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Earl Davis
08-29-2015, 09:33 PM
It's been a wonderful year for DF27 with over 100 of the very early subclades now discovered as well as thousands of downstream snips revealed. That said there is still some way to go however. The Big Tree suggests that there are are at least 14 more subclades yet to be discovered at just the second level under DF27. With more testing this could well turn out to be 20 subclades or more. At just three or four levels under DF27 there are many snips still to be discovered.

With the commercial success of the FTDNA R1b panel, an early release DF27 panel must seem tempting. There are still too many gaps in the early branching however. There are also large blocks of snips that still need splitting to determine what really is the lead SNP in the block. This is already evident in the R1b panel where DF27 lead snips that looked really old only a couple of months ago are now known to be 5, 6 or 7 levels below DF27 itself whilst much older snips are missing simply because their seniority was unknown just a couple of months ago.

I hope we can wait at least another 3 to 6 months or more before rushing to design a DF27 panel at FTDNA.

Earl.

Mikewww
09-01-2015, 03:15 PM
It's been a wonderful year for DF27 with over 100 of the very early subclades now discovered as well as thousands of downstream snips revealed. That said there is still some way to go however. The Big Tree suggests that there are are at least 14 more subclades yet to be discovered at just the second level under DF27. With more testing this could well turn out to be 20 subclades or more. At just three or four levels under DF27 there are many snips still to be discovered.

With the commercial success of the FTDNA R1b panel, an early release DF27 panel must seem tempting. There are still too many gaps in the early branching however. There are also large blocks of snips that still need splitting to determine what really is the lead SNP in the block. This is already evident in the R1b panel where DF27 lead snips that looked really old only a couple of months ago are now known to be 5, 6 or 7 levels below DF27 itself whilst much older snips are missing simply because their seniority was unknown just a couple of months ago.

I hope we can wait at least another 3 to 6 months or more before rushing to design a DF27 panel at FTDNA.

Earl.
This is the constant problem of fixed SNP panels and packs of all sorts. The next Big Y test result could bring some valuable new information. Hence fixed SNP packages are doomed to be obsolete on the day they are released or soon thereafter.

Earl, I've argued your point on this in knock down drag out discussions with the Thomas Krahn on the R1b-L21-project yahoo group. It essentially comes down to that you should get a Next Generation Sequencing test (Big Y or FGC Elite) if you can and are inclined to at all and are interested in genetic genealogy. That's always a good investment. I also say upgrading to 111 STRs is always a good investment.

... but in the discussions I've had with Mr. Krahn, I have to concede that if Big Y is not in the picture then fixed SNP packages are a good value and have a time value. It is worth something to know something now rather than later.

On another thread, another project administrator emphasizes this time value in relation to SNP pack availability.

... My primary concern is that with every passing year, more testees die and more account custodians become unreachable or simply disinterested. Delay has its own cost--in knowledge lost.
http://www.anthrogenica.com/showthread.php?5027-R1b-M343-Backbone-SNP-Pack-FTDNA&p=100059&viewfull=1#post100059

Oftentimes (maybe all of the time), one's view depends on one's position. I've found that generally Big Y testers that have results in from multiple members of the cluster are oftentimes anxious to have all of their SNPs out their in the market on these fixed SNP tests. Those that have NGS results waiting and want just a little more time.

If interested in NGS testing, the good news is there is no need to wait, The below posting is from the U106 group. This is NOT the rule but he says he as seen a turn around of only 16 days. There is hope for those who want Big Y results included.
---------- Forwarded message ----------
From: Charles Moore .... [R1b1c_U106-S21] ....

The coupon code swede2015 will apparently reduce the price of Big Y from $575 to $488.75. We recently had a Big Y result received only 16 days after it was ordered during this slow time of year. Who knows, but something to consider.
Surprisingly, SNPs can be added to packs and panels at the last minute.

Kvenlander
09-02-2015, 05:38 AM
Do you know, generally, how many people need to share an SNP before it is taken into offering of FTDNA?

Mikewww
09-02-2015, 10:58 PM
Do you know, generally, how many people need to share an SNP before it is taken into offering of FTDNA?
At least two. That's the minimum I've seen. Of course, I would think it helps if they are of different surnames.

Mikewww
09-02-2015, 11:02 PM
What does Razyn think about packs and panels? He's Mr. DF27.

razyn
09-03-2015, 12:34 AM
What does Razyn think about packs and panels? He's Mr. DF27.

Whoa. Mr. DF27, heavy responsibility.

Well, I think it's coming along, at YSEQ -- but I'm not supposed to say that at FTDNA, which is where I have the actual reins of the project. Last weekend Thomas sent me the current version of his DF27 panel and it's really obvious, visually or graphically, how much better-defined (as a tree) the Z195+ side is -- compared with the ZZ12 side. That still looks more like a comb structure, or "haircomb" as the Brits seem to say. This is pretty apparent on the Big Tree, too; it's just more obvious in the vertical format Thomas uses. Maybe I can do a couple of illustrative screen shots or something. I'm trying to reduce these to a size you can't actually read, just to illustrate the difference between how well we have sorted the Z195+ branch in 4 1/2 years of testing it (and that's the one, part of which exploded in Iberia in the past 2-3 millennia), versus the rest of DF27. Those of us who believe palindromic SNPs are important call it the ZZ12+ branch, but anyway, it's the rest of DF27.

