O2a2b-P164
.....O2a2b1-M134
......O2a2b1a-M117
.......O2a2b1a1
........O2a2b1a1a
.........O2a2b1a1a1
..........Oα
...........Oα1
............Oα1a
.............Oα1a1
............Oα1b
.............Oα1b1
..............Oα1b1a
...........Oα2
...........Oα3
...........Oα4
......O2a2b1b-F444
.......O2a2b1b1
........Oβ
.........Oβ1
..........Oβ1a
.........Oβ2
..........Oβ2a
.........Oβ3
..........Oβ3a
...........Oβ3a1
.........Oβ4
.........Oβ5
.......O2a2b1b2
.....O2a2b2-N6
......O2a2b2a-N7
.......O2a2b2a1
......O2a2b2b
.......O2a2b2b1
..O2b
...O2b1
....O2b1a

Erik_Maher
11-23-2013, 09:29 AM
Thank you, Rock, for this updated information. I do have one question: I looked at the diagram in the scientific paper that you mentioned, and the 5.4 is pointing towards the right end of the line entitled M117. The left side of that line corresponds more with what looks like 15,000 ybp, and there is a note below the image, saying that the number in red is the coalescence time. I could be wrong, but I think 5.4K ybp refers to the coalescence time of O-M117, not the first appearance of the SNP in haplogroup O?

rock
12-01-2013, 07:17 AM
M117 should be a little older than 5.4k y.Another M117 22754 ordered big Y,he is F438+

rock
04-01-2015, 06:32 PM
288248 I saw his SNP is F3599+, F1870+. this branch likely related to Fujian Minnan or neighbouring area. You can compare with 1000 Genomes sample's SNPs

F3599+, F1870+
HG02122 KHV
HG01852 KHV
HGDP00822 Han

F3599+, F1870-
HGDP00821 Han
NA18623 CHB
HG00592 CHS

I find closest STR match is
2 steps at 23 STRs
Sq0173 Singapore [Han] difference at DYS385a and DYS458
2 steps at 26 STRs
24 Shanghai Han difference at DYS390 and DYS458 (PP23+DYS388, DYS449, DYS460)

288250's closest match at 23 STRs is 5 steps
Sq0134 Singapore [Han] difference at DYS389b, DYS456, DYS576, DYS481(2 steps)
Have you analyse the big Y result,what branch is 288250?

fjnj
10-12-2015, 05:16 PM
There are 5 1kgenome samples under F438. Four are positive for Y17728, one is negative. So Y17728 breaks the F438 into 2 subgroups. The four samples under Y17728 then break into 3 groups: CTS1304/F318; F1754; and CTS12122.

william0509
01-04-2016, 03:21 AM
I've got my result of Big Y last week, and confirmed as M117+,F8+, CTS5063+, and two of my friends are testing Big Y who are under the subclade of CTS1304 . Hopefully, we can see better picture of O2-M117.

Huntergatherer1066
01-04-2016, 04:16 AM
I've got my result of Big Y last week, and confirmed as M117+,F8+, CTS5063+, and two of my friends are testing Big Y who are under the subclade of CTS1304 . Hopefully, we can see better picture of O2-M117.

That's good to hear. Out of curiosity, how many novel variants are you showing in the BigY results page at FTDNA?

william0509
01-04-2016, 03:10 PM
It says 267 entries (filtered from 274 total entries).

fjnj
01-10-2016, 10:32 PM
Some of these snps are known snps, and the list used by FTDNA is not up to date. There are probably also wrong calls because they mixed up the ancestral vs the derived allele. If you plan to have the BAM file analyzed by Y-Full or someone else, you will have better ideas about exactly which are really useful novel snps.

william0509
01-12-2016, 04:09 PM
Some of these snps are known snps, and the list used by FTDNA is not up to date. There are probably also wrong calls because they mixed up the ancestral vs the derived allele. If you plan to have the BAM file analyzed by Y-Full or someone else, you will have better ideas about exactly which are really useful novel snps.
I've already submitted the BAM to ISOGG, and just waiting for the confirmation.

fjnj
01-12-2016, 07:55 PM
Great. Hopefully they will find some useful novel snps.

william0509
01-13-2016, 11:17 PM
The administrator Owen had updated the O tree in ISOGG.

• • • • • • • • • O2a2b1a1a4 Z25853
• • • • • • • • • • O2a2b1a1a4a CTS5492, CTS4789, CTS5063, CTS7418, CTS8299, CTS12655
• • • • • • • • • • • O2a2b1a1a4a1 CTS6987, Z25902, Z25903, Z25905

william0509
01-20-2016, 08:44 PM
Great. Hopefully they will find some useful novel snps.

Fjnj, I've only 12 private SNPs. I guess it means that the subclade CTS6987 is young compare to the other F5 subclades.

william0509
02-23-2016, 08:00 PM
15 private SNPs are calculated for the subclade M117-CTS5492.

william0509
02-23-2016, 08:03 PM
7948


7949

Update: This is my result of age of estimation. A Long bottleneck for this subclade, but the good news for me is that it is the first subclade which is under 2000 yrs in the Haplogroup O.

fjnj
02-23-2016, 08:10 PM
7948
7949

Update: This is my result of age of estimation. Long bottleneck for this subclade, but the good news for me is that it is the first subclade which under 2000 yrs in Haplogroup O.

That is surprisingly young. So we are looking at an MCA at the age of the three kingdoms :-).

lgmayka
02-24-2016, 03:08 AM
15 private SNPs are calculated for the subclade M117-CTS5492.
YFull has CTS5492 at the O-CTS5063 level (http://yfull.com/tree/O-CTS5063/), TMRCA 2500 ybp.

william0509
02-25-2016, 09:58 PM
YFull has CTS5492 at the O-CTS5063 level (http://yfull.com/tree/O-CTS5063/), TMRCA 2500 ybp.

