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ataneojr1
01-24-2018, 12:46 AM
It is always missing from any list, lol???

lgmayka
01-24-2018, 10:36 AM
It is always missing from any list, lol???
The FTDNA employee (an assistant manager) wrote that "I don't think I have ever seen a P in the database." He promised to honor the discount price of the Big Y if, indeed, your Y-DNA12 confirms you to belong to Px(Q,R).

I must point out, of course, that this is a multi-step procedure:
1) Your Y-DNA12 results arrive. Since FTDNA has never seen a P*, your haplogroup is left unpredicted.
2) FTDNA runs a Y-Hap-Backbone test. If done correctly, it should return Px(Q,R).
3) We crowdfund your Big Y.

I have a couple worries:
1) Your Y-DNA12 (actually 14 markers) may appear to match some other haplogroup such as R1b, such that FTDNA assigns you an incorrect haplogroup prediction. This is unlikely but possible. If it happens, we will consider our options.
2) Your Y-Hap-Backbone test may falsely return an R1b-M269 result. This is unlikely, but has happened in the past. :( If it happens, we will consider our options.

On the other hand...It's too early to worry about such things! Let's just wait calmly for your Y-DNA12 results.

ataneojr1
01-25-2018, 01:15 AM
Thank You.....I am not worried just find it funny that when it comes to list of Ydna in almost all Forums...P is always missing....

lgmayka
01-30-2018, 04:11 PM
Thank You.....I am not worried just find it funny that when it comes to list of Ydna in almost all Forums...P is always missing....
You received your 12 markers. As expected, FTDNA is unable to predict your haplogroup. However...

You have one exact 12-marker match, who tested M89+ and hence is classified as F-M89. The question is whether he was ever tested for M9 (haplogroup K) or M45 (haplogroup P)? I have asked FTDNA this question, although I am not sure whether they are permitted to answer (since this person is not a project member).

ataneojr1
01-30-2018, 09:05 PM
I called them and ask why there is no Haplogroup Designation. The lady said she will put in a Request for a Backbone Test???
Whats the deal with F=M89? Wikipedia says it is common in South/Southeast Asia?

swid
01-31-2018, 03:28 PM
Just so you know, these are the SNPs FTDNA will test as part of their Backbone SNP test (https://www.familytreedna.com/learn/project-administration/gap-interpretation/snp-assurance-program-2/); this test is run when they cannot reliably predict a (high-level) haplogroup from your 12-marker results.

A-M91
B-M181
C-RPS4Y711
D-M174
E-M96
E-M2
E-M35.1
F-M89
G-M201
H-M69
I-M170
I-M253
I-P37.2
I-M223
J-M304
J-M267
J-M172
K-M9
L-M20
M-M106
N-M231
O-M175
P-M45
Q-M242
Q-M3
R-M207
R-M173
R-M198
R-M269
R-M124
S-M230
T-M70

As alluded to in post 2, if your P-P295 result from elsewhere is accurate, the backbone test *should* come back with a K-M9 result (since P-P295 is not part of the test and P-M45 is below it).

Squad
01-31-2018, 04:22 PM
Can I have a look at the haplotype so that I could try to infer something about it ? Although the resolution is low (12 markers), it would be extremely helpful to see how does it look like.

lgmayka
02-22-2018, 11:57 PM
As alluded to in post 2, if your P-P295 result from elsewhere is accurate, the backbone test *should* come back with a K-M9 result (since P-P295 is not part of the test and P-M45 is below it).
And indeed it did: result K-M9. I have now asked FTDNA to order the Big Y for this kit at the discount/coupon price on a pay-later basis. I will then post a request for crowdfunding.

ataneojr1
04-20-2018, 12:53 AM
FTDNA Big Y haplogroup P-BY49600

parasar
04-20-2018, 03:03 AM
FTDNA Big Y haplogroup P-BY49600

809841 Taneo Patricio D. Taneo Philippines P-BY49600 14 22 15 9 12-16 11 14 11 13 13 29

This is my first look at a P STR sequence.
Of course it has changed since the first P, but I notice that DYS426 is 11.

ataneojr1
04-24-2018, 08:03 PM
809841 Taneo Patricio D. Taneo Philippines P-BY49600 14 22 15 9 12-16 11 14 11 13 13 29

This is my first look at a P STR sequence.
Of course it has changed since the first P, but I notice that DYS426 is 11.

FTDNA STR just changed to Y500, from panel1 to then direct to panel6(???)...I have NO IDEA what the STRs are for and what they have to do with my haplogroup...it is something to do with matching???

Osiris
04-24-2018, 08:59 PM
FTDNA STR just changed to Y500, from panel1 to then direct to panel6(???)...I have NO IDEA what the STRs are for and what they have to do with my haplogroup...it is something to do with matching???
Yes, potentially. There are a great many positions on the Y chromosome which can be considered STR. FTDNA has a 111 STR test with what is supposed to contain 111 very important markers for matching. They then used the data from the Big Y to extract out enough to get at least another 389 to make 500 strings total. They only gave the 111 markers free to people that ordered the Big Y during the Christmas sale. Others will have to fill those in separately.

I'd presume you'd use these to match against Big Y matches where there's no node defining SNP. Like say if you had 7 cousins who knew their grandparents but not their parents and all had the same SNP values. But some fast mutating STR could indicate a structure to their ancestry. Rather than 7 cousins with 7 separate fathers some of them had the same father. But presumably you'd want this to happen further back in time.