So, here's the part that looks like a tree -- Z195+ with its numerous subclades:
5770

And here's the rest of DF27 -- the ZZ12+ part that still looks like a comb. All of those little tags in red at the right mean "new," not always in discovery sequence, but in having been added to the YSEQ panel for DF27:
5771

That's as of 8/28/15 -- and as perceived by a guy who does not intend to test for SNPs on palindromes, or in repeat regions, mirroring the X chromosome, near the centromere, etc. (so it is never going to agree completely with Alex Williamson's Big Tree). If we were to include those additional known SNPs -- and/or wait about a month, while new discoveries (and matches with older ones) keep trickling in -- it would look substantially different. Mainly, it would look like a wider comb. That being the case, my instincts are to wait a bit -- and get it a little closer to right, before trying to sell it. YMMV. I have no veto at YSEQ -- and as far as I know, no voice whatever with the lab side of FTDNA.

YFull shares most of the preconditions I attributed to YSEQ, plus one against indels (that I think Thomas will test, anyhow). Some of these distinctions exclude the basic documentation of SNPs that form, or once formed, major branching points on the phylogenetic tree of DF27. NextGen testing, coupled with creative analysis of many results, can get around these lab-specific or technology-limited problems. The desired quick-and-cheap pre-loaded panel, pack, and chip tests cannot get past those obstacles; and unless either attitudes or technological capabilities at the relevant labs change quite a bit, will not.

So, Mr. DF27 does not really carry much of a torch for them. I kind of like targeted NextGen testing; analysis by the people who are good at that; sorting the project by SNP trees to see what STR patterns might point toward what SNPs -- and then testing a handful of one's most likely SNPs for a reasonable price, maybe more like $20 than $40 each.

Another thing I would like, were it ever to happen, would be intelligent revision of the woefully inadequate criteria that generate the Novel Variants list, after a BigY test. If that feature worked as it should, perhaps we wouldn't need to jump a hopscotch path through a maze wearing a blindfold, to learn what useful results our $575 test has found.

Cofgene
09-03-2015, 01:52 AM
Whoa. Mr. DF27, heavy responsibility.

SNIP
I'm trying to reduce these to a size you can't actually read, just to illustrate the difference between how well we have sorted the Z195+ branch in 4 1/2 years of testing it (and that's the one, part of which exploded in Iberia in the past 2-3 millennia), versus the rest of DF27.
SNIP27.


You should be able to see haplogroup "bottlenecks" corresponding to the Iron Age cold epoch (https://en.wikipedia.org/wiki/Iron_Age_Cold_Epoch) around DF27... There are explosions of new haplogroups after things warmed up appearing in the U106 region.

lgmayka
09-03-2015, 02:51 AM
Last weekend Thomas sent me the current version of his DF27 panel and it's really obvious, visually or graphically, how much better-defined (as a tree) the Z195+ side is -- compared with the ZZ12 side.
...
If we were to include those additional known SNPs -- and/or wait about a month, while new discoveries (and matches with older ones) keep trickling in -- it would look substantially different. Mainly, it would look like a wider comb.
That is not a difference in "definition," as if greater testing would reduce the difference. What you are describing is a major difference in fanout, which roughly but accurately reflects the actual speed of expansion. A tree node which has two or three subclades indicates steady expansion, whereas a tree node with ten subclades (or singletons) suggests a demographic and/or geographic explosion.

This kind of difference is not unique to DF27. Take a look at the tree for I-CTS10228 (http://yfull.com/tree/I-CTS10228/) (sometimes called "Dinaric"). We see:
- One singleton, CTS10228*, that barely survived
- The Z17855 clade, which did only a little better
- The Y4460 clade, which shows substantial growth
- The S17250 clade, which in its Y3548 subclade shows a veritable population explosion of singletons as well as several subclades.

If we were to test the "Dinaric" population more heavily, this difference would not disappear. The subclades would become bushier, and the singletons would become small subclades, but the basic difference in fanout would remain, and in fact probably increase.

To be fair, there is indeed a way to reduce the fanout (i.e., make the tree bushier): To increase the number of base pairs tested. If everyone were to order FullGenomes' higher-coverage product rather than the Big Y, we would find additional SNPs to consolidate some of the fanout. But we have to live with the current practicalities of pricing, sample availability, etc.

Kvenlander
09-03-2015, 05:08 AM
At least two. That's the minimum I've seen. Of course, I would think it helps if they are of different surnames.

