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View Full Version : SNP pack for Z209+ (N/S cluster, Z210, Z220, etc.)



razyn
10-29-2015, 03:57 PM
I just saw a notice of such a test, on sale for $99, on the FTDNA home page of a Z295+ person. It is supposed to test 109 SNPs, but I don't know which ones. It would almost certainly be a good deal for people who are Z195+, and not positive for any of the DF27 project's major groups below B in the alphabet.

People in group E and below, definitely, need to avoid it. Well, except for group Ub (STR pattern matches the North/South cluster).

Subsequent to my posting this, Mike W has informed us that a DF27 pack has been released (that's the one for group E, and should cover anything later in the alphabet through R).

Also a Z198 pack, which covers the D (yellow) groups.

I'm not sure if DF17 is covered by any of them.

gotten
10-29-2015, 04:59 PM
Here's the description:

Z210 SNP PACK

Includes 12 SNPs on the Haplotree:
Z210, Z295, Z211, CTS12074, M153, CTS10504, CTS4065, Z279, Z214, Z299, Z270, Z209

Includes 97 SNPs not on the Haplotree:
ZZ11, BY3189, BY3190, BY3191, Z29694, A5000, A5001, A5362, A5376, ZS822, Z697, Z694, Z419, Z298, Z29687, CTS10029, CTS11473, CTS2142, CTS2379, CTS3423, CTS3702, CTS3889, CTS4183, CTS4531, CTS4558, CTS7359, CTS7870, CTS8087, CTS8196, CTS9050, CTS9053, CTS9164, FGC13557, FGC15329, FGC15710, Z29664, Z29661, Z29658, Z29652, Z29650, Z294, Z272, Z271, FGC15714, FGC15730, FGC15731, FGC15735, FGC15742, FGC17318, FGC23176, FGC23178, FGC23184, FGC23196, FGC23342, FGC23343, FGC23347, FGC23349, FGC23350, FGC23351, FGC23353, FGC23355, FGC23356, FGC23363, FGC29721, FGC29729, FGC29730, FGC29733, FGC29757, FGC35766, FGC35767, FGC39263, PH1354, PH1859, PH312, PH4283, PH5341, S11482, S16864, S19290, S21184, S25783, Z221, Z218, Z217, Z216, Z213, Y11215, Y11216, Y11217, Y11219, Y11285, Y11286, Y11287, Y11288, Y11880, Z29663, FGC15726

ZZ11 is a strange inclusion in this pack.

razyn
10-29-2015, 05:22 PM
A lot of the listed SNPs have synonyms (same mutation, but called by a different name at some other lab or analytical service). The SNP pack in question may include one you are expecting, but calling it something else -- and not necessarily what I have called it in the DF27 project. Many of the synonyms can be found here, if you use your browser's "find" function: http://www.ytree.net/DisplayTree.php?blockID=629&star=false

gotten
10-29-2015, 10:31 PM
And within hours the number of SNPs expanded:

Z210 SNP PACK Includes 15 SNPs on the Haplotree:
PF2462, Z210, Z295, Z211, CTS12074, M153, CTS10504, F2735, CTS7927, CTS4065, Z279, Z214, Z299, Z270, Z209

Includes 129 SNPs not on the Haplotree:
Z220, Z268, Z212, Z278, ZZ11, BY3189, BY3190, BY3191, Z29694, A5000, A5001, A5362, A5376, ZS822, Z697, Z694, Z419, Z298, Z29687, CTS10029, CTS11473, CTS2142, CTS2379, CTS3423, CTS3702, CTS3889, CTS4183, CTS4531, CTS4558, CTS7359, CTS7870, CTS8087, CTS8196, CTS9050, CTS9053, CTS9164, FGC13557, FGC15329, FGC15710, Z29664, Z29661, Z29658, Z29652, Z29650, Z294, Z272, Z271, FGC15714, FGC15730, FGC15731, FGC15735, FGC15742, FGC17318, FGC23176, FGC23178, FGC23184, FGC23196, FGC23342, FGC23343, FGC23347, FGC23349, FGC23350, FGC23351, FGC23353, FGC23355, FGC23356, FGC23363, FGC29721, FGC29729, FGC29730, FGC29733, FGC29757, FGC35766, FGC35767, FGC39263, PH1354, PH1859, PH312, PH4283, PH5341, S11482, S16864, S19290, S21184, S25783, Z221, Z218, Z217, Z216, Z213, Y11215, Y11216, Y11217, Y11219, Y11285, Y11286, Y11287, Y11288, Y11880, Z29663, FGC15726, A8256, BY3281, BY3282, BY3284, BY3285, Z29690, Z29689, Z29684, Z29666, Y17687, Y17458, Y17154, Y17146, Y17144, Y17143, S16785, PF7203, FGC34881, FGC29756, FGC29751, A7066, BY3033, CTS517, CTS8780, FGC15737, FGC29731, FGC29738, FGC29750