Since you have no Big Y matches in the last 50,000 years probably not a big deal for you. But maybe someday ...

ataneojr1
04-24-2018, 09:12 PM
I had ONE match for the Y12 test who was/is haplogroup F-M89 but he is nowhere to be found, UTC(unable to contact) at the moment,,,,,currently No matches. Its Lonesome but as soon as more Filipinos, Indonesians,Melanesians, Australian Aborigines, Papauans test Big Y, I think there will be hundreds.

ataneojr1
04-24-2018, 09:37 PM
@parasar Curious???...what is the significance of having DYS426-11?

parasar
04-25-2018, 02:52 PM
@parasar Curious???...what is the significance of having DYS426-11?

Most Y-Q and Y-R happen to be DYS426=12.
Most Y-K, C etc. are 11. So the change on this stable marker happened perhaps at the M45 level.

lgmayka
01-04-2019, 04:26 PM
At long last, YFull's haplotree (https://yfull.com/tree/P/) has reclassified this entry as P* (by redefining P to be the P295 SNP level).

parasar
01-04-2019, 05:55 PM
So we have about 575 SNPs at P and after, and YF13223 has 84 of those derived and rest ancestral.
Assuming P is about 50000 years old (+10% correction applied to YFull ages), we have the YF13223 split at about 43ybp.

Yana splits P1 (now defined differently due to YF13223), as Yana is derived at 60% and ancestral at 40% ISOGG P SNPs so about 30000ybp. Pretty close in time to the ~31.6 thousand-year-old Yana site.

Andaman P is no doubt basal to Yana.

I had previously thought that Andaman P was SE Asian derived (still most likely due to F, K, M, S and other Ps).

But now that we know that YF13223 has 84 derived SNPs at the P level, is Andaman P also basal to YF13223? Looks like it is: for example YF13223 is L536+ while Andaman P is L536-.
http://science.sciencemag.org/highwire/filestream/718083/field_highwire_adjunct_files/2/aav2621_TableS11.xlsx

lgmayka
01-05-2019, 02:49 AM
for example YF13223 is L536+ while Andaman P is L536-.
Sorry, YF13223 has a no-call at L536. (I have custody of the YFull entry.)

I can check some others for you if you wish.

parasar
01-05-2019, 07:21 PM
Sorry, YF13223 has a no-call at L536. (I have custody of the YFull entry.)

I can check some others for you if you wish.
lgmayka,
If possible please check the ones below.
Thanks

M1187
PF5867
M1191
M1194
M1195
M1197
CTS4944
CTS5673
CTS6948
CTS7244
CTS7481
CTS7886
CTS8356
CTS9604
CTS10081
CTS10168
CTS10454
M1255
M1261
M1262
M1267
CTS12648

lgmayka
01-06-2019, 04:01 AM
If possible please check the ones below.

No Call:
M1187
M1191
M1194
M1197
CTS4944
CTS5673
CTS7244
CTS7481
CTS7886
CTS8356
CTS10081
CTS10168
CTS10454
M1255
M1261
M1262
M1267
CTS12648

Positive:
PF5867 (2 reads)

Negative:
CTS9604 (10 reads)

Mixed:
M1195 (1 positive vs. 2 negative reads)
CTS6948 (4 positive vs. 12 negative reads)

For comparison, FTDNA's definition of P cites only two SNPs, P295 and F115. For these, YF13223 has:
P295+ (1 read)
F115+ (6 reads)

parasar
01-06-2019, 05:11 PM
No Call:
M1187
M1191
M1194
M1197
CTS4944
CTS5673
CTS7244
CTS7481
CTS7886
CTS8356
CTS10081
CTS10168
CTS10454
M1255
M1261
M1262
M1267
CTS12648

Positive:
PF5867 (2 reads)

Negative:
CTS9604 (10 reads)

Mixed:
M1195 (1 positive vs. 2 negative reads)
CTS6948 (4 positive vs. 12 negative reads)

For comparison, FTDNA's definition of P cites only two SNPs, P295 and F115. For these, YF13223 has:
P295+ (1 read)
F115+ (6 reads)

Thanks.
The Andaman P is also positive for P295 and F115, but negative for the rest including PF5867 which I guess near all other P,Q,R are positive for.

Megalophias
01-06-2019, 06:23 PM
P2-B252 from Karmin et al is also positive for P295 and F115, but PF5867 (7996768 A>G) is not among the SNPs covered. M1197 and CTS8356 are also not listed, all the rest of the above SNPs including CTS9604/M1244, M1195, and CTS6948/M1231 are put under P1-M45 in that study. I don't know how many of these SNPs were actually covered in the P2-B252 sample (an Agta from the Philippines), though.

Lgmayka, would it be possible to check YF13223 for P2 SNPs, such as B252 7104989 C>A (in GRCh37)?

lgmayka
01-06-2019, 08:54 PM
Lgmayka, would it be possible to check YF13223 for P2 SNPs, such as B252 7104989 C>A (in GRCh37)?
YF13223 is a no-call at B252.

Megalophias
01-06-2019, 09:19 PM
Thanks! I guess given differences in coverage it might require a lot of slogging through equivalent SNPs to find one that's informative. :(

ataneojr1
01-06-2019, 09:57 PM
At long last, YFull's haplotree (https://yfull.com/tree/P/) has reclassified this entry as P* (by redefining P to be the P295 SNP level).