Thanks Mike. Then there is hope for FGC17112, as apart from Earl and another Davis, and myself (Kainulainen/Kajnul), there is also Rice?

razyn
09-03-2015, 01:21 PM
That is not a difference in "definition," as if greater testing would reduce the difference. What you are describing is a major difference in fanout, which roughly but accurately reflects the actual speed of expansion. A tree node which has two or three subclades indicates steady expansion, whereas a tree node with ten subclades (or singletons) suggests a demographic and/or geographic explosion.
That may be true theoretically; but in practice [noting that the practice is virtually limited to (a) FTDNA testers at the BigY level and (b) the heavily skewed sample of the 1000 Genomes project] a tree node that has two or three (or zero) subclades indicates a very small tested sample, like two to four guys. Whereas the Z195 side has a very large sample, many hundreds of guys (they don't have to have NGS testing if they tested the individual SNP in question, mainly with Sanger sequencing since 2011). Additionally, much of the apparent Z195+ "explosion" happened in the population toward which 1000 Genomes is skewed.

I think the ZZ12 side of the DF27 project -- or at least several specific, recently-discovered branches of it -- might be as bushy as the Z195 side. We lack the sample, so far, with which the rest of its bushiness can be discovered and differentiated. I don't for a moment believe that the fifty or so subsets of DF27+, ZZ12+ [my second illustration, plus the ones Alex includes but YSEQ doesn't test, plus over a dozen who have NextGen results or 1000 Genomes sequencing with no match yet found, plus some unknown number we have yet to discover at all] are "basal," or almost basal (DF27**) -- meaning they have had one or two mutations in 4900 years.

I think it's a sampling difference.

Mikewww
09-03-2015, 02:53 PM
Razyn, can you post a higher resolution of the DF27 tree charts? I can barely read those.

razyn
09-03-2015, 03:53 PM
Reducing the screen shots to near-illegibility was deliberate, and stated when I posted them. It was my intent to show the contrasting pattern -- Z195 a bush, ZZ12 (or the rest of DF27) a comb. Not to advertise the SNPs currently available from YSEQ. I think that is interesting, but a little off topic; and Thomas sent the list to me privately.

Mikewww
09-03-2015, 04:15 PM
..
That's as of 8/28/15 -- and as perceived by a guy who does not intend to test for SNPs on palindromes, or in repeat regions, mirroring the X chromosome, near the centromere, etc. (so it is never going to agree completely with Alex Williamson's Big Tree). If we were to include those additional known SNPs -- and/or wait about a month, while new discoveries (and matches with older ones) keep trickling in -- it would look substantially different. Mainly, it would look like a wider comb. That being the case, my instincts are to wait a bit -- and get it a little closer to right, before trying to sell it. YMMV. I have no veto at YSEQ -- and as far as I know, no voice whatever with the lab side of FTDNA....
I think you are saying what I am observing but have not researched - the YFull CombBed regions eliminate the same things that YSEQ eliminates. Is that true, except YSEQ also does not support InDels on the tree? I didn't know that, but I did know ISOGG doesn't allow InDels to be added (at least mine.)

I will work with FTDNA on DF27's haplotree. It will be long slog as they do their own research after you've hit them on them on the head and provided them with a recommendation.

Mikewww
09-03-2015, 04:20 PM
Reducing the screen shots to near-illegibility was deliberate, and stated when I posted them. It was my intent to show the contrasting pattern -- Z195 a bush, ZZ12 (or the rest of DF27) a comb. Not to advertise the SNPs currently available from YSEQ. I think that is interesting, but a little off topic; and Thomas sent the list to me privately.
umm... I embolded the one sentences because Thomas doesn't have direct access to NGS results, at least he told me doesn't access FGC results although I invited him to a shared L21yresearch profile at FGC. Of course, Alex's Big Tree is completely public.

It's strange that he has an updated DF27 YSEQ panel but hasn't updated his web page for it since April 8th.
http://www.yseq.net/product_info.php?products_id=10749

To all DF27ers:
If anyone sees anything wrong with Alex's Big Tree or as an addition, please post it here. I should try to get it into FTDNA's haplotree. You can only go to the well so many times so I'd like to do it all at once.

Earl Davis
09-03-2015, 04:40 PM
Just running some numbers again. This time against the now 306 samples at the Big Tree which we know is a biased sample for several reasons.

The R1b backbone panel appears to have found some sort of home for DF27 people in about 54% of cases. In general this will place the successful 54% at 2 to 5 levels under DF27 based on the currently known 'blocks'.

If a DF27 panel was launched tomorrow that included all the known 'lead' snips at levels 1-4 under DF27 plus the well known and well tested big hitters it would offer little advancement to those 54% of DF27 people that had a successful R1b backbone result although a level 2 or 3 person might advance a step or two.

If all the known leads down to level 4 were included in a DF27 panel and successfully testable (which is highly unlikely given the large number of problematic regions in the early DF27 branching) then how would the remaining 46% of people (the main audience of a high level DF27 panel?) gain?

Based on the 306 people at the Big Tree; at DF27 level 4 in 25% of cases the level 4 lead SNP has simply not been discovered yet. The real situation is likely worse than that as many of the arbitrary leads may that might be selected for the panel may turn out to really be less significant branches several levels lower when more samples come in. For now however lets assume a minimum of 25% of DF27 level 4 has not been identified yet.

I am now looking at this from the point of view of someone who took the R1b backbone.

