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TigerMW
04-18-2013, 09:47 PM
I've created a separate descendency tree graphic for DF27. I'll keep it posted on this URL so you can bookmark it. I'll try to keep this graphic current. It is the Y DNA tree/phylogeny for DF27 and subclades. I need help, though, to stay abreast the newly discovered SNPs and where they fit in.

https://dl.dropboxusercontent.com/u/17907527/R1b-DF27_Descendency_Tree.jpg

FTDNA's haplotree is way behind so for source data for the graphic I use International Society of Genetic Genealogy's (ISOGG) Y haplogroup R tree at
http://isogg.org/tree/ISOGG_HapgrpR.html

Another source of data is FTDNA's lab director Thomas Krahn and the draft tree he posts for DF27.
http://ytree.ftdna.com/index.php?name=Draft&parent=99813460

Of course, another source is new news from our R1b-P312 project Y DNS SNP report screen. I check it about once a week.
http://www.familytreedna.com/public/atlantic-r1b1c/default.aspx?section=ysnp

I'll also check the SRY2627/L176.2 and L165 projects, but do so only occasionally.
http://www.familytreedna.com/public/R1b1c6/default.aspx?section=ysnp
http://www.familytreedna.com/public/R-L165Project/default.aspx?section=yresults

It's okay to be in more that one project, so it helps me keep things updated if you join the R1b-P312 project at this link.
http://www.familytreedna.com/public/atlantic-r1b1c/

Henry Zenker, the P312 project admin is a good source of info too, along with our citizen-science research team.

Is there anyone that creates a comparison table of newly discovered SNPs from WTY/Geno 2.0 (raw) results for DF27? This is critical. Here is an example of what David Reynolds does for L21: http://daver.info/geno/results/R-L21.pdf

TigerMW
04-27-2013, 10:12 PM
I did some fine tuning based on the input and here is what I have now. Look okay? I can't find much information on Z198. Is it really approximate to L176.2?

http://tinyurl.com/R1b-DF27-Tree

thetick
04-28-2013, 01:53 AM
Great post. I'm SRY 2627+. I should probably get the Gen2.0 test since I suspect my SRY2627 A1 cluster probably has a unidentified SNP downstream.

TigerMW
06-13-2013, 08:53 PM
Here is the latest update.
http://tinyurl.com/R1b-DF27-Tree

TigerMW
07-09-2013, 02:58 PM
Below is the latest update. I've moved DF81 up. There still remains testing to be done but I think it will make ISOGG. A Mr. Uriarte contacted me to let me know.
259851 Uriarte DF27+, DF79-, DF81+, DF83-, DF84-, L1231-, L1245-, L194-, L617-, L86.2-, L881-, Z196-, Z225-
B3142 Ziga DF27+, DF79-, DF81+, DF83-, DF84-, Z196-, Z209-, Z220-, Z225-, Z229-

Is anyone pursuing ISOGG qualifications for this?

I think these guys are potentially Basque, but they have branched away from the Z220+ M153+ long ago. That indicates some diversity, which keeps Iberia and/or South France as critical to understanding DF27's origin. I guess that's for another thread though.

http://tinyurl.com/R1b-DF27-Tree

TigerMW
07-14-2013, 06:58 PM
What is the placement of Z215, Z268, and Z274?

This was posted today on another forum in response to this question.

all three were placed by Richard Rocca as approximate to Z209 when he did his research with the 1000 genomes project. Z268 was chosen to replace Z209 in the Geno 2.0 test, Henry Zenker wasn't quite sure why. The other two have not been confirmed as far as placement. They are probably somewhere between Z209 and Z220, but until someone ends up having one as either a terminal or as beginning a new branch, such as Z295 beginning the branch for the L484 guys, it's hard to say. Henry and I corresponded via email quite often and he explained to me that when Richard Rocca placed these snps, he wasn't quite sure where they went, so he clustered them around a snp that had a known placement.

We've already heard that FTDNA is not likely to develop an a la carte test for Z210 so it is just additional info, not really helpful for the official phylogenetic trees.

I'd like to know about why Z268 was chosen as a substitute for Z209 or what exactly that means. On ISOGG, Z268 is not listed as equivalent to Z209. It is just listed in their SNP index as under "investigation."

Webb
07-14-2013, 08:18 PM
What is the placement of Z215, Z268, and Z274?

This was posted today on another forum in response to this question.


We've already heard that FTDNA is not likely to develop an a la carte test for Z210 so it is just additional info, not really helpful for the official phylogenetic trees.

I'd like to know about why Z268 was chosen as a substitute for Z209 or what exactly that means. On ISOGG, Z268 is not listed as equivalent to Z209. It is just listed in their SNP index as under "investigation."

Here's a thought. Just like replacing Z195 for Z196. Maybe the goal of placing these "new" snps on the list to test for was a test in itself. If you have a list of snps and you think you know roughly where they are, the more people you can get to test for them might help you figure where they really belong.

Webb
07-14-2013, 10:23 PM
Also, Z274 is somewhere between Z195/Z196 and Z268/Z209. So if DF17 people are testing positive for Z274 then that is possibly the location of where they break off.

1st Edit: Mike, I went back and looked at my spreadsheet and I one individual who is Z195+ and Z274+. There are no other Z series snps in the results. My guess is this individual is in actuality DF17. So I'm pretty sure that DF17 broke off just before Z209.