razyn
10-30-2015, 01:59 AM
Here's the description:

Z210 SNP PACK

Includes 97 SNPs not on the Haplotree:
ZZ11,
...
ZZ11 is a strange inclusion in this pack.

I noticed that, too. ZZ40 would actually be a good one for this pack, if they are willing to catch some Zs after all. It's actually under Z210, is new, and has nine branches so far ( a few of which they were already testing).

I'd love to see some major pool of data on ZZ11, this pack just is an odd place to park it. Everybody who tests Z210+ should be ZZ11+, unless they have one of the back-mutations. I suppose those are mildly interesting, but they don't prove a thing about the early history of DF27.

Mikewww
11-03-2015, 10:20 PM
The web link has been updated again for the Z209 SNP Pack. I'm now counting 146 SNPs.

SNP Pack R1b - Z209 SNP Pack $99 Add

Includes the following SNPs on the haplotree:
PF2462, Z210, Z215, Z295, Z211, CTS12074, M153, CTS10504, F2735, CTS7927, CTS4065, Z279, Z214, Z299, Z270, Z209

Includes the following SNPs that are NOT on the haplotree:
Z220, Z268, Z212, Z278, BY3190, BY3191, Z29694, A5000, A5001, A5362, A5376, ZS822, Z697, Z694, Z419, Z298, Z29687, CTS10029, CTS11473, CTS2142, CTS2379, CTS3423, CTS3702, CTS3889, CTS4183, CTS4531, CTS4558, CTS7359, CTS7870, CTS8087, CTS8196, CTS9050, CTS9053, CTS9164, FGC13557, FGC15329, FGC15710, Z29664, Z29661, Z29658, Z29652, Z29650, Z271, FGC15714, FGC15730, FGC15731, FGC15735, FGC15742, FGC17318, FGC23176, FGC23178, FGC23184, FGC23196, FGC23342, FGC23343, FGC23347, FGC23349, FGC23350, FGC23351, FGC23353, FGC23355, FGC23356, FGC23363, FGC29721, FGC29729, FGC29730, FGC29733, FGC29757, FGC35766, FGC35767, FGC39263, PH1354, PH1859, PH312, PH5341, S11482, S16864, S19290, S21184, S25783, Z221, Z218, Z217, Z216, Z213, Y11215, Y11216, Y11217, Y11219, Y11285, Y11286, Y11287, Y11288, Y11880, Z29663, FGC15726, BY3279, BY3281, BY3282, BY3284, BY3285, Z29690, Z29689, Z29684, Z29666, BY3275, Y17458, BY3278, BY3280, BY3277, BY3276, S16785, PF7203, FGC34881, FGC29756, FGC29751, A7066, BY3033, CTS517, CTS8780, FGC15737, FGC29731, FGC29738, FGC29750, BY3275, BY3276, BY3278, BY3277, BY3279, BY3283, BY3280, FGC15712, FGC15713, FGC29739, ZZ40_1, Y16854

This has good coverage of Z209. There are no dependencies in this bundle where SNPs are selectively tested. Since it is all one fell swoop there is some cross-validation support. There are selected phylogenetic equivalents included so there is a chance to break up lightly tested blocks of SNPs.

I want to thank Dick on this one in particular. He apparently spends his evenings communicating with people all over the world and searching through Big Y matching screens and multiple experimental trees. He's definitely a Z209 North-South guy all the way through. He probably needs some kind of ten gallon cowboy hat with DF27 stamped on it.