If 25% can't be helped to level 4 by a panel test right now as their level 4 SNP remains undiscovered and thus can not be included anyway and another 53% found some sort of home from the R1b backbone test anyway (though not always down four levels) then someone looking to test a DF27 panel as their next step is limited to 23% of the DF27 audience anyway.

So a DF27 panel launched today and taken by as a next step by a R1b backbone tester would only be of major benefit to about 23% of DF27 people.

A DF27 panel launched today and taken by someone who has done no other panels or testing under DF27 would be of some benefit to about 75% of DF27 people.

About half of the R1b backbone panel testers who who only reached level 2 or 3 under DF27 may be able to advance a little.

For context that well know SNP SRY2627 is currently in a block 5 levels under DF27. It may stay there or may one day be 10 levels under DF27. Who knows. There are already over 70 DF27 'leads' that are older in the DF27 branching than SRY2627. One day as block continue to get split there may be several hundred. The point being that even today 70+ snips would need to be included in a panel to get 75% of people to a level in the DF27 hierarchy above DF27.

I am aware these numbers have more than an echo of Mark Twains 'Lies, damned lies, and statistics' and depending on what snips are included and what branching level you choose to quote makes the situation appear much better or much worse. For this I elected to include problematic regions but selected level 4 as that's when most (but not all) of the problematic regions currently seem to even out.

Percy Bysshe Shelley (For Razyn).

Mikewww
09-03-2015, 05:21 PM
... I am now looking at this from the point of view of someone who took the R1b backbone.
....
Percy Bysshe Shelley (For Razyn).

This reminds of my reply #2 of this thread. One's viewpoint makes all of the difference. For a person sitting at DF27+ and having no other downstream testing, should they not be able to buy a pack or panel if they want? Meanwhile, Lawrence is legitimately concerned that everyone doesn't have the health to wait. The view of an M343 Backbone tested person is different than untested or a North-South cluster haplotype person. The price points and budgets make a difference too on an individual basis.


Oftentimes (maybe all of the time), one's view depends on one's position. I've found that generally Big Y testers that have results in from multiple members of the cluster are oftentimes anxious to have all of their SNPs out their in the market on these fixed SNP tests. Those that have NGS results waiting and want just a little more time.

If interested in NGS testing, the good news is there is no need to wait, The below posting is from the U106 group. This is NOT the rule but he says he as seen a turn around of only 16 days. There is hope for those who want Big Y results included.
---------- Forwarded message ----------
From: Charles Moore .... [R1b1c_U106-S21] ....

Surprisingly, SNPs can be added to packs and panels at the last minute.

It never seems to be a bad deal to buy Big Y or FGC Elite. Guessing timing and considering all tester positions and starting viewpoints is an ever changing battle for fixed SNP pack testing. Buying Big Y + 111 Y STRs is always a good investment.


Percy Bysshe Shelley (For Razyn).
I'm confused by your sign-off. Is Percy posting under this alias on behalf of Razyn?

REWM
09-03-2015, 06:06 PM
This is what I know of for Z2573 so far.
5780

Earl Davis
09-03-2015, 06:15 PM
I'm confused by your sign-off. Is Percy posting under this alias on behalf of Razyn?

Sorry, I can't help myself sometimes. I should know better by know. Dick suggested one of my other threads had a ring of Ozymandais about it.

Earl.

Earl Davis
09-03-2015, 06:41 PM
This reminds of my reply #2 of this thread. One's viewpoint makes all of the difference. For a person sitting at DF27+ and having no other downstream testing, should they not be able to buy a pack or panel if they want? Meanwhile, Lawrence is legitimately concerned that everyone doesn't have the health to wait. The view of an M343 Backbone tested person is different than untested or a North-South cluster haplotype person. The price points and budgets make a difference too on an individual basis.

I have read a few comments around the net recently about people who may not have long to wait. It's an important point and one I had not originally considered.

Earl.

lgmayka
09-03-2015, 07:16 PM
I am now looking at this from the point of view of someone who took the R1b backbone.

If 25% can't be helped to level 4 by a panel test right now as their level 4 SNP remains undiscovered and thus can not be included anyway and another 53% found some sort of home from the R1b backbone test anyway (though not always down four levels) then someone looking to test a DF27 panel as their next step is limited to 23% of the DF27 audience anyway.

So a DF27 panel launched today and taken by as a next step by a R1b backbone tester would only be of major benefit to about 23% of DF27 people.
So is it true that someone like #196199 of Poland, who is DF27** now (after the M343 panel), should not waste his money on a DF27-specific panel any time soon?

Mikewww
09-03-2015, 07:22 PM
Sorry, I can't help myself sometimes. I should know better by know. Dick suggested one of my other threads had a ring of Ozymandais about it.

Earl.
I expose my literary shortcomings, but who is Ramses the Great in our scene?
"Look on my works, ye Mighty, and despair!'
Nothing beside remains"

REWM, thanks for the update.

Does anyone know if the Chromo 2 tree for S250/DF27 has additional branching?