THANK YOU Mr. L....you made it possible.

lgmayka
01-06-2019, 10:11 PM
Thanks! I guess given differences in coverage it might require a lot of slogging through equivalent SNPs to find one that's informative. :(
Does YFull have access to a P2 BAM file?

lgmayka
01-06-2019, 10:17 PM
THANK YOU Mr. L...….you made it possible.
I am happy to accept credit for my advocacy, but if I recall correctly, the majority of the cost of your Big Y came from contributions by Anthrogenica members. So a hearty thanks to all who contributed!

lgmayka
01-06-2019, 10:20 PM
The Andaman P is also positive for P295 and F115, but negative for the rest including PF5867 which I guess near all other P,Q,R are positive for.
YFull gives PF5867 four stars, implying reliability. So perhaps the Andaman P is indeed an earlier offshoot.

ataneojr1
01-06-2019, 10:26 PM
I am happy to accept credit for my advocacy, but if I recall correctly, the majority of the cost of your Big Y came from contributions by Anthrogenica members. So a hearty thanks to all who contributed!

Thank You all to the Big Y contributors

Megalophias
01-06-2019, 11:10 PM
Does YFull have access to a P2 BAM file?

Data is here: http://evolbio.ut.ee/chrY/GS000036476-DID/ but I don't think it's BAM format? I don't think YF has done any of the Karmin et al samples, maybe too low coverage or something?

igor1961
01-23-2019, 01:21 PM
I am glad to Larry for the access to STR data of ataneojr1. I browsed YHRD database and found 8 apparent matches of him in Philippines. Below is their list in 23-marker PowerPlex format (DYS393, DYS390, DYS19, DYS391, DYS385a, DYS385b, DYS439, DYS389I, DYS392, DYS389II, DYS458, DYS437, DYS448, YGATAH4, DYS456, DYS576, DYS570, DYS438, DYS481, DYS549, DYS533, DYS635, DYS643)

809841 Philippines 14 22 15 9 12 16 11 13 13 29 17 16 20 12 14 18 19 10 23 12 12 22 14
PNPDB-325 Luzon [Filipino] 14 22 15 9 12 16 11 13 13 29 17 16 20 13 14 18 19 10 23 12 12 22 14
202-12-A348 Luzon [Filipino] 14 22 15 9 12 17 11 14 13 31 17 16 20 13 14 16 18 10 23 12 13 21 14
230-11-A1187 Luzon [Filipino] 14 22 15 9 12 17 11 14 13 31 17 16 20 13 14 16 17 10 23 12 12 21 14
99-13-A480A Luzon [Filipino] 14 22 15 9 12 16 11 13 13 29 18 16 20 13 14 17 18 10 23 12 12 22 14
PH-5784 Philippines [Filipino] 14 22 15 9 12 17 11 14 13 31 17 16 20 13 14 17 18 10 23 12 13 22 15
PNPDB-166 Luzon [Filipino] 14 22 15 9 12 16 11 14 13 30 17 16 20 12 14 17 19 10 23 12 14 22 14
PH-5829 Philippines [Filipino] 14 22 16 9 12 17 11 14 13 31 18 16 20 13 14 15 19 10 22 12 12 21 14
PH-5840 Philippines [Filipino] 14 22 15 9 10 17 11 15 13 32 17 16 21 13 14 17 18 10 23 12 12 21 14

Note that YGATA_H4 marker is shown in YHRD convention form (FTDNA+1).

This group has TMRCA of 2300440 year ago. I have no idea what events in the history South-East Asia fits this date. There were no matches outside Philippines.

This group constitutes a tiny (8 of 795) but still measurable fraction YHRD dataset of Filipinos. It corresponds to about 500 thousand men belonging to this unique branch. It's 3 times more than an entire male population of Iceland. Quite far from extinction ;)

Шад
02-02-2019, 04:06 PM
Data is here: http://evolbio.ut.ee/chrY/GS000036476-DID/ but I don't think it's BAM format? I don't think YF has done any of the Karmin et al samples, maybe too low coverage or something?

Unfortunately, this will not work. We need a file in a different format (BAM).
If someone has the competencies and resources to convert several FASTQ to BAM - please contact me. I think we can do something with 'Karmin's files problem'.

Шад
02-02-2019, 04:11 PM
Does anyone know the details about the sample P-M45 on the FTDN tree? It is indicated that he is from Mongolia. It was better to contact the donor and convince him to analyze the data in YFull

Pribislav
08-19-2019, 09:55 PM
I sent an e-mail to Yfull today with links to BAM files for paleolithic samples Yana1 and Yana2 from Sikora paper, and for 19th century Andaman islander from Moreno-Mayar paper, these samples should help in resolving P and P1 phylogeny. Andamanese is the most basal P sample to date, with only several derived P-level SNPs, and two Yana samples have at least 14 ancestral SNPs at P level, and at least 37 (38) derived SNPs at P1 level, which means lots of SNPs at these two levels aren't placed properly. It seems they've already put one of the Yana samples on the tree:

https://www.yfull.com/tree/P/

artemv
08-21-2019, 12:42 AM
I sent an e-mail to Yfull today with links to BAM files for paleolithic samples Yana1 and Yana2 from Sikora paper, and for 19th century Andaman islander from Moreno-Mayar paper, these samples should help in resolving P and P1 phylogeny. Andamanese is the most basal P sample to date, with only several derived P-level SNPs, and two Yana samples have at least 14 ancestral SNPs at P level, and at least 37 (38) derived SNPs at P1 level, which means lots of SNPs at these two levels aren't placed properly. It seems they've already put one of the Yana samples on the tree:

https://www.yfull.com/tree/P/

That's cool, nice to see Yana samples on Y-full.

Pribislav
08-21-2019, 01:29 AM
That's cool, nice to see Yana samples on Y-full.