2nd Edit: I confirmed that the one DF17 Geno test I have access to at Semargl is positive for Z274. So DF17 actually broke off at Z274, or thereabouts, which as of now is right above Z209.

razyn
07-15-2013, 03:51 AM
B. Webb, I can't "reply" to what Mike quotes you as saying (it disappears), but I believe it is CTS4065 and not Z295 that "leads" to L484+ (and to other guys who are L484-, but are Z295+ -- like all those other guys, such as Z216, Z278, M153). That mostly Iberian fork under Z295 may be defined by CTS 12074, though I'm not sure the case has been proven. I suspect it could be -- and if so, CTS12074 should also be in Mike's chart. There may be somebody out there who proves whether CTS12074 is above Z216 etc. I haven't yet had time to work on it much.

Webb
07-15-2013, 01:30 PM
B. Webb, I can't "reply" to what Mike quotes you as saying (it disappears), but I believe it is CTS4065 and not Z295 that "leads" to L484+ (and to other guys who are L484-, but are Z295+ -- like all those other guys, such as Z216, Z278, M153). That mostly Iberian fork under Z295 may be defined by CTS 12074, though I'm not sure the case has been proven. I suspect it could be -- and if so, CTS12074 should also be in Mike's chart. There may be somebody out there who proves whether CTS12074 is above Z216 etc. I haven't yet had time to work on it much.

My plan is once I think I have the Geno "Z" series snps roughly figured out, I am going to go back and track the "CTS" series snps and start comparing them.

Edit: I checked my notes and CTS12074 is the snp I noticed that the "Iberian" fork carries. Henry thought it was right around Z278, maybe just upstream. Please see my post above about DF17. I think it is huge. Huge, I tell you.

TigerMW
07-15-2013, 06:34 PM
Here's a thought. Just like replacing Z195 for Z196....

Richard D on the P312 group posted this.

I was recently paging through the list of SNP results for the new DF27 project. I was confused when I noticed a L617+ and Z195+ result for kit N115093. It is my understanding that these two SNP's are on different branches under DF27. Any one know if this is an error by FTDNA or am I mixing things up? http://tech.groups.yahoo.com/group/R1b-P312-Project/message/5954

We've been assuming Z196 and Z195 are phylogenetically equivalent, but that can only be an assumption because you can never prove it. All it takes is one new person to pop up to prove one is older than the other.

N115093 Hall L617+, Z195+, Z210+, Z215+, Z220+, Z268+, Z274+

5928 Marsh L617 5928 Marsh L617+, Z196-

As long as Z196 and Z195 are all stable SNPs, it appears that Z195 is older than Z196 since L617+ is Z195+ but Z196-.

Can Z195 be ordered a la carte? It would be good idea for Marsh to test for Z195 and possibly for Hall to test for Z196.

DavidCar
07-15-2013, 06:36 PM
Note: There is still the untestable Z294 between Z274 and Z209.

As far as Z274 being above DF17, there is the Hart kit which is DF17+, CTS7768+ and Z274+, and also kit N30509 in the French Heritage Project that is CTS7768+ and Z274+. CTS7768+ is apparently "phylogenetically equivalent" to DF17+.

razyn
07-16-2013, 12:03 PM
Re: N115093 Hall L617+, Z195+, Z210+, Z215+, Z220+, Z268+, Z274+

I can't find this recently deceased guy in either the R1b-P312 project (which his sister says he joined) nor the Hall family project. I would like to look at his STR results. We wouldn't see them in a Geno2 report, anyway -- but his sister says he has only one vial left, and that sounds like a regular FTDNA customer (maybe with a different kit number, as such?) who might be found in the above mentioned projects under an ID other than his Geno kit number.

One Hall family (group 006 in their FTDNA surname project, with 8 members currently) is Z210+, Z220+, CTS4065+, L484+. In case that is at all relevant for identifying N115093 John Hall. We have a very strong off-modal signature, and it's not at all similar to that of L617+ (unless it turns out that L617 occurs in more than one place, and needs decimal places after it).

TigerMW
07-16-2013, 01:48 PM
Re: N115093 Hall L617+, Z195+, Z210+, Z215+, Z220+, Z268+, Z274+
..

L617 is perplexing. Here is my best shot at things right now. Is there anything wrong on this?

Should Z268 be in a cloud underlaying Z209 as phylogenetically equivalent?

Should be CTS12074 be in a cloud underlaying Z216 as phylogenetically equivalent? Do we know if it is above or below?

http://tinyurl.com/R1b-DF27-Tree

razyn
07-16-2013, 03:55 PM
I think CTS12074 is where it should be (cloud is fine, until we know how far up or down to hang it, but it's in the right lineage). But you have a typo in the chart, it's CTS12074, not CTS12704.

I don't know why L484.NS is still in a cloud, we've known for over a year where we are -- a couple or three more SNPs above us have surfaced since then, because they are on Geno2, but one of our guys (Travis) also has a Geno2 test reported. I guess waiting for his L484+ to post is OK, but the guy is after all my cousin from Tennessee, not some mysterious line from Poland (which we also have in the L484+ group).

I'm waiting to hear back from N115093 John Hall's sister, I emailed her off-list today. That might settle some of the dust around the tree placement of L617 (or, it might not).