The price has not gone up to $119 yet but it might Wednesday when they start a new batch cycle. I'm trying to update a tree-like spreadsheet format for this so you can see the position numbers, etc.

Mikewww
11-03-2015, 10:42 PM
... I'm trying to update a tree-like spreadsheet format for this so you can see the position numbers, etc.
This has been a bit of a tedious experience but at least I have a preset format for doing this kind of stuff. I had contact FTDNA to get the details of the new BY SNPs not in YBrowse, but here is my depiction of a draft tree using the SNPs in the Z209 Pack.
https://dl.dropboxusercontent.com/u/17907527/R1b-Z209-Pack.pdf

This stuff is always doomed to be out of date but I believe this is very close in alignment with the Big Tree, the YFull experimental tree and stuff FTDNA has from years of accumulation.

Ric
11-05-2015, 05:41 PM
What is the level referring to, the number of branching event?

Mikewww
11-06-2015, 09:02 PM
What is the level referring to, the number of branching event?
The # of branching generations (not real generations) away from the trunk.
In other words the trunk is #1, the next oldest branches are #2, then next #3, etc.

Ric
11-06-2015, 09:28 PM
got it. thanks Mike.

Ric
11-13-2015, 09:48 PM
Do you guys, Mike and Razyn, have some ideas of the kind of results to expect, that you could share, or you prefer not to speculate, yet ?

There is a long way from Spain to Scotland, and it is hard to imagine that the z209 (or df27) populations expanded at the same pace and the same way, with the same founder effects everywhere, the same genetic bottlenecks effects, the same selection for phenotypes, all the way from Spain to Scotland.

PaddyOHannon
11-30-2015, 06:25 PM
Debut post here -- and first, I'd like to thank everyone for the information on this thread!

I'm trying to decide if purchasing the Z209 Pack is worth it or not. My curious nature is getting expensive, what with one test after another, seemingly.

I discovered my "R-Z209-ness" after purchasing a R-M269 pack. I tested negative, though, for Z295, as part of the aforementioned test. If I'm reading the pdf correctly, that eliminates a fair amount of what is tested in the 209 pack; pretty much isolating it to Z210 and everything under ZZ40_1 (inclusive). Is that a correct interpretation?

Thoughts on the value of the pack?

Thanks!

Ric
11-30-2015, 07:45 PM
Paddy, if you are not sure you can still wait for mid-December when the first results 'should' come and ask the z209+ z295- guys what they think their 'return for the money'.
I am z295+ so I can't tell you what you are missing exactly out of the 152 tested snp, but personally I'd like to get down to a relatively recent snp, with a bit better geographical location than 'somewhere in between the South tip of Spain to the North tip of Scotland', which the m243 pack didn't help much to resolve, but I guess I had to go through it before I could go further. Any test that improves the location/time is an acceptable return for the money don't you think?

PaddyOHannon
11-30-2015, 08:09 PM
Ric,

Good point! 'Spain to Scotland' really didn't help me, either... I was reasonably certain I'd come back with L21 or DF27 based on our *very* limited knowledge of my paternal tree. We know there's a combination of Irish/Spanish on his side; we're just not sure the sources of the various contributions, so to speak -- i.e. what is lurking in the pure paternal line vs. paternal/maternal stuff?

I'm leaning toward giving myself the Z-209 pack as a Christmas present unless I hear screams to the contrary from the experts.

ADW_1981
11-30-2015, 08:17 PM
Debut post here -- and first, I'd like to thank everyone for the information on this thread!

I'm trying to decide if purchasing the Z209 Pack is worth it or not. My curious nature is getting expensive, what with one test after another, seemingly.

I discovered my "R-Z209-ness" after purchasing a R-M269 pack. I tested negative, though, for Z295, as part of the aforementioned test. If I'm reading the pdf correctly, that eliminates a fair amount of what is tested in the 209 pack; pretty much isolating it to Z210 and everything under ZZ40_1 (inclusive). Is that a correct interpretation?

Thoughts on the value of the pack?

Thanks!