Yes, rather important ancient samples IMO, it would be a shame if they weren't on Yfull tree, considering the high quality of samples. They also added Andaman islander, but he's only K2b for now:

https://www.yfull.com/tree/K2b/

VytautusofAukstaitija
08-21-2019, 01:29 AM
That's cool, nice to see Yana samples on Y-full.

Do you know how to get ancient samples uploaded to yfull? Are there any requirements?

Pribislav
08-21-2019, 01:39 AM
Do you know how to get ancient samples uploaded to yfull? Are there any requirements?

The procedure seems to be rather straightforward: I sent an e-mail with attached Y-calls and links to BAM files, and explained why are Yana samples so important for resolving phylogeny of macro-haplogroups P and P1. And that was it. Haven't got any response, but the samples were on the tree the same day. As for requirements, the samples must be shotgun sequenced (so almost none of samples sequenced by Harvard and Max Planck groups can make it to the Yfull tree), and they need to have at least ~1 depth of coverage IIRC.

Pribislav
09-12-2019, 12:38 AM
The new tree is here, and boy, putting Yana samples and Andaman islander on the tree really paid off, there are two new levels now, P337 and P226:

https://www.yfull.com/tree/P/ (https://www.yfull.com/tree/P/)

EDIT:

New clade, V2219, will be soon added between L754 and V88 thanks to OC1 and SC2, Iron Gates HGs from Romania.

ataneojr1
09-13-2019, 10:54 PM
YFULL YTREE P Update
I went from P* to under P1 as P-BY49600 (ftdna Y500)

alchemist223
09-14-2019, 12:01 AM
Hello ataneojr1

Have you thought about upgrading your STRs at Family Tree DNA? That would be a big help in learning more about your haplogroup.

lgmayka
09-14-2019, 01:53 AM
Have you thought about upgrading your STRs at Family Tree DNA? That would be a big help in learning more about your haplogroup.
Note that an upgrade to Big Y-700 would include an upgrade to 700 Y-STRs, including the original 111. My understanding is that ataneojr1 plans to order the Big Y-700 upgrade at a later date. Now if only FTDNA would subsidize it. ;)

ataneojr1
12-25-2019, 08:27 PM
Hello ataneojr1

Have you thought about upgrading your STRs at Family Tree DNA? That would be a big help in learning more about your haplogroup.

DONE!!! Will download the FTDNA Big Y700 BAM file sometime after New Years to send to YFULL.

Pribislav
04-21-2020, 10:16 PM
DONE!!! Will download the FTDNA Big Y700 BAM file sometime after New Years to send to YFULL.

Hi ataneojr1, are you planning to send your BigY-700 BAM to YFull anytime soon? It would really help refining phylogenetic tree of macrohaplogroup P, together with Yana samples and Andaman islander, whose analysis isn't done yet.

parasar
04-21-2020, 10:35 PM
Hi ataneojr1, are you planning to send your BigY-700 BAM to YFull anytime soon? It would really help refining phylogenetic tree of macrohaplogroup P, together with Yana samples and Andaman islander, whose analysis isn't done yet.

I think he is YF13223
https://yfull.com/tree/P/

Pribislav
04-21-2020, 10:54 PM
I think he is YF13223
https://yfull.com/tree/P/

Yeah, but that's his BigY-500 result, which hasn't covered a lot of SNPs on all 4 P-levels.

ataneojr1
04-24-2020, 07:41 PM
Yes, once I have the extra funds.

alchemist223
04-24-2020, 08:35 PM
Hi ataneojr1, are you planning to send your BigY-700 BAM to YFull anytime soon? It would really help refining phylogenetic tree of macrohaplogroup P, together with Yana samples and Andaman islander, whose analysis isn't done yet.

How long do you think it will take to finish the analysis? These samples have been up on YFull for quite a while.

Pribislav
04-24-2020, 10:00 PM
How long do you think it will take to finish the analysis? These samples have been up on YFull for quite a while.

I'm not really sure why is analysis of Yana samples taking them so long, the only reasonable explanation is they are preoccupied with their day-to-day business (i.e. analysing results of paying customers). The same situation is with all ancient samples recently added to YFull tree, but Yana samples are far too important to be left unfinished for almost 8 months, IMO. In case anybody missed the reason why these two samples are so important, it's this:
Population of several hundred people which Yana1 and Yana2 were part of more than 30.000 years ago wasn't just a dead end "cousin" population of distant ancestors of all living R&Q men, it was THE population in which those ancestors lived for at least several hundred years, and probably much longer.

I've analysed Y-calls of both Yana samples and of the 19th century Andaman islander, and discovered that Yana2 has three more derived SNPs than Yana1, so those three mutations which are carried by all living R&Q men must've happened in the population Yana1 and Yana2 were part of. Three SNPs that are derived in Yana2, but ancestral in Yana1 (and Andaman islander) are: P284 (currently at P337 level), and PF5482 and PF5883/M1197 (currently at P1 level). All three SNPs have multiple reads (>3) in all three ancient samples, and moreover P284 and PF5482 are transversions, so very unlikely to be the result of aDNA damage. So when I sent my analysis to YFull, along with BAM files, I proposed Yana2 forming another level (P284) between levels P337 and P226, but that still hasn't happened.