DavidCar
07-16-2013, 04:16 PM
The Hall kit has 5 false positives and 91 no-calls, like the Borquez kit that has 4 false positives and 116 no-calls. Consider the Hall L617 to be bogus.

DavidCar
07-16-2013, 04:23 PM
For the record the false positives in the Hall kit are:

CTS11067, L617, PAGES00022, PF3236, PF3303

The false positives in the Borquez kit are:

CTS5318, L160, U175, Z6.

And to add to the fun, the Crandall kit has 4 or 5 bogus SNPs in the FTDNA upload that are not in the raw data, including:

L99, Z38, Z70, and some others.


--- I should say "likely" false positives. Maybe one could be real, but it would be expensive to prove which one.

Webb
07-17-2013, 10:28 AM
For the record the false positives in the Hall kit are:

CTS11067, L617, PAGES00022, PF3236, PF3303

The false positives in the Borquez kit are:

CTS5318, L160, U175, Z6.

And to add to the fun, the Crandall kit has 4 or 5 bogus SNPs in the FTDNA upload that are not in the raw data, including:

L99, Z38, Z70, and some others.


--- I should say "likely" false positives. Maybe one could be real, but it would be expensive to prove which one.

I did a search on semargl.me for L617 and I found it among the Geno 2.0 results for a few L21, U152, and DF27 individuals. I would agree with David that it is an unreliable result in regards to Geno 2.0.

TigerMW
07-17-2013, 02:51 PM
I think CTS12074 is where it should be (cloud is fine, until we know how far up or down to hang it, but it's in the right lineage). But you have a typo in the chart, it's CTS12074, not CTS12704.

I don't know why L484.NS is still in a cloud, we've known for over a year where we are -- a couple or three more SNPs above us have surfaced since then, because they are on Geno2, but one of our guys (Travis) also has a Geno2 test reported. I guess waiting for his L484+ to post is OK, but the guy is after all my cousin from Tennessee, not some mysterious line from Poland (which we also have in the L484+ group).
....

Here is an update.

http://tinyurl.com/R1b-DF27-Tree

The reason I put things in a cloud is that they are uncertain or some extra precaution is needed - that's all. I have put L617 in a cloud now because an L617+ result apparently does not (essentially) guarantee membership in the particular subclade with DF27+ Z196- that we think is out there.

Likewise, L484, has multiple occurrences and will never be on ISOGG. If it'll never be on ISOGG it'll never be safe position-wise. One of the functions ISOGG does is ensures that any new SNP must be proven in its positioning through a combination of testing of potential children, brothers and parents. I consider that safe. I still record it in the spreadsheet and it has its own subgrouping in the DF27 project sense. I think I put L484.NS in the cloud because of the appearance of CTS4065.

So if Hans is L484- and CTS4065+, that should be the proof I was looking for that L484 is clearly below CTS4065
http://www.anthrogenica.com/showthread.php?911-Z209-(DF27-gt-Z196-gt-Z209)-and-subclades-including-NS-Cluster-and-M153&p=8870&viewfull=1#post8870

Maybe I misinterpreted David's statement about CTR4065's placement.

There is something similar to L484.NS in L21 land, so I guess this calls for a new graphic depiction. I'll put these types of situations in rectangles but with dotted edging so we know that new SNPs in the vicinity won't be cross-checked and documented by ISOGG vis a vis this occurrence of L484+.

DavidCar
07-17-2013, 07:26 PM
Here is an update.

Maybe I misinterpreted David's statement about CTR4065's placement.



Your graph correctly illustrates what I intended regarding CTS4065 and L484.

razyn
07-17-2013, 08:43 PM
Likewise, L484, has multiple occurrences and will never be on ISOGG. If it'll never be on ISOGG it'll never be safe position-wise.

I don't want to seem combative, but I don't think either of those sentences is true as stated. L176 has multiple occurrences, as do numerous other SNPs, and the phylogenetically meaningful ones routinely are positioned on the ISOGG tree after someone gets around to assigning them decimal places. There are testing issues with L484 (and it may be impossible with the Next-Gen chip technology, which is clearly the way they'd like to go), but not stability issues. The four or five lines that have it, under Z295 etc., have had it for many hundreds of years. It's just as "safe" now as it was at the Battle of Hastings. Life is full of little problems, and getting on ISOGG isn't one of the biggest, but I still contend that we are in every sense qualified, and one day soon I'll submit the case.

But that aside, I agree with the current version of your excellent chart.

TigerMW
07-18-2013, 04:06 AM
Likewise, L484, has multiple occurrences and will never be on ISOGG. If it'll never be on ISOGG it'll never be safe position-wise.


I don't want to seem combative, but I don't think either of those sentences is true as stated. L176 has multiple occurrences, as do numerous other SNPs, and the phylogenetically meaningful ones routinely are positioned on the ISOGG tree after someone gets around to assigning them decimal places...

It's okay to disagree. I should clarify that I'm not guaranteeing that L484 will never be on ISOGG. I'm just pretty sure it won't. David Reynolds is our ISOGG R1b rep and he's already said that FTDNA and ISOGG will resist adding any SNP that occurs more than twice. L176 has two known occurences. L484 already has several.

I've got your quote for David.