Mikewww
09-03-2015, 07:25 PM
So is it true that someone like #196199 of Poland, who is DF27** now (after the M343 panel), should not waste his money on a DF27-specific panel any time soon?
I haven't studied the YSEQ DF27 panel, perhaps produced rashly premature, but it might have more SNPs in it now if Thomas is working on an update. We've seen the comb-like charts from insiders like Rayzn.

I don't think we can comment on an FTDNA DF27 pack until we see it, but as has been noted, with every NGS result, every FGC or YFull interpretation, things change.

Oh my, oh my... market overhang seems to abound. :) Sorry, I couldn't resist, Lawrence. We must have some poetry and humour so we don't bore ourselves.

Earl Davis
09-03-2015, 07:37 PM
So is it true that someone like #196199 of Poland, who is DF27** now (after the M343 panel), should not waste his money on a DF27-specific panel any time soon?

That would be my view although they could strike it lucky of course.

I have tested 5 of my ancestral lines so far. One is Nordic-Q, one is I1>Z60, one is DF27>ZZ12>FGC11712, one is under the North South Cluster of DF27 and another is stuck at P312. I considered the R1b panel for the latter but as the STR's don't match much anything I took it was an obscure group and gambled that taking the panel would not reveal much and took a pass at this point. I have run two ancestral lines through BigY so far and am waiting to see how they progress before potentially investing further in more BigY or elsewhere. The ZZ12 test has got me down several levels so far and the I1>Z60 line has no matches under I1>Z60, so nothing really learned in the first 18 months after BigY that we didn't already know. Hopefully some good matches will come in soon.

I got really lucky on the north south cluster line as it was a close STR match to the Zenker family who had tested their line well so I was able to jump straight to CTS4065 without taking any panels and just that single SNP test.

Earl.

Earl Davis
09-03-2015, 07:45 PM
Mike this may be useless but it's an extension of something I posted about in another thread. It's the first four levels under DF27 with selected lead snips which may not always be the best selections. It tries to avoid picking lead snips from very large SNP blocks and instead classifies those as undiscovered. It's far from perfect but does give some idea how common the subclades may be. Also I was not aware until a few hours ago that the YSEQ panel may include more snips than they advertise on their website. It also highlights where some of the biggest knowledge gaps might lie.

5785

Mikewww
09-04-2015, 08:37 PM
Reducing the screen shots to near-illegibility was deliberate, and stated when I posted them. It was my intent to show the contrasting pattern -- Z195 a bush, ZZ12 (or the rest of DF27) a comb. Not to advertise the SNPs currently available from YSEQ. I think that is interesting, but a little off topic; and Thomas sent the list to me privately.
The more I look at the ZZ12 side of things and the "comb" the more I see the diversity. This reminds of DF13 under L21 and L2 under U152 - a tremendous burst of lineages that survived until today.

razyn
09-04-2015, 09:59 PM
Also I was not aware until a few hours ago that the YSEQ panel may include more snips than they advertise on their website. It also highlights where some of the biggest knowledge gaps might lie.

My posting of that was misleading. In his accompanying email, Thomas called that "my current draft tree" for DF27. For many years his Draft Tree was a good reality check versus the ISOGG tree -- I had it bookmarked -- and I thought it had gone away forever. Maybe it's just no longer public?

Anyway, the "new" SNPs are, I suppose, new to his Draft Tree -- not necessarily newly added to the DF27 panel test YSEQ offers. Once again -- my purpose was to illustrate the Comb vs. Bush picture, not to sell kits for the Krahns. I wish them well, like them, and am a customer. I just think we should know the phylogeny better, before designing one DF27 SNP pack that seems likely to be the last good look at this haplogroup that a certain large company will take for the next decade or so.


The more I look at the ZZ12 side of things and the "comb" the more I see the diversity. This reminds of DF13 under L21 and L2 under U152 - a tremendous burst of lineages that survived until today.

I'm no authority on those other lines, but I suspect they also are to some extent looking like combs temporarily -- because relatively few have yet done NextGen testing (and match finding) to reveal the bushiness that may exist in the separate "teeth" of these combs. I may be mistaken, but it's my opinion that we can't tell yet whether these are caused by ancient explosion(s) of mutating, or the recent tsunami of testing for them. If I'm wrong, Larry Mayka is right (about what this pattern is showing us). Either way, it's real -- and not much explored, yet. Exploring it will take some time, and cost some money. In a sense, this thread is about the best route cum timetable by which to get that exploration done.

Mikewww
09-05-2015, 03:31 AM
..
Anyway, the "new" SNPs are, I suppose, new to his Draft Tree -- not necessarily newly added to the DF27 panel test YSEQ offers. Once again -- my purpose was to illustrate the Comb vs. Bush picture, not to sell kits for the Krahns. I wish them well, like them, and am a customer. I just think we should know the phylogeny better, before designing one DF27 SNP pack that seems likely to be the last good look at this haplogroup that a certain large company will take for the next decade or so.
I'm joking with you a bit here but it seems like a double standard if one company has been allowed even supported to have a fixed SNP panel for several months but another is company is recommended not to put one out yet.