Here is my analysis of these three samples:

https://drive.google.com/file/d/1L_w0bM-TzmLRuoNA8d_SKKXz7Jmeks5g/view?usp=sharing

And here is how the tree should actually look like:

37287

rock
05-13-2020, 09:50 AM
I see yfull listed PF5482, M1208, CTS3446, CTS3509 at P1 level, is yfull wrong? Shouldn't these SNPs at P-M45 level?

rock
05-13-2020, 06:21 PM
I think Yfull is wrong, as FTDNA listed P-BY49600 under P-F19020, the Andaman sample should join YF13223 as Andman also F19020+

F19020 Andaman,Agta1,SSM050,SSM097
F19416 Andaman,Agta1,SSM050,SSM097
F20149 Andaman,Agta1,SSM050,SSM097
F20897 Andaman,Agta1,SSM050,SSM097
F23629 Andaman,Agta1,SSM050,SSM097
F23794 Andaman,Agta1,SSM050,SSM097
F24383 Andaman,Agta1,SSM050,SSM097
F18982 Andaman,Agta1
F26197 Andaman,SSM050,SSM097
BY49659 Andaman,SSM050,SSM097
F20148 Agta1,SSM050,SSM097 (Andaman no call)

Andaman NEG:
FGC14876 Agta1,SSM050,SSM097
FT142537 Agta1,SSM050,SSM097
FT1044 SSM050,SSM097,YF13223
BY49746 SSM050,SSM097,YF13223

TuaMan
05-14-2020, 07:16 PM
I've analysed Y-calls of both Yana samples and of the 19th century Andaman islander, and discovered that Yana2 has three more derived SNPs than Yana1, so those three mutations which are carried by all living R&Q men must've happened in the population Yana1 and Yana2 were part of. Three SNPs that are derived in Yana2, but ancestral in Yana1 (and Andaman islander) are: P284 (currently at P337 level), and PF5482 and PF5883/M1197 (currently at P1 level). All three SNPs have multiple reads (>3) in all three ancient samples, and moreover P284 and PF5482 are transversions, so very unlikely to be the result of aDNA damage. So when I sent my analysis to YFull, along with BAM files, I proposed Yana2 forming another level (P284) between levels P337 and P226, but that still hasn't happened.

Here is my analysis of these three samples:

https://drive.google.com/file/d/1L_w0bM-TzmLRuoNA8d_SKKXz7Jmeks5g/view?usp=sharing

And here is how the tree should actually look like:

37287


Are you able to determine how many private SNPs the Andaman sample has?

rock
05-15-2020, 04:30 PM
a new P branch just displayed on the FTDNA's tree: P-FT289115 (xP-M45, P-F20148)

alchemist223
05-16-2020, 04:46 AM
Hoping there are some big updates on YFull soon... Nonetheless, props to FTDNA for such important changes.

rock
05-16-2020, 11:38 AM
P-F20148 has 4 Big Y participants, while P-FT292000 has only 1 Big Y participant, don't understand how to formed a new P branch, maybe FTDNA has additional scientific samples?

Pribislav
08-19-2020, 10:01 PM
I think Yfull is wrong, as FTDNA listed P-BY49600 under P-F19020, the Andaman sample should join YF13223 as Andman also F19020+

Both YFull and FTDNA are wrong in some ways, there's a bunch of misplaced SNPs in both trees. For example, current FTDNA haplogroup P tree is (or should've been, to be more precise) redefined by Yana samples as follows:

- level M45 is defined by SNPs derived in both Yana1 and Yana2;

- level P284 is defined by SNPs derived in Yana2 but ancestral in Yana1;

- level P226 is defined by SNPs derived in all living R & Q males, but ancestral in both Yana1 & Yana2;

And here are the mistakes made by FTDNA:

- seven SNPs that are derived in both Yana1 and Yana2 are for some reason at level P226 instead at level M45 (F4, F29, F506, F640, F671, YSC0000270 and YSC0000279)

- two SNPs at level P284 have no reason to be there: PF5854 is ancestral in both Yana1 and Yana2, so it should be at level P226; and PF5958 isn't covered in either Yana1 or Yana2

- and the most hilarious one: SNP L779/PF5907/YSC0000251/V2974 (hg38: 13368667 C>G) is listed at both M45 and P226 levels under different names (L779 and YSC0000251, respectively)

As for YFull, you're right about Andamanese, he indeed has 9 out of 11 SNPs derived at level F20148, so he should be in the same clade as YF13223. The problem could be that BigY-500 doesn't cover those SNPs, so we'll probably have to wait for YF13223 to submit his BigY-700 BAM to YFull.

For a long time, my main objection to YFull was that they haven't added P284 level, but on closer inspection I get why YFull was/is reluctant to do so. Of the three SNPs that are without a doubt derived in Yana2 and ancestral in Yana1, PF5482 is heterochromatic and PF5883/M1197 is in LINE1 (https://en.wikipedia.org/wiki/LINE1), so not in the Karmin regions (and consequently not in the combBed regions). But P284, although in the palindromic region, is accepted by both Poznik and Karmin as a SNP in a "good region", and is not recurrent. And Yana1 is clearly ancestral (25C), while Yana2 is clearly derived (3G), so P284 simply can not be at level P337 as he currently is. YFull will eventually have to add level P284, or their tree will remain inaccurate.