David Reynolds has mentioned (on a WorldFamilies thread about Z209) that "L484 is a case where one is actually looking at an STR, not an SNP, so one sees multiple 'state' changes as the repeat count goes up/down."
http://tech.dir.groups.yahoo.com/group/R1b-P312-Project/message/4782

I don't care. I hope ISOGG takes L484 on but I'm not going to say something is that isn't. I think the odds are bleak and you should look for additional SNPs that could substitute for L484.NS. If you want to pursue L484 with ISOGG I'm on your side, but effectively David is ISOGG for us. He is not the bad guy in this though. He's just doing his best to weigh the information objectively and apply to a process that is manageable.

My definition of "safety" in regards to all of this is my own. I use ISOGG as a safety blanket because I know they do the cross-checking.

TigerMW
07-18-2013, 01:15 PM
Speaking of L176.2, is Z198 still holding as equivalent to L176.2? How many tested L176.2* Z198+ folks are out there?

TigerMW
07-19-2013, 03:53 PM
Can Z295 be ordered via FTDNA a la carte?

Can CTS4065 be ordered via FTDNA a la carte?

Webb
07-19-2013, 04:28 PM
Can Z295 be ordered via FTDNA a la carte?

Can CTS4065 be ordered via FTDNA a la carte?

No Mike, neither are being offered at this point.

TigerMW
07-19-2013, 08:07 PM
No Mike, neither are being offered at this point.

Thank you, Webb. That means on the project screen I should probably back off the requirement of Z295- for Z220* and go back to Z216-.

razyn
07-19-2013, 08:53 PM
Seems to me there's still a difference of opinion here about the nuances of a testing requirement, a function of what FTDNA can currently sell us, vs the definition of the phylogeny, which has more to do with the documented facts as we know them, from whatever reliable source (including, but not limited to, other lab work FTDNA and its Houston sister companies are doing, but not selling as individual orders).

I'm very much more interested in the latter (as shown e.g. in your descendency graphics). I don't perceive that [definition of the phylogeny] as a function of whether the SNP (test) is for sale by FTDNA, or it was discovered in WTY, 1000 Genomes, any other tested genomes or Y chromosomes, the Geno2 chip, Adriano's parsing of 23andMe data... have I skipped any reliable sources? Didn't mean to.

If this just has to do with the "further testing" advice we give people, we should be able to write that in a way that narrows such advice to the possible.

TigerMW
07-20-2013, 06:48 AM
Seems to me there's still a difference of opinion here about the nuances of a testing requirement, a function of what FTDNA can currently sell us, vs the definition of the phylogeny, which has more to do with the documented facts as we know them, from whatever reliable source (including, but not limited to, other lab work FTDNA and its Houston sister companies are doing, but not selling as individual orders).

I'm very much more interested in the latter (as shown e.g. in your descendency graphics). I don't perceive that [definition of the phylogeny] as a function of whether the SNP (test) is for sale by FTDNA, or it was discovered in WTY, 1000 Genomes, any other tested genomes or Y chromosomes, the Geno2 chip, Adriano's parsing of 23andMe data... have I skipped any reliable sources? Didn't mean to.

If this just has to do with the "further testing" advice we give people, we should be able to write that in a way that narrows such advice to the possible.

I agree that the phylogeny is what it is. We are just discovering it as we go and you are right, that's what I try to depict in those graphics but it is just a best effort.

Ultimately, are you talking about the use of asterisks/paragroups in subgroupings? ... that I said below "I should probably back off the requirement of Z295- for Z220* and go back to Z216-". I apologize, but I did not intend to use the word "requirement" as meaning every Z220 needed to test for Z295 or not or Z216 or not. I just meant as a "requirement" for the use of the asterisk but that is a loose thing I use in the spreadsheets and subgroupings and I think are a nice way to highlight people who have done a lot of testing. Asterisks are a forever shifting thing and there are shades of gray between testing for all potential next level down SNPs versus formal ones on ISOGG versus testing absolutely everthing including private SNPs. We can use Z295- in the Z220 case but that will pretty much close off that subcategory that would be the asterisk to a limited few people. Do you want Z220* to be Z220+ Z295-? I'm okay with that. It actually could be Z210 in their between Z220 and Z216, anyway but the status of that Z210 a bit iffy. Even though Geno 2 reports it as a terminal SNP (I'm told), FTDNA is telling Reynolds that Z210 sits on an unstable segment so they won't support it.

As far as testing advice, what I'd really to see, is for people to come on to the yahoo group and ask us (project admins, other experts, other members in a similar position) for help. I'm leery of giving precise advice as there are oftentimes a couple of ways to go and it really is the individual's decision. It's good to have a discussion with multiple inputs and then the individual decides. Unfortunately, not everyone will join in those discussions but there is no way to adequately make all of the recommendations by using the FTDNA project screens. We can't get all of the nuances of testing options right on a the project screens.

As far as what some other projects do, I know L21 pretty much follows the ISOGG line. If it is in ISOGG it gets a subgrouping. If it isn't, it doesn't. The U106 group is much more aggressive and takes the leading edge knowledge to have more elaborate subgroupings, although still pretty much entirely based on SNP testing. Maintenance becomes a factor.

Webb
07-20-2013, 05:37 PM
I agree that the phylogeny is what it is. We are just discovering it as we go and you are right, that's what I try to depict in those graphics but it is just a best effort.