What do you mean by decade? Granted FTDNA is slow as molasses (per Lawrence) but a decade is a bit of of an overstatement, don't you think?

Maybe all comers should put out whatever tests they want and let their customers decide? Never mind, I am just one of those crazy free market guys. We don't want project members and hobbyists to have too many choices.


...I'm no authority on those other lines, but I suspect they also are to some extent looking like combs temporarily -- because relatively few have yet done NextGen testing (and match finding) to reveal the bushiness that may exist in the separate "teeth" of these combs. I may be mistaken, but it's my opinion that we can't tell yet whether these are caused by ancient explosion(s) of mutating, or the recent tsunami of testing for them. If I'm wrong, Larry Mayka is right (about what this pattern is showing us). Either way, it's real -- and not much explored, yet. Exploring it will take some time, and cost some money. In a sense, this thread is about the best route cum timetable by which to get that exploration done.

The key thing that I was trying to point out is that given that most, if not nearly all Y DNA lines go extinct or are killed off in one manner or another (in ancient times) it's amazing to me that so many branches of ZZ12 still live. We have NOT found downstream (of ZZ12) shared SNPs for all of these other branches that form the "comb". That means they branched away almost immediately directly from ZZ12.

This makes ZZ12 like DF13 and L2. The implication was that these distant cousins had some technical, cultural or biological advantage that allowed them to quickly diversify into various other cultures and geographies in a very successful (hegemonious) way. I don't know how else to interpret it other than just plain dumb luck, but why were the early P311 descendants so lucky?

razyn
09-05-2015, 06:11 AM
I'm joking with you a bit here but it seems like a double standard if one company has been allowed even supported to have a fixed SNP panel for several months but another is company is recommended not to put one out yet.

FTDNA put out a sort of general request (around the time the BigY test was offered) that all creatures great and small with any suggestions for haplogroup-specific panels might want to design those, and hand them over, to see if they agree.

By contrast, Thomas sent me an email this spring, said he was going to put one out (enclosing an outline of it), and asked if I had any corrections to suggest. I suggested a bunch, all on the Z195+ side. And he incorporated most of them. But it was almost the deadline set by my tax preparer (mid-March), so I had to mess with that stuff for a week or so. Just before I came up for air, ready to tackle what I now call the ZZ12 side of the Great Divide -- I saw the YSEQ announcements that their DF27 panel was for sale. So I had no input to that part, though I had been invited to offer it.

I did learn a couple of things from the exercise, though. One was that the project could use some radical reorganizing (which I finally did, less than two weeks ago). And another was that I agree with Earl -- it's possible to go off half-cocked with this kind of test; and if we wait a bit (while continuing to test and compare), we can make a better initial effort.


What do you mean by decade?

Ten years. If we see a second DF27 panel from FTDNA within a shorter time, I'll be both pleased and surprised. That assumes that there will be a first draft, before much longer, with or without my valuable assistance. I'm just extrapolating from how long it took to replace the old Deep Clade, revise the 2010 Haplotree, things like that. Those things didn't take ten years, but they took a lot longer than they needed to -- and were much higher priority than DF27 has yet appeared to be, for those folks.


We have NOT found downstream (of ZZ12) shared SNPs for all of these other branches that form the "comb". That means they branched away almost immediately directly from ZZ12.

I don't think it means that the branching was immediate; just that a lot of branches have happened (since the parent SNP was "born") -- and for all we know, from some "basal" form of the parent. But more likely, we just haven't found and named the intervening branches. They may even have back-mutated away (an example being ZZ12 in the Plant family -- who alone among L617 people seem no longer to have that ancient mutation, on either side of the palindrome). We can see perhaps thirty or forty "teeth" under ZZ12; there may have been hundreds, but the rest have daughtered out -- or are in populations still below our radar.


This makes ZZ12 like DF13 and L2. The implication was that these distant cousins had some technical, cultural or biological advantage that allowed them to quickly diversify into various other cultures and geographies in a very successful (hegemonious) way. I don't know how else to interpret it other than just plain dumb luck, but why were the early P311 descendants so lucky?

They served wine at feasts.

Mikewww
09-05-2015, 04:52 PM
FTDNA put out a sort of general request (around the time the BigY test was offered) that all creatures great and small with any suggestions for haplogroup-specific panels might want to design those, and hand them over, to see if they agree. As far as I can tell, no one has submitted a request to FTDNA for a DF27 fixed SNP panel before me and that was about 1.5-2 months ago, not last March and April.


By contrast, Thomas sent me an email this spring, said he was going to put one out (enclosing an outline of it), and asked if I had any corrections to suggest. I suggested a bunch, all on the Z195+ side. And he incorporated most of them. But it was almost the deadline set by my tax preparer (mid-March), so I had to mess with that stuff for a week or so. Just before I came up for air, ready to tackle what I now call the ZZ12 side of the Great Divide -- I saw the YSEQ announcements that their DF27 panel was for sale. So I had no input to that part, though I had been invited to offer it. I emboldened your responses that were related to actions you took or were requested to take. Yes, I've seen you bring up the DF27 YSEQ panel to tester inquiries. That's okay. There is no need to be shy about it. People need to know what's available. YSEQ panels, in general, have done much good. I do agree with Earl's general point that fixed SNP panels are doomed to be out of date, I just add that they will always be doomed to this status. It's okay, though, as long as people know what they are getting.