I bought about 3 SNPs a la carte, one of which was negative, so this might be a hair cheaper. I'm not an SNP expert, but it seems to have some good ones you are likely to be positive for as well.

razyn
11-30-2015, 10:25 PM
Do you guys, Mike and Razyn, have some ideas of the kind of results to expect, that you could share, or you prefer not to speculate, yet ?
I didn't actually see this question when you asked it, had just returned from a trip and had a bunch of music gigs in a row. Anyway, I'm cautiously optimistic that the SNPs in the graphic posted above by Mike (#7 on this thread) will be tested, the tests will work, and Z209+ people will learn a lot. In some cases we know more levels below Z209 than in others; but this SNP pack drills down as deeply as we knew to tell it, just a few weeks ago.

If you have already spent a wad on testing for subclades below Z209 -- and some were negative -- you aren't really starting at the starting line. So you may feel it was kind of expensive to pay another $119 (or $109 if you buy it before Dec.31), and just get one or two new SNPs. But the pack will also give you results for a lot of equivalent SNPs you haven't tested (FTDNA has not offered them before as single tests) -- fill in rungs on the ladder that you can assume, but have not tested, etc. For Z209 guys, it is both broad and deep. Those who go into it without having tested any of the SNPs on it (for instance, guys currently in group Ub) will presumably get the most for their money.

gotten
11-30-2015, 10:31 PM
OK, because this question pops up regularly I saved the Bigtree (ytree.net) downstream of Z209 and made a python script that adds a * before the SNPs that are in the Z209 pack.
Link to image (http://i.imgur.com/bsalgme.png?1) - 3000 pixels wide !

The SNPs that are also tested but not yet placed on the Bigtree are:
S16785 (this one is below ZZ40>S21184>S19290)
CTS7927 F2735 CTS8780 Z299 Z29666 A5376 PF2462 A5362 BY3333 FGC17318 CTS517 FGC29751 FGC29750 A5000 Z29690 PF7203 Z29689

As you can see from the image the Z209 pack is quite complete below ZZ40 (at least based on the current knowledge of the tree) so its a pretty economic choice.
Note that if you do take the pack and new discoveries are made you need to take more SNPs tests to keep up with developments. Doing a Big-Y or Y-elite 2.0 evades this problem because it discovers your private SNPs and the results directly contribute to improving the knowledge of the Y-tree.

It's a trade-off that you have to make yourself.

Ric
11-30-2015, 11:11 PM
. In some cases we know more levels below Z209 than in others; but this SNP pack drills down as deeply as we knew to tell it, just a few weeks ago.
wow, it's good to read that. I cross my fingers....


Note that if you do take the pack and new discoveries are made you need to take more SNPs tests to keep up with developments. Doing a Big-Y or Y-elite 2.0 evades this problem because it discovers your private SNPs and the results directly contribute to improving the knowledge of the Y-tree.
I start to think so too. Thanks for annotating the tree.

thetick
12-01-2015, 10:26 PM
OK, because this question pops up regularly I saved the Bigtree (ytree.net) downstream of Z209 and made a python script that adds a * before the SNPs that are in the Z209 pack.
Link to image (http://i.imgur.com/bsalgme.png?1) - 3000 pixels wide !

Very cool. Any chance you can share your code with Alex and get this in the DF-27 Big Tree ? It would nice see the above for the rest of DF-27.

gotten
12-01-2015, 11:33 PM
Very cool. Any chance you can share your code with Alex and get this in the DF-27 Big Tree ? It would nice see the above for the rest of DF-27.

The code is very hackish because it only does a string replace in the .htm code for matching SNP names. I'm sure Alex can do something way smarter in more native code.

Here are the Z198, Z209 and DF27 packs highlighted in the DF27 branch of www.ytree.net 's Bigtree. (18000 pixels wide, 860 kb each)
Z198 (http://i.imgur.com/Ana3Dwk.png), Z209 (http://i.imgur.com/Tip6mrV.png), DF27 (http://i.imgur.com/RBJVGy5.png)
I'll try something smart with colored *'s in the future.