Ultimately, are you talking about the use of asterisks/paragroups in subgroupings? ... that I said below "I should probably back off the requirement of Z295- for Z220* and go back to Z216-". I apologize, but I did not intend to use the word "requirement" as meaning every Z220 needed to test for Z295 or not or Z216 or not. I just meant as a "requirement" for the use of the asterisk but that is a loose thing I use in the spreadsheets and subgroupings and I think are a nice way to highlight people who have done a lot of testing. Asterisks are a forever shifting thing and there are shades of gray between testing for all potential next level down SNPs versus formal ones on ISOGG versus testing absolutely everthing including private SNPs. We can use Z295- in the Z220 case but that will pretty much close off that subcategory that would be the asterisk to a limited few people. Do you want Z220* to be Z220+ Z295-? I'm okay with that. It actually could be Z210 in their between Z220 and Z216, anyway but the status of that Z210 a bit iffy. Even though Geno 2 reports it as a terminal SNP (I'm told), FTDNA is telling Reynolds that Z210 sits on an unstable segment so they won't support it.

As far as testing advice, what I'd really to see, is for people to come on to the yahoo group and ask us (project admins, other experts, other members in a similar position) for help. I'm leery of giving precise advice as there are oftentimes a couple of ways to go and it really is the individual's decision. It's good to have a discussion with multiple inputs and then the individual decides. Unfortunately, not everyone will join in those discussions but there is no way to adequately make all of the recommendations by using the FTDNA project screens. We can't get all of the nuances of testing options right on a the project screens.

As far as what some other projects do, I know L21 pretty much follows the ISOGG line. If it is in ISOGG it gets a subgrouping. If it isn't, it doesn't. The U106 group is much more aggressive and takes the leading edge knowledge to have more elaborate subgroupings, although still pretty much entirely based on SNP testing. Maintenance becomes a factor.

Mike, what makes the whole Z209 tree so unstable that FTDNA is hesitant to test the new snps?

TigerMW
07-21-2013, 04:26 AM
Mike, what makes the whole Z209 tree so unstable that FTDNA is hesitant to test the new snps?

From what I've seen, FTDNA is not treating Z209 differently than any other subclade. Besides whether an SNP has potential for being public or not they seem to evaluate both thee stability of the segment of the Y chromosome that SNP in question is on as well as the reliability of their test process for that particular SNP.

I'm not a biochemist, but that is just my interpretation. David Reynolds communicates with Thomas Krahn quite a bit. He'd probably be able to answer correctly. I'm just guessing.

TigerMW
09-12-2013, 09:01 PM
Seems to me there's still a difference of opinion here about the nuances of a testing requirement, a function of what FTDNA can currently sell us, vs the definition of the phylogeny, which has more to do with the documented facts as we know them, from whatever reliable source (including, but not limited to, other lab work FTDNA and its Houston sister companies are doing, but not selling as individual orders).

I'm very much more interested in the latter (as shown e.g. in your descendency graphics). .....
I've been kind of waiting to upgrade that descendency tree for more Geno 2 test results and some comparative analysis to see how things settle out. http://tinyurl.com/R1b-DF27-Tree

It appears Chris Morley's tool is doing a good job of that comparative analysis. We need to integrate that with other sources, such as WTY and now Fullgenomes. Page 41 of the 9/7/2013 version is where we see Z274 so I'm trying to understand that.
http://ytree.morleydna.com/ExperimentalGenoPhylogeny20130907.pdf

Here is what I see on the Morley tool.

Z274
. Z209 Z210 Z215 Z220 Z268
. . Z295
. . . Z270
. . . . CTS12074 Z211 Z212 Z273
. . . . . Z214 Z299
. . . . . . Z279
. . . . . . . M153
. . . . . . . L160/PF4013 U175 Z6
. . . . PF5535
. . . CTS4065
. . . . L484.NS
. . CTS11067 L617 PAGES00022 PF3236 PF3303
. CTS7768 DF17

I don't see Z294 in the tool. Does Geno 2 test for it? Can we say certainly that Z274 is above Z294? I think that is true.

We know that Z220 is above Z210, right? I wonder why the tool isn't showing that.

Are Z270, PF5535 and CTS12074 all considered stable? It looks like I should insert them. With Thomas Krahn gone, I'm not sure how we can handle questions of stability. I guess we have to fend for ourselves and just observe what's working and what isn't (SNP consistency wise.)

Can any of these three be ordered a la carte?

I'm a little confused by L617. He has it showing up in two places.

Perhaps things are settled enough (unfortunately in some regards due to Krahn's departure) that I should go ahead and use some symbol/color coding to mark SNPs that are in Geno 2 or are available a la carte.

TigerMW
09-12-2013, 11:53 PM
Here is what I see on the Morley tool.

Z274
. Z209 Z210 Z215 Z220 Z268
. . Z295
. . . Z270
. . . . CTS12074 Z211 Z212 Z273
. . . . . Z214 Z299
. . . . . . Z279
. . . . . . . M153
. . . . . . . L160/PF4013 U175 Z6
. . . . PF5535
. . . CTS4065
. . . . L484.NS
. . CTS11067 L617 PAGES00022 PF3236 PF3303
. CTS7768 DF17


These appear to be available on the FTDNA a la carte advanced order system.
Z209 Z209 Z268 Z214 M153 L160 Z6 CTS7768 DF17 L617

These do not.
Z274 Z294 Z210 Z295 Z270 CTS12074 Z211 Z212 Z273 Z299 Z279 PF4013 PF5535 CTS4065 CTS11067 PF3236 PF3303

razyn
09-13-2013, 03:28 AM
I don't see Z294 in the tool. Does Geno 2 test for it? Can we say certainly that Z274 is above Z294? I think that is true.