I did learn a couple of things from the exercise, though. One was that the project could use some radical reorganizing (which I finally did, less than two weeks ago).
You've done great work on the project. Thank you. We all are indebted to you and most probably don't realize how much work you've done.


And another was that I agree with Earl -- it's possible to go off half-cocked with this kind of test; and if we wait a bit (while continuing to test and compare), we can make a better initial effort.


Ten years. If we see a second DF27 panel from FTDNA within a shorter time, I'll be both pleased and surprised. You are worried about others being half-cocked? These decade/ten year statements must be sarcasm. :) I feel more comfortable with Lawrence's terminology. They are slow as molasses. If FTDNA produces a refresh to their M222 SNP Pack this year will you eat your words?


That assumes that there will be a first draft, before much longer, with or without my valuable assistance. I'm just extrapolating from how long it took to replace the old Deep Clade, revise the 2010 Haplotree, things like that. Those things didn't take ten years, but they took a lot longer than they needed to -- and were much higher priority than DF27 has yet appeared to be, for those folks.
Other parts of the tree are being updated. My father's lineage is now a formal haplogroup assignment, R-ZW02. There is no reason why DF27 folks shouldn't have this. It takes an advocate slugging it out and getting in the queue. Sugar works better than vinegar, but rational and empathetic presentation with civility can do wonders.

Are we really looking out for the DF27 community if we are not providing the request to FTDNA and not providing the detail for a haplotree update? If not now, when? There is never a perfect day. We've had NGS testing for almost two years now. As I've said, I've been reticent and ambivalent on SNP packs/panels from day one. Thomas can attest to this. However some people just won't do NGS and we need to get things going for those before they retire or otherwise are lost, per Lawrence.

I think there is something not well understood. A newly discovered SNP can be added to a Pack at the last minute. Since FTDNA is slow as molasses in their general processes (i.e. haplotree updates and product introductions) we have to get in the queue and be ready for last minute add recommendations.

Mikewww
09-09-2015, 06:14 PM
It's been a wonderful year for DF27 with over 100 of the very early subclades now discovered as well as thousands of downstream snips revealed. That said there is still some way to go however. The Big Tree suggests that there are are at least 14 more subclades yet to be discovered at just the second level under DF27. With more testing this could well turn out to be 20 subclades or more. At just three or four levels under DF27 there are many snips still to be discovered.

With the commercial success of the FTDNA R1b panel, an early release DF27 panel must seem tempting. There are still too many gaps in the early branching however. There are also large blocks of snips that still need splitting to determine what really is the lead SNP in the block. This is already evident in the R1b panel where DF27 lead snips that looked really old only a couple of months ago are now known to be 5, 6 or 7 levels below DF27 itself whilst much older snips are missing simply because their seniority was unknown just a couple of months ago.

I hope we can wait at least another 3 to 6 months or more before rushing to design a DF27 panel at FTDNA.

Earl.
It looks like YSEQ didn't wait. They plunged ahead with a major update to their spring product.

I recognize that Thomas is on this forum so I don't there is any secret that an FTDNA DF27 pack is coming too. I'll check on the timing but it should about right. Over in U106 land, the project admins seem to be saying wait until see what's available.

I think people should do what they want and this YSEQ panel is no doubt good. If you have time to wait, I expect to see FTDNA DF27 pack(s) out soon so you will have more options to choose from and pricing tends to get better when we see competition like this.

razyn
09-09-2015, 07:31 PM
It looks like YSEQ didn't wait. They plunged ahead with a major update to their spring product.

It is somewhat more complete than the version I used (above) to illustrate the bush versus comb structures each side of the major DF27 divide. Anyway, since Thomas has now made it public, you can see the big version on his commercial site: http://www.yseq.net/product_info.php?products_id=10749

Mikewww
09-10-2015, 03:39 PM
Earl, from the surface it seems strange that you start this post and Razyn refers to it from Facebook.... then less than two weeks later your or someone using your name on the DF27 yahoo group is saying.
"Thomas thanks for making these improvements to your DF27 panel. This version appears to be a very inclusive and well rounded test.

Earl." https://groups.yahoo.com/neo/groups/R1b-DF27-Project/conversations/messages/3029;_ylc=X3oDMTJxMGttNWpxBF9TAzk3MzU5NzE0BGdycElk Azg4OTExOTYwBGdycHNwSWQDMTcwNTE4Nzk4MgRtc2dJZAMzMD I5BHNlYwNmdHIEc2xrA3JwbHkEc3RpbWUDMTQ0MTg5MDUyMA--?act=reply&messageNum=3029

Can you comment? I may totally misunderstand, but the purpose of this thread does not seem be what it is portrayed as. I admit I just may be confused, but help me understand.