The unmatched SNPs are

for Z198: Y1238 PF4280 CTS4015 F1697 PF4354 F1287 Y7729 FGC20084 PF1023 PF2462 F2536 Y9114 Y8412 CTS7416 BY3252 BY3254 CTS9454 Y8421 BY3268 BY3264 CTS10893 CTS9615 F3198 CTS5284 CTS3437 Y8417 Y8411 FGC9381 S16419 S23468 S4415 F3161 BY3271
for Z209: CTS7927 F2735 CTS8780 S16785 Z29666 A5376 PF2462 A5362 BY3333 FGC17318 CTS517 FGC29751 FGC29750 A5000 Z29690 PF7203 Z29689
for DF27: Y13115 FGC8127 Z226 BY3235 BY3332 BY3330 BY3331 S400 BY3329 BY3327 Y16018 Y14084 A6104 M225 A6456 BY3328 Y4867 Y14468 FGC14934

Ric
01-19-2016, 07:49 PM
The results are coming according to the admins of the df27 group at ftdna. I was found R-CTS4065 and negative for all snps downstream of it.

PaddyOHannon
01-19-2016, 08:32 PM
Well, I took the plunge and bought the Z209 pack. Apparently my results are back, although my Haplogroup still shows as R-Z209.

I downloaded the results as a CSV. I had 14 "no calls" in my results, along with the following showing as "TRUE" from the Z209 pack:
Z215
Z220
Z268
Z271
Z29689
Z694

What I don't understand is where these fall downstream from Z209. It isn't immediately clear from the Y-DNA Haplotree on FTDNA exactly where these fit. And, of course, the follow-on confusion of "what is this telling me?" is present. So much to learn, so little time!

gotten
01-19-2016, 09:34 PM
Z220, Z268, Z694, Z271 and Z215 are phylogenetically equivalent to Z209.
I think Z29689 is below CTS8087. What does it say about Z295, Z216 and CTS8087?

razyn
01-19-2016, 10:47 PM
Well, I took the plunge and bought the Z209 pack. Apparently my results are back, although my Haplogroup still shows as R-Z209.
Are you B54298? Of the 13 kits that returned Z209 SNP pack results last night, that's the only one I see with no subgroup named below the Z209 level. It just means you are Z209* as far as that test knows. That kit is probably in an undiscovered subclade, or one discovered since the test was designed (late October). If you aren't B54298, you need to join the DF27 haplogroup project.

Speaking more generally, this test worked very well for its intended purpose. Z210 was called negative in every sample, I believe incorrectly in all cases (they are positive for three others at the same level). Otherwise it looks credible. There may be quibbling about the stability of PF2462, which apparently occurs also below haplogroup E. But if you are positive for the instance of it beneath CTS12074, rest assured you aren't in the E group.

I guess I should post the breakdown of "terminal" SNPs as I can detect them easily. (A few could still be hiding in the .csv underbrush.)

1 - S16785 (below S21184)
1 - A7066
1 - FGC15710
1 - S21184
2 - CTS12074*
1 - CTS4065*
1 - Z295
1 - Z279*
1 - FGC23343
1 - PF2462 (below CTS12074)
1 - Z209*
1 - FGC34881

gotten
01-19-2016, 11:12 PM
I think Z29689 is below CTS8087.
Hmmm. I see many more Z209-pack-tested kits with Z29689+ that aren't CTS8087. False positive or ...? Big Y coverage is poor.

PaddyOHannon
01-20-2016, 07:49 PM
Thanks for the information -- very interesting!

I confess to being a little underwhelmed at my Y-DNA experiences thus far. I expect the solution is a generous application of patience and research. In retrospect, I can't help but wonder if I would've been better off going directly to Big-Y rather than spending the time/money doing incremental steps. That is, of course, water under the bridge at this point, but should someone inquire, I'd like to be able to give a more reasoned answer. It will be interesting to see where all this goes!

Cheers!

Mikewww
01-21-2016, 04:21 PM
What is the level referring to, the number of branching event?
This is a reference to the base or trunk of the tree. In this case, I used DF27 as the the base or level #1. Z209 is three branching events downstream (more recent) at level #4.

Ric
01-21-2016, 05:03 PM
This is a reference to the base or trunk of the tree. In this case, I used DF27 as the the base or level #1. Z209 is three branching events downstream (more recent) at level #4.

The tree indicates CTS4065 is level 7, therefore 3 branching events downstream of z209.
In Y tree here http://yfull.com/tree/R-DF27/
indicates df27 formed 4500 bp and z209 formed 4400 years ago with a Time of MostRecentCommonAncestor about the same at 4300 bp
and
cts4065 also formed around 4300 bp but with a TMRCA of only 3400 bp.