I've thought so, from work Rich Rocca posted to DNA-Forums over two years ago, but Z294 has never become an available SNP test.


We know that Z220 is above Z210, right? I wonder why the tool isn't showing that.

I think the tool is an algorithm, and doesn't report what Geno 2 doesn't tell it. Chris Morley can sort of force-feed it with additional data we provide to him from our other reliable sources. I think the only statement about the positioning of Z210 I've seen was more or less a rumor started by you (Mike), probably based on good evidence in your Excel documents that I've not yet mastered.


Are Z270, PF5535 and CTS12074 all considered stable? It looks like I should insert them. With Thomas Krahn gone, I'm not sure how we can handle questions of stability. I guess we have to fend for ourselves and just observe what's working and what isn't (SNP consistency wise.)

I concur, about the fending part. There are other well informed friends out there besides Thomas, but he ran the lab most of us have been using, and we are getting through the X stages of grief or whatever.


I'm a little confused by L617. He has it showing up in two places.

Yeah, so? It's recurrent; I still don't think that means "unstable." That false equation reflects either laziness in the lab, sloppy semantics, or some economic thing (whether solid positioning of that SNP is worth what testing for it costs) that doesn't matter, to the actual science of it. That place on the chromosome has a tendency to mutate more often than we might wish; TS. Some specific loci have been seen to mutate two or three times within one haplogroup; yet there are old and widely dispersed lineages bearing one of those mutations, a thousand or more years thereafter. How on earth can that be considered phylogenetically unstable?


Perhaps things are settled enough (unfortunately in some regards due to Krahn's departure) that I should go ahead and use some symbol/color coding to mark SNPs that are in Geno 2 or are available a la carte.

Your co-administrators stand ready to assist. It takes a village.

TigerMW
09-13-2013, 11:52 AM
I think the tool is an algorithm, and doesn't report what Geno 2 doesn't tell it. Chris Morley can sort of force-feed it with additional data we provide to him from our other reliable sources. I think the only statement about the positioning of Z210 I've seen was more or less a rumor started by you (Mike), probably based on good evidence in your Excel documents that I've not yet mastered.

I wouldn't really say it is a rumor, just a comparison of the data. It's not really the spreadsheet. That's just a tool that helps find and sort stuff versus manually scanning or manually doing ctrl-F's or something.


I just ran through the same exercise as David C did.

I found theses Geno 2.0 results with Z210+

N94262 Victoriano Perez/Peres Z210+, Z214-, Z216+, Z220+, Z274+, Z278+

N8661 Ramon Borquez Z210+, Z214+, Z220+, Z274+, Z278+

211471 Unknown Z210+, Z216-, Z220+, Z274+

N50965 Joseph Trinquier Z209+, Z210+, Z214+, Z216+, Z220+, Z274+, Z278+

N2640 John Chalmers Z209+, Z210+, Z214-, Z216-, Z220+, Z274+, Z278-

The highest level SNP that we know is below Z210 is Z216 because we see both
Z216+ and Z216- folks above.

Assuming that the draft by the citizen-scientists is correct at
http://www.u152.org/images/stories/Draft_P312_Tree_v005.png
then Z210 is below Z220.

Hence, Z210 is above Z216 and below Z220 and should be moved up the line
halfway on the draft tree.
http://groups.yahoo.com/neo/groups/R1b-P312-Project/conversations/topics/5647

This is all Morley's tool is doing, just making comparisons based on Geno 2 results. Morley would not have the knowledge of Rocca's draft tree, though. Apparently the Rocca citizen-scientist team found Z210 downstream of Z220 and equivalent approximately to Z216. That comparative process is also no different than Morley's tool or what we can see by looking at results manually.

The above test kits show Z210 has to be above Z216....

assuming these test results are correct and the SNP is not recurrent or otherwise unstable... which we'd need someone like a lab director to help on that.

I concur, about the fending part. There are other well informed friends out there besides Thomas, but he ran the lab most of us have been using

How do we assess what is reliable or not?

I just noticed that Morley's tool does not have Z216 in the tree below Z274. I surmise Z216 is not in Geno 2, or gives false calls in Geno 2. Is either true? Is there any way you can research that? Is here is the full question - What SNPs below Z274 are available from FTDNA or somewhere else but are not in Geno 2?

Webb
09-13-2013, 09:18 PM
This was an email I recieved from Henry during some of our correspondence. I can confirm his placements of most of the snp's through my own spreadsheet I have been keeping of the North/South Cluster and DF17 results from the Geno 2.0 tests. My data is a little old as I use Semargl's website to view the test results, and it seems to take a few weeks for Geno 2.0 results to get posted there. Again, that is where I mistakenly added a DF17 person to my spreadsheet, because they were positive for Z274. It took Torres mentioning that he noticed that DF17 was also positive for Z274 that made me realize that it was in fact true. Morley's current tree looks more like Rocca's draft tree than it does the actual tree of the North/South Cluster. It places the snp's fairly close to where they are supposed to be, but an algorithm is not able to reason through results to correctly place these snp's where they belong based on whether an individual tested negative or positive. Only human eyes can do that. This is how I came to the conclusion that Geno is probably not testing for Z216, despite Henry thinking they were. Kits 289627, N58888, N8661 are positive for Z278 but do not show negative for Z216. There are no negative results for these kit numbers, making me assume they have only ever tested with Geno. The other kits that show both Z278 and Z216 also show a whole slew of other negative results, leading me to believe they have also tested with FTDNA for other SNPs.