On a good note, while rereading McColl et al. 2018 (https://science.sciencemag.org/content/sci/361/6397/88.full.pdf), I noticed a modern male Jehai (https://en.wikipedia.org/wiki/Jahai_people) sample from Malaysia that was sequenced to a high coverage along with ancient samples. I analysed his Y-calls, and it turned out he has only 6 derived, and 135 ancestral SNPs across four P levels. More importantly, he's ancestral for P295, which is currently at the first/oldest level in FTDNA tree, which means he represents the earliest split to date, earlier even than Filipino and Andaman branch (F20148). So he has been submitted to YFull, and he will further split the clade when the next version of the tree is released (he is currently at K2b level: ERS2589709 (https://www.yfull.com/tree/K2b/)).

alchemist223
08-22-2020, 07:09 PM
Both YFull and FTDNA are wrong in some ways, there's a bunch of misplaced SNPs in both trees. For example, current FTDNA haplogroup P tree is (or should've been, to be more precise) redefined by Yana samples as follows:

- level M45 is defined by SNPs derived in both Yana1 and Yana2;

- level P284 is defined by SNPs derived in Yana2 but ancestral in Yana1;

- level P226 is defined by SNPs derived in all living R & Q males, but ancestral in both Yana1 & Yana2;

And here are the mistakes made by FTDNA:

- seven SNPs that are derived in both Yana1 and Yana2 are for some reason at level P226 instead at level M45 (F4, F29, F506, F640, F671, YSC0000270 and YSC0000279)

- two SNPs at level P284 have no reason to be there: PF5854 is ancestral in both Yana1 and Yana2, so it should be at level P226; and PF5958 isn't covered in either Yana1 or Yana2

- and the most hilarious one: SNP L779/PF5907/YSC0000251/V2974 (hg38: 13368667 C>G) is listed at both M45 and P226 levels under different names (L779 and YSC0000251, respectively)

As for YFull, you're right about Andamanese, he indeed has 9 out of 11 SNPs derived at level F20148, so he should be in the same clade as YF13223. The problem could be that BigY-500 doesn't cover those SNPs, so we'll probably have to wait for YF13223 to submit his BigY-700 BAM to YFull.

For a long time, my main objection to YFull was that they haven't added P284 level, but on closer inspection I get why YFull was/is reluctant to do so. Of the three SNPs that are without a doubt derived in Yana2 and ancestral in Yana1, PF5482 is heterochromatic and PF5883/M1197 is in LINE1 (https://en.wikipedia.org/wiki/LINE1), so not in the Karmin regions (and consequently not in the combBed regions). But P284, although in the palindromic region, is accepted by both Poznik and Karmin as a SNP in a "good region", and is not recurrent. And Yana1 is clearly ancestral (25C), while Yana2 is clearly derived (3G), so P284 simply can not be at level P337 as he currently is. YFull will eventually have to add level P284, or their tree will remain inaccurate.

On a good note, while rereading McColl et al. 2018 (https://science.sciencemag.org/content/sci/361/6397/88.full.pdf), I noticed a modern male Jehai (https://en.wikipedia.org/wiki/Jahai_people) sample from Malaysia that was sequenced to a high coverage along with ancient samples. I analysed his Y-calls, and it turned out he has only 6 derived, and 135 ancestral SNPs across four P levels. More importantly, he's ancestral for P295, which is currently at the first/oldest level in FTDNA tree, which means he represents the earliest split to date, earlier even than Filipino and Andaman branch (F20148). So he has been submitted to YFull, and he will further split the clade when the next version of the tree is released (he is currently at K2b level: ERS2589709 (https://www.yfull.com/tree/K2b/)).

Apparently, YFull has finished analyzing the Yana samples, but they ultimately did not change their SNP placements or odd TMRCA dates.

parasar
08-22-2020, 10:46 PM
Both YFull and FTDNA are wrong in some ways, there's a bunch of misplaced SNPs in both trees. For example, current FTDNA haplogroup P tree is (or should've been, to be more precise) redefined by Yana samples as follows:

- level M45 is defined by SNPs derived in both Yana1 and Yana2;

- level P284 is defined by SNPs derived in Yana2 but ancestral in Yana1;

- level P226 is defined by SNPs derived in all living R & Q males, but ancestral in both Yana1 & Yana2;

And here are the mistakes made by FTDNA:

- seven SNPs that are derived in both Yana1 and Yana2 are for some reason at level P226 instead at level M45 (F4, F29, F506, F640, F671, YSC0000270 and YSC0000279)

- two SNPs at level P284 have no reason to be there: PF5854 is ancestral in both Yana1 and Yana2, so it should be at level P226; and PF5958 isn't covered in either Yana1 or Yana2

- and the most hilarious one: SNP L779/PF5907/YSC0000251/V2974 (hg38: 13368667 C>G) is listed at both M45 and P226 levels under different names (L779 and YSC0000251, respectively)

As for YFull, you're right about Andamanese, he indeed has 9 out of 11 SNPs derived at level F20148, so he should be in the same clade as YF13223. The problem could be that BigY-500 doesn't cover those SNPs, so we'll probably have to wait for YF13223 to submit his BigY-700 BAM to YFull.

For a long time, my main objection to YFull was that they haven't added P284 level, but on closer inspection I get why YFull was/is reluctant to do so. Of the three SNPs that are without a doubt derived in Yana2 and ancestral in Yana1, PF5482 is heterochromatic and PF5883/M1197 is in LINE1 (https://en.wikipedia.org/wiki/LINE1), so not in the Karmin regions (and consequently not in the combBed regions). But P284, although in the palindromic region, is accepted by both Poznik and Karmin as a SNP in a "good region", and is not recurrent. And Yana1 is clearly ancestral (25C), while Yana2 is clearly derived (3G), so P284 simply can not be at level P337 as he currently is. YFull will eventually have to add level P284, or their tree will remain inaccurate.