Does the difference indicate a bottleneck ?
If so, very little individuals must have carried CTS4065 3400 years ago and therefore their modern descendants, with all their snps downstream of cts4065, should be a representative sample of that small group. How come then, was I found with NONE of these downstream snps if the sampling is representative?
French people don't test much dna kits in general, not to mention BigY or snp paks, which means that the sampling may have excluded those 'French' cts4065 branches. But is it really a credible explanation?
After all, if we admit the TMRCA is 3400 bp down to one man, he can't be everywhere at the same time. If this man was in the Basque country, he can't be in France to make a new branch, and then in the British Isles to start another one etc., unless he traveled very fast and had sons everywhere.

razyn
01-21-2016, 05:55 PM
The branching below CTS4065 that we know about (and for which the Z209 chip is searching) has for the most part been discovered within the past 2 1/2 years, from NextGen testing (FGC and BigY). In several cases, matching samples were found in the older (and lower-resolution) 1000 Genomes project, and in the Genomes of the Netherlands project.

If FTDNA had a lot of French customers, or if there were a Genomes of France project on the shelf, we would know more about subclades found there and not elsewhere. They would be on the Z209 chip, and you would test positive; also if you had a BigY test, you would be much more likely to have a good match and a younger terminal SNP.

Ric
01-21-2016, 06:30 PM
also if you had a BigY test, you would be much more likely to have a good match and a younger terminal SNP.
Next Christmas maybe, I'm thinking about it.

For the French people testing, they are so far behind, even if they started now with a dna kit, which is unlikely, they would start with a cheap generic autosomal. I know there is a huge interest in genealogy in France, there are clubs everywhere, almost in every city. My mom stated a tree, that's how It started for me. Tests like the 23andme would sale in mass, this is guaranteed. But no, the French Elite has ruled that it's no good for the populace 'to know'. And I am certain that this elite uses dna kit for itself without any remorse while forbidding it for the mass, what a chutzpah!
But whoever company will get the French DNA genealogy market first, that's the jackpot for them.

Ric
01-24-2016, 04:59 PM
The branching below CTS4065 that we know about (and for which the Z209 chip is searching) has for the most part been discovered within the past 2 1/2 years, from NextGen testing (FGC and BigY). In several cases, matching samples were found in the older (and lower-resolution) 1000 Genomes project, and in the Genomes of the Netherlands project.

So does that mean CTS4065 is commonly found in the Netherlands? I assume the Netherland project was well representative of the Netherlander men, so me not sharing any SNP with them, means that my particular branch of CTS4065 is most likely NOT from the Netherlands, is that correct?

Unfortunately the French political issue with DNA testing won't resolve, not anytime soon I am afraid. There will be only a trickle of French testers like me, US residents or other. Which means that if my particular branch of cts4065 is French, I may never know.

razyn
01-24-2016, 05:16 PM
So does that mean CTS4065 is commonly found in the Netherlands? I assume the Netherland project was well representative of the Netherlander men, so me not sharing any SNP with them, means that my particular branch of CTS4065 is most likely NOT from the Netherlands, is that correct?
Well, your branch might not match one of the 500 or so males tested for that project, but could still match some other person of Dutch (or Flemish, Frisian, or some other nearby population) ancestry whose lineage has yet to be tested. France is far from the only possibility.

But, yes, it's the one with the most North American descendants (especially colonial ones who don't know where their immigrant ancestor originated), that has governmental roadblocks against testing people in the homeland.

gotten
01-24-2016, 05:22 PM
3 out of 250 fathers out of the GoNL project were CTS4065, 2 of which were in the van der Vliet/Bjorkman branch S11482. One was in the Pastore/Chernik/Zima branch S16864. You tested negative for both branches but this doesn't mean your branch doesn't exist in the Netherlands. It just wasn't tested in your SNP pack and there aren't more CTS4065 people in the GoNL project.

It is hard to derive a percentage out of this with such a small sample. The amount of CTS4065 in the Netherlands might be on the order of 1% but this could be proven to be wrong when a larger sample is tested.

One thing is clear: we need more Continental Europeans with Full Genome tests.