"Billy,

I have extensive spreadsheets on all this, and can sort you out a bit with the following:

CTS12074 is new and appears approximate Z278; possibly above Z278

M269, M173, P25 are tests from different versions of FTDNA's Deep Clade Test; these were not tested by Geno2. Whether they appear in one and not others only reflects that they had different versions of the Deep Clade test.

Z148 ............ under U152; discard since it is appearing positive in R1b Geno2 tests; offered by FTDNA
Z191 ............ under U152; discard since it is appearing positive in R1b Geno2 tests; not offered by FTDNA
Z195 ............ approximate to Z196 and replaces Z196 in Geno testing; offered by FTDNA
Z196 ............ result comes from FTDNA Advanced Testing; not tested by Geno where it is replaced by Z195; offered by FTDNA
Z209 ............ result comes from FTDNA Advanced Testing; not tested by Geno where it is replaced by Z268; offered by FTDNA
Z210 ............ appears approximate to Z216 according to R. Rocca's research, but may be between Z220 and Z216; tested by Geno; not offered by FTDNA

Z211 ............ appears approximate to Z278 according to R. Rocca's research; tested by Geno; not offered by FTDNA
Z212 ........... appears approximate to Z278 according to R. Rocca's research; tested by Geno; not offered by FTDNA
Z214 ........... result comes from FTDNA Advanced Testing and tested by Geno; offered by FTDNA
Z215 ............ appears approximate to Z209 according to R. Rocca's research; not offered by FTDNA
Z216............. result comes from FTDNA Advanced Testing and tested by Geno; offered by FTDNA
Z220 ............ result comes from FTDNA Advanced Testing and tested by Geno; offered by FTDNA
Z268 ............ approximate to Z209 and replaces Z209 in Geno testing; offered by FTDNA
Z270 ........... appears approximate to Z216 according to R. Rocca's research; tested by Geno; not offered by FTDNA
Z273........... appears approximate to Z216 according to R. Rocca's research; tested by Geno; not offered by FTDNA
Z274 ............ placed between Z195/Z196 and Z209/Z268 on tree; not offered by FTDNA
Z278............ result comes from FTDNA Advanced Testing and tested by Geno; offered by FTDNA
Z279 ........... appears approximate to Z214 according to R. Rocca's research; tested by Geno; not offered by FTDNA
Z295 ........... appears approximate to Z209 according to R. Rocca's research, but may be incorrect and equiv to Z278; tested by Geno; not offered by FTDNA
Z299 ........... appears approximate to Z214 according to R. Rocca's research; tested by Geno; not offered by FTDNA
Z365 ............ under U106; discard since it is appearing positive in R1b Geno2 tests; not offered by FTDNA






R1b-P312
.............DF27
................Z196/Z195
..............................Z274
..................................Z209/Z268, Z215, Z295

......................................Z220
...........................................[Z210] .....possibly between Z220 and Z216 according to N2640's results .... needs confirmation

.................................................. Z216, Z210[?], Z270, Z273
.................................................. .......Z278, Z211, Z212
.................................................. ...........Z214, Z279, Z299
.................................................. ..................M153





Henry"

razyn
09-14-2013, 12:10 AM
It places the snp's fairly close to where they are supposed to be, but an algorithm is not able to reason through results to correctly place these snp's where they belong based on whether an individual tested negative or positive. Only human eyes can do that.

I don't think this is a truism. Depends on the algorithm, and the eyes. This particular algorithm doesn't tell about negatives that weren't reported by FTDNA (though the chip tested them), or about cells that failed, or about SNPs that weren't on the chip. Some of that info is available from other sources and has been provided to Chris Morley, who overrides the algorithm if that's phylogenetically useful.


Z295 ........... appears approximate to Z209 according to R. Rocca's research, but may be incorrect and equiv to Z278; tested by Geno; not offered by FTDNA

Henry had insufficient data and this one is wrong, Z295 is above Z278 and also above CTS4065, an entirely separate lineage that is more northeastern, and doesn't include Z278.

There may be other minor corrections needed, but I didn't notice anything else that made me break out in hives.

R.Rocca
09-14-2013, 12:36 AM
I don't think this is a truism. Depends on the algorithm, and the eyes. This particular algorithm doesn't tell about negatives that weren't reported by FTDNA (though the chip tested them), or about cells that failed, or about SNPs that weren't on the chip. Some of that info is available from other sources and has been provided to Chris Morley, who overrides the algorithm if that's phylogenetically useful.



Henry had insufficient data and this one is wrong, Z295 is above Z278 and also above CTS4065, an entirely separate lineage that is more northeastern, and doesn't include Z278.

There may be other minor corrections needed, but I didn't notice anything else that made me break out in hives.

Correct. on the updated tree I had from earlier in the spring, Z295 is without a doubt above Z278 and CTS4065 which are separate brother clades.