On a good note, while rereading McColl et al. 2018 (https://science.sciencemag.org/content/sci/361/6397/88.full.pdf), I noticed a modern male Jehai (https://en.wikipedia.org/wiki/Jahai_people) sample from Malaysia that was sequenced to a high coverage along with ancient samples. I analysed his Y-calls, and it turned out he has only 6 derived, and 135 ancestral SNPs across four P levels. More importantly, he's ancestral for P295, which is currently at the first/oldest level in FTDNA tree, which means he represents the earliest split to date, earlier even than Filipino and Andaman branch (F20148). So he has been submitted to YFull, and he will further split the clade when the next version of the tree is released (he is currently at K2b level: ERS2589709 (https://www.yfull.com/tree/K2b/)).

Reminds me of Maju's map pointing to the middle of old Sundaland:
http://4.bp.blogspot.com/-wsNAS_dNkfg/U5L1ztBrjfI/AAAAAAAACso/DsrzZsJRtM4/s1600/Y-DNA-K-Sundaland-arrows.png
http://1.bp.blogspot.com/-xIyCVSPSm3I/U5LqVD5nawI/AAAAAAAACsM/TEjs1OTRu7k/s1600/Karafet-Y-DNA-K-tree-annotated.png
https://upload.wikimedia.org/wikipedia/commons/d/d7/Geographical_location_of_Orang_Asli_communities_re cruited_in_the_study.jpg
By Farhang Aghakhanian, Yushima Yunus, Rakesh Naidu, Timothy Jinam, Andrea Manica, Boon Peng Hoh, and Maude E. Phipps - Aghakhanian F, Yunus Y, Naidu R, et al. Unravelling the Genetic History of Negritos and Indigenous Populations of Southeast Asia. Genome Biology and Evolution. 2015;7(5):1206-1215. doi:10.1093/gbe/evv065. http://gbe.oxfordjournals.org/content/7/5/1206.full, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=54911106

alchemist223
09-13-2020, 07:20 AM
Both YFull and FTDNA are wrong in some ways, there's a bunch of misplaced SNPs in both trees. For example, current FTDNA haplogroup P tree is (or should've been, to be more precise) redefined by Yana samples as follows:

- level M45 is defined by SNPs derived in both Yana1 and Yana2;

- level P284 is defined by SNPs derived in Yana2 but ancestral in Yana1;

- level P226 is defined by SNPs derived in all living R & Q males, but ancestral in both Yana1 & Yana2;

And here are the mistakes made by FTDNA:

- seven SNPs that are derived in both Yana1 and Yana2 are for some reason at level P226 instead at level M45 (F4, F29, F506, F640, F671, YSC0000270 and YSC0000279)

- two SNPs at level P284 have no reason to be there: PF5854 is ancestral in both Yana1 and Yana2, so it should be at level P226; and PF5958 isn't covered in either Yana1 or Yana2

- and the most hilarious one: SNP L779/PF5907/YSC0000251/V2974 (hg38: 13368667 C>G) is listed at both M45 and P226 levels under different names (L779 and YSC0000251, respectively)

As for YFull, you're right about Andamanese, he indeed has 9 out of 11 SNPs derived at level F20148, so he should be in the same clade as YF13223. The problem could be that BigY-500 doesn't cover those SNPs, so we'll probably have to wait for YF13223 to submit his BigY-700 BAM to YFull.

For a long time, my main objection to YFull was that they haven't added P284 level, but on closer inspection I get why YFull was/is reluctant to do so. Of the three SNPs that are without a doubt derived in Yana2 and ancestral in Yana1, PF5482 is heterochromatic and PF5883/M1197 is in LINE1 (https://en.wikipedia.org/wiki/LINE1), so not in the Karmin regions (and consequently not in the combBed regions). But P284, although in the palindromic region, is accepted by both Poznik and Karmin as a SNP in a "good region", and is not recurrent. And Yana1 is clearly ancestral (25C), while Yana2 is clearly derived (3G), so P284 simply can not be at level P337 as he currently is. YFull will eventually have to add level P284, or their tree will remain inaccurate.

On a good note, while rereading McColl et al. 2018 (https://science.sciencemag.org/content/sci/361/6397/88.full.pdf), I noticed a modern male Jehai (https://en.wikipedia.org/wiki/Jahai_people) sample from Malaysia that was sequenced to a high coverage along with ancient samples. I analysed his Y-calls, and it turned out he has only 6 derived, and 135 ancestral SNPs across four P levels. More importantly, he's ancestral for P295, which is currently at the first/oldest level in FTDNA tree, which means he represents the earliest split to date, earlier even than Filipino and Andaman branch (F20148). So he has been submitted to YFull, and he will further split the clade when the next version of the tree is released (he is currently at K2b level: ERS2589709 (https://www.yfull.com/tree/K2b/)).

YFull has now added P-P284 to their tree (https://www.yfull.com/tree/P-P284/). They have added a few SNPs on the P284 level: PF5958/M1160, PF5883/M1197, PF5482, and PF5854. The Malaysian Jehai sample remains at K2b*. Interestingly, the most basal sample of Haplogroup S (mostly found in Papuans and Australian Aboriginals) is from the Selangor region of Malaysia, possibly from another Negrito ethnic group. This may give credence to the theory that K2b split in Southeast Asia/Sundaland.

Pribislav
09-13-2020, 12:15 PM
YFull has now added P-P284 to their tree (https://www.yfull.com/tree/P-P284/). They have added a few SNPs on the P284 level: PF5958/M1160, PF5883/M1197, PF5482, and PF5854. The Malaysian Jehai sample remains at K2b*. Interestingly, the most basal sample of Haplogroup S (mostly found in Papuans and Australian Aboriginals) is from the Selangor region of Malaysia, possibly from another Negrito ethnic group. This may give credence to the theory that K2b split in Southeast Asia/Sundaland.