I'm the one who tested (YF05177), You are right, it is equivalent to CTS5063. YF05177

william0509
09-27-2016, 03:35 PM
288248 I saw his SNP is F3599+, F1870+. this branch likely related to Fujian Minnan or neighbouring area. You can compare with 1000 Genomes sample's SNPs

F3599+, F1870+
HG02122 KHV
HG01852 KHV


HGDP00822 Han

F3599+, F1870-
HGDP00821 Han
NA18623 CHB
HG00592 CHS

I find closest STR match is
2 steps at 23 STRs
Sq0173 Singapore [Han] difference at DYS385a and DYS458
2 steps at 26 STRs
24 Shanghai Han difference at DYS390 and DYS458 (PP23+DYS388, DYS449, DYS460)

288250's closest match at 23 STRs is 5 steps
Sq0134 Singapore [Han] difference at DYS389b, DYS456, DYS576, DYS481(2 steps)
Have you analyse the big Y result,what branch is 288250?

Rock, can you tell me how did you find the STRs and haplogroup for HGDP00821 Han and HGDP00822 Han?

william0509
09-27-2016, 03:54 PM
https://yfull.com/tree/O-M1706/

Many subclades of M117-M1706 had been updated this year, and CTS1642 is the only subclade that still lags behind.

kukuku
01-09-2019, 03:47 PM
Hello,

Recently I got the DNA result from Geno2.0 and my haplogroup is O-F438.

I would be very glad if you teach me about this haplogroup.
I am from Japan.

Thank you!

palamede
01-09-2019, 10:54 PM
Hello,

Recently I got the DNA result from Geno2.0 and my haplogroup is O-F438.

I would be very glad if you teach me about this haplogroup.
I am from Japan.

Thank you!

Results in Yfull https://yfull.com/tree/O-F438/
But, maybe, more Chinese people than Japonese ones used Yfull service. altogether Yfull has got Japonese users for the specific Jomon haplogroup D1b-M64 (old D2) which represent 30-35% of Japonese men.

https://yfull.com/tree/D-M64.1/

Other old specific Japonese haplogroup C1a1 about 5 % of Japonese men. https://yfull.com/tree/C-M8/

For (probably) Yayoi haplogroups, we have O1b (old O2) and O2 (Old O3). O1b is frequent in Korea and Japan. O2 more frequent in China.

F438 is now designed by O2a2b1a1a1 by ISOGG classification
https://isogg.org/tree/ISOGG_HapgrpO.html

For wikipedia information
https://en.wikipedia.org/wiki/Haplogroup_O-M175

kukuku
01-12-2019, 04:23 PM
Thank you for your quick response and your information!

Do you know the suclades of Tibeto-Burman and Mongolian populations?

This is what I got in the internet:
O-M133 subgroups
(1) 第1支=姒(夏)、嬴(秦)、姫姓劉
O2a2b1a1a1 (F438)⇐日本・北京。(BC3000年)
O2a2b1a1a1a (Y17728)(BC1500年)
O2a2b1a1a1a1 (F155)⇐漢王室ー湖南・重慶・湖北(姓氏:劉24%、土家族地域) 。前300年頃起源。
-----------------------------------
(2) 第2支=姚・媯(舜)?
O2a2b1a1a2 (FGC23469/Z25852)
妫纳五姓:姚、虞、陈、胡、田。
-----------------------------------
(3) 第3支=陳( 舜系、媯姓)?
O2a2b1a1a3 (CTS7634)ー福建・広東・浙江(姓氏:陳25%)。
-----------------------------------
(4) 第4支=姬姓林氏?
O2a2b1a1a4 (Z25853)ー福建・広東・浙江(姓氏:林14%)
------------------------------------
(5) 第5支 周王室・姫姓王氏
O2a2b1a1a5 (CTS10738/M1707)
O2a2b1a1a5a (CTS9678)⇐周王室ー福建・雲南・河南(姓氏:王9%)

palamede
01-14-2019, 09:00 PM
I can't help you.

william0509
04-30-2020, 03:46 PM
Thank you for your quick response and your information!

Do you know the suclades of Tibeto-Burman and Mongolian populations?

This is what I got in the internet:
O-M133 subgroups
(1) 第1支=姒(夏)、嬴(秦)、姫姓劉
O2a2b1a1a1 (F438)⇐日本・北京。(BC3000年)
O2a2b1a1a1a (Y17728)(BC1500年)
O2a2b1a1a1a1 (F155)⇐漢王室ー湖南・重慶・湖北(姓氏:劉24%、土家族地域) 。前300年頃起源。
-----------------------------------
(2) 第2支=姚・媯(舜)?
O2a2b1a1a2 (FGC23469/Z25852)
妫纳五姓:姚、虞、陈、胡、田。
-----------------------------------
(3) 第3支=陳( 舜系、媯姓)?
O2a2b1a1a3 (CTS7634)ー福建・広東・浙江(姓氏:陳25%)。
-----------------------------------
(4) 第4支=姬姓林氏?
O2a2b1a1a4 (Z25853)ー福建・広東・浙江(姓氏:林14%)
------------------------------------
(5) 第5支 周王室・姫姓王氏
O2a2b1a1a5 (CTS10738/M1707)
O2a2b1a1a5a (CTS9678)⇐周王室ー福建・雲南・河南(姓氏:王9%)

Just saw your post today, F438 is one of major subclades of M133, we share the same common ancestor back to 6000-7000 years ago. Most likely related to the Yangshao Culture population in China.If you are interested on deep Y-DNA testing you should get Big Y from Familytree DNA or Y Elite Ancestry Test from FGC. https://www.fullgenomes.com/