Webb
09-14-2013, 12:45 AM
I don't think this is a truism. Depends on the algorithm, and the eyes. This particular algorithm doesn't tell about negatives that weren't reported by FTDNA (though the chip tested them), or about cells that failed, or about SNPs that weren't on the chip. Some of that info is available from other sources and has been provided to Chris Morley, who overrides the algorithm if that's phylogenetically useful.



Henry had insufficient data and this one is wrong, Z295 is above Z278 and also above CTS4065, an entirely separate lineage that is more northeastern, and doesn't include Z278.

There may be other minor corrections needed, but I didn't notice anything else that made me break out in hives.

You are correct about Z295. Your cousin was the first to test positive for Z295 and negative for the Z216/Z278 cluster, I believe. I think this happened after Henry was no longer able to serve as admin.

razyn
09-14-2013, 01:42 AM
Your cousin was the first to test positive for Z295 and negative for the Z216/Z278 cluster, I believe.

Maybe the first in the DF27 project -- I think Ware and Sarabia had already tested that way, of whom Ware has subsequently joined the project. And we've picked up a few more from elsewhere; Cartier is in the project but doesn't have any STRs visible yet. van Vliet is in the project but his Full Genome results (Z295+, CTS4065+) are invisible; SNPs he had tested earlier at FTDNA are visible. A bunch of guys are working on this. There's even breaking news, sort of... F2302+ may be under CTS4065, some of these guys have it and some don't. Trouble is, it's also found elsewhere in DF27 (a "recurrent" mutation, I guess -- or perhaps a malfunctioning cell, a marker that needs to be read in two directions, or whatever). It's at least another thing to watch, in that fascinating lineage.

cmorley
09-14-2013, 03:17 AM
I just noticed that Morley's tool does not have Z216 in the tree below Z274. I surmise Z216 is not in Geno 2, or gives false calls in Geno 2. Is either true? Is there any way you can research that? Is here is the full question - What SNPs below Z274 are available from FTDNA or somewhere else but are not in Geno 2?

The PDF is searchable. Z216 is reported a few lines below Z274, approximately equivalent to Z278. Consistent with ISOGG tree v. 8.75. The coverage statistic for Z216 is 10/16 (8/8 a la carte + 2/8 Geno). Looks like its Geno probe is bad.

The legend (page 4) will tell you which SNPs are Geno-tested. The description beside "M343" (black text) should actually read "Geno-tested SNPs with positions known to ISOGG." (Previous versions of the algorithm did not report results for non-Geno SNPs unmentioned in the ISOGG tree, so it previously wasn't necessary for the legend to make this distinction.)



This particular algorithm doesn't tell about negatives that weren't reported by FTDNA (though the chip tested them), or about cells that failed, or about SNPs that weren't on the chip.


The algorithm actually does think about whether each Geno-tested SNP not reported positive is negative or a no-call. It can't be accurate all the time. This would be moot if the FTDNA SNP reports reported no-calls.



Some of that info is available from other sources and has been provided to Chris Morley, who overrides the algorithm if that's phylogenetically useful.

The algorithm is already capable of fusing Geno and non-Geno data (in the form of a la carte-ordered SNPs and deep clade results). WTY calls and Full Genomes calls aren't much different from the present form of non-Geno data. If you can provide some WTY or FG data, I'll feed it to my algorithm and see what happens.




F2302+ may be under CTS4065, some of these guys have it and some don't. Trouble is, it's also found elsewhere in DF27 (a "recurrent" mutation, I guess -- or perhaps a malfunctioning cell, a marker that needs to be read in two directions, or whatever).


I have 739 kits in my collection that are F2302+. Had to add it to my list of erratic SNPs. It's either a bad cell, or the SNP analogue to CDY.

razyn
09-14-2013, 04:29 AM
I have 739 kits in my collection that are F2302+. Had to add it to my list of erratic SNPs. It's either a bad cell, or the SNP analogue to CDY.

Ah well. Kind of thought it might be that way. We'll keep looking, a lot of those genome-ish Y chromosome tests should be flooding in soon.

Mythtown
11-13-2014, 06:57 PM
FTDNA is suggesting a Z211 test to those of us who are Z295*. How valid is this recommendation?

razyn
11-13-2014, 10:35 PM
FTDNA is suggesting a Z211 test to those of us who are Z295*. How valid is this recommendation?

Not at all valid. It's only downstream for the people who are Z216+ (it's on the same level, i.e. equivalent). And you tested Z216- in 2011, I think. [Edit: OK, March 2012; anyway we have known for a long time. It seems longer.]

Another edit: I don't think it's particularly useful, but FYI the babbling brook designation for your category (Z295*) on the ISOGG R tree is now R1b1a2a1a2a1a1a*. It's under Z295 and above Z216, as I suppose it should be. You probably have a SNP (or some SNPs) on that level, we just haven't been able to name one yet.

Mythtown
11-14-2014, 02:09 AM
Thanks! I'll buy you a $39 dinner when you're next on Washington's outer coast.

Tltos
03-05-2015, 05:19 PM
Any R1b experts I have a question.

There is a man who tested with Geno 2.0 he is Q-L245+, but he also tested Z6+. http://forums.familytreedna.com/showthread.php?p=403723#post403723

Is Z6 a reliable SNP, is it one of those SNPs that reoccur in haplogroups? When I looked at the SNPs for other Q1b men that have taken the more extensive tests including the Geno 2.0, no one else has the Z6+. What do you guys make of it? Thanks.