Finally! I'm not sure why they haven't moved Jehai sample below P, since he has six derived SNPs at various P-levels. And most importantly, he's negative for P295 (which is currently at the oldest level on FTDNA block tree), so these six derived SNPs should make the oldest level now, and P295 would be at the second oldest.


P level: F115/PF5870/M1189/V1651+ A>T (34T); PF5850+ T>A (18A); P295/S8/PF5866- T>G (22T)

P1 level: M1218/CTS4944/PF5909/V3240+ C>T (17T)

P337 level: PF5861/F83/M1185/V1195+ A>T (14T); M1216/YSC0000176/PF5908/V2979+ C>G (16G)

P226 level: M1264/YSC0000227/F597+ A>G (17G)


As for haplogroup S, those two recently submitted samples from Australia that split subclade M230 (https://www.yfull.com/tree/S/) are in fact ancient Aborigines from Wright et al. 2018 (https://advances.sciencemag.org/content/4/12/eaau5064):

ERS2897884 is PA86; date unknown; Cairns, Queensland

ERS2897881 is KP1; ~350 AD; Barham, New South Wales

alchemist223
09-13-2020, 05:54 PM
Finally! I'm not sure why they haven't moved Jehai sample below P, since he has six derived SNPs at various P-levels. And most importantly, he's negative for P295 (which is currently at the oldest level on FTDNA block tree), so these six derived SNPs should make the oldest level now, and P295 would be at the second oldest.


P level: F115/PF5870/M1189/V1651+ A>T (34T); PF5850+ T>A (18A); P295/S8/PF5866- T>G (22T)

P1 level: M1218/CTS4944/PF5909/V3240+ C>T (17T)

P337 level: PF5861/F83/M1185/V1195+ A>T (14T); M1216/YSC0000176/PF5908/V2979+ C>G (16G)

P226 level: M1264/YSC0000227/F597+ A>G (17G)


As for haplogroup S, those two recently submitted samples from Australia that split subclade M230 (https://www.yfull.com/tree/S/) are in fact ancient Aborigines from Wright et al. 2018 (https://advances.sciencemag.org/content/4/12/eaau5064):

ERS2897884 is PA86; date unknown; Cairns, Queensland

ERS2897881 is KP1; ~350 AD; Barham, New South Wales

I was actually referring to kit YF09913 in Haplogroup S, a kit submitted by a YFull customer. I would love to know more about his origin.

alchemist223
10-08-2020, 08:07 PM
delete

alchemist223
10-08-2020, 08:08 PM
Finally! I'm not sure why they haven't moved Jehai sample below P, since he has six derived SNPs at various P-levels. And most importantly, he's negative for P295 (which is currently at the oldest level on FTDNA block tree), so these six derived SNPs should make the oldest level now, and P295 would be at the second oldest.


P level: F115/PF5870/M1189/V1651+ A>T (34T); PF5850+ T>A (18A); P295/S8/PF5866- T>G (22T)

P1 level: M1218/CTS4944/PF5909/V3240+ C>T (17T)

P337 level: PF5861/F83/M1185/V1195+ A>T (14T); M1216/YSC0000176/PF5908/V2979+ C>G (16G)

P226 level: M1264/YSC0000227/F597+ A>G (17G)


As for haplogroup S, those two recently submitted samples from Australia that split subclade M230 (https://www.yfull.com/tree/S/) are in fact ancient Aborigines from Wright et al. 2018 (https://advances.sciencemag.org/content/4/12/eaau5064):

ERS2897884 is PA86; date unknown; Cairns, Queensland

ERS2897881 is KP1; ~350 AD; Barham, New South Wales

Although the YFull tree has been updated, the Jehai sample still remains at the K2b level.

Pribislav
10-08-2020, 09:26 PM
Although the YFull tree has been updated, the Jehai sample still remains at the K2b level.

It seems they forgot about him in the avalanche of ancient samples they've added recently. At least all three ancient Q samples I recently submitted turned out to be useful, all of them split their clades:


https://www.yfull.com/tree/Q-YP1500/ (https://www.yfull.com/tree/Q-YP1500/)

https://www.yfull.com/tree/Q-Y18330/ (https://www.yfull.com/tree/Q-Y18330/)

https://www.yfull.com/tree/Q-YP832/ (https://www.yfull.com/tree/Q-YP832/)

parasar
12-29-2020, 03:48 PM
P* xP-M1254
id:ERS2589709MYS [MY-08]
https://www.yfull.com/tree/K2b/

alchemist223
03-02-2021, 09:45 PM
Can someone double check if the ancient Andaman sample is positive for M45? I keep finding contradictory information as to what level of P M45 appears, but I know that it is negative/ancestral at the oldest level (Jehai sample).

davit
03-02-2021, 09:50 PM
When did Andaman P migrate to mainland Asia?

Pribislav
03-02-2021, 10:00 PM
Can someone double check if the ancient Andaman sample is positive for M45? I keep finding contradictory information as to what level of P M45 appears, but I know that it is negative at the oldest level (Jehai sample).

M45 is not covered in Andaman, Jehai and Yana samples. I'm not sure how reliable is this SNP, but there must be a reason why YFull doesn't use it.

alchemist223
03-02-2021, 10:05 PM
delete

Pribislav
03-02-2021, 10:07 PM
I assume the same is true with PF5962?

PF5962 is another name for the same SNP.

alchemist223
03-02-2021, 10:08 PM
Thanks for the clarification.

Pribislav
03-02-2021, 10:09 PM
Thanks for the clarification.

You're welcome. :)