It's been a wonderful year for DF27 with over 100 of the very early subclades now discovered as well as thousands of downstream snips revealed. That said there is still some way to go however. The Big Tree suggests that there are are at least 14 more subclades yet to be discovered at just the second level under DF27. With more testing this could well turn out to be 20 subclades or more. At just three or four levels under DF27 there are many snips still to be discovered.

With the commercial success of the FTDNA R1b panel, an early release DF27 panel must seem tempting. There are still too many gaps in the early branching however. There are also large blocks of snips that still need splitting to determine what really is the lead SNP in the block. This is already evident in the R1b panel where DF27 lead snips that looked really old only a couple of months ago are now known to be 5, 6 or 7 levels below DF27 itself whilst much older snips are missing simply because their seniority was unknown just a couple of months ago.

I hope we can wait at least another 3 to 6 months or more before rushing to design a DF27 panel at FTDNA.

Earl.

On one hand, we think FTDNA takes decades to do things while at the same time we are afraid they may be too quick and rash. Meanwhile YSEQ has had a product for some time and now we think their update yesterday is "very inclusive" and "well rounded". ?????

The YSEQ product is excellent. I'm glad they had one in the spring and glad they have a good update now. I just don't understand the positions taken.

REWM
09-10-2015, 06:37 PM
I don't see the problem with it. It seems to me that Earl was just complementing YSEQ on their excellently updated DF27 Panel.
I'm sure he has the same opinion as before.
If FTDNA comes out with their panel (I hope they do) that is anywhere near as good. One would think he would have posted the same complement.

Mikewww
09-10-2015, 07:50 PM
I don't see the problem with it. It seems to me that Earl was just complementing YSEQ on their excellently updated DF27 Panel.
I'm sure he has the same opinion as before.
If FTDNA comes out with their panel (I hope they do) that is anywhere near as good. One would think he would have posted the same complement.

I just wonder why an imminent FTDNA panel is "rash" and is recommended to be "deferred 3 to 6 months" while a YSEQ panel is "very inclusive and well rounded" ?

Earl Davis here on August 28th
".... There are still too many gaps in the early branching however. There are also large blocks of snips that still need splitting to determine what really is the lead SNP in the block. ....
I hope we can wait at least another 3 to 6 months or more before rushing to design a DF27 panel at FTDNA."

earljdavis on DF27 yahoo group today, Sept. 10th.
"... This version appears to be a very inclusive and well rounded test."

If the answer is along the lines of I don't like FTDNA and I like YSEQ or I think YSEQ's tests are more reliable, that's all fair. Everyone has a right to an opinion. Let's just be plain about it so folks listening and just look at the facts and make their minds based on an open display of the data.

What's good or not, might be an eye of the beholder but I'll bet FTDNA has many more SNPs in their DF27 Pack. You might be surprised what they can do. It's all good for competition and individual choice. YSEQ may decide to drop their price. They've done it before.

I'm being a little harsh. I apologize, but the purpose of the thread is hard to understand and I'm not sure if it is what is best for the community. As far as that goes, I'll defer back to let's get all of the companies working in our areas and have a good free for all. This has worked well for L21 for some time. It is about to work for U106 although they are of the wait until the ready, set, go mindset. It's not a bad way to go. I give them credit.

REWM
09-10-2015, 09:18 PM
I just don't think that was Earl's intention. From what I have read here any on other sites he has posted to.

I personally think the more options the better.
I'm looking forward to seeing what FTDNA has to offer. Since I don't have that option now at FTDNA.
There's nothing I could test for, so I've been doing it at YSEQ and been happy with the results.

Mikewww
09-10-2015, 11:01 PM
I just don't think that was Earl's intention. From what I have read here any on other sites he has posted to.

I personally think the more options the better.
I'm looking forward to seeing what FTDNA has to offer. Since I don't have that option now at FTDNA.
There's nothing I could test for, so I've been doing it at YSEQ and been happy with the results.

Perhaps Earl will share his intentions rather than us guessing. I get the feeling there is a team or alliance in place.:)

I agree heartily the more options the better and it might be a good idea to wait and see like the U106 folks. Unless someone is about to retire or otherwise no longer be engaged in genetic genealogy then waiting is actually a good thing when it comes to fixed SNP panels and packs. This has always been a bone of contention as fixed SNP sets are doomed to be out of date.

Come to think of it, the best kind of pack/panel is one with very early branching and well-tested sets of SNPs... exactly like what the R1b-M343 Backbone SNP Pack should evolve into. Everything else is a compromise to Next Generation Sequencing... until a member of your known genealogical family tests NGS.

Well, let's let it rest. I suspect Earl and Razyn are happy enough and have plenty to do. It's all good in the long run.

razyn
09-11-2015, 01:06 AM
On one hand, we think FTDNA takes decades to do things while at the same time we are afraid they may be too quick and rash.

I just don't understand the positions taken.

Earl and I are not an alliance, AFAIK. We are customers at FTDNA, and have at no charge carried some tons of their organic fertilizer for them. We aren't stupid, so I assume that we agree that more informed analysis, more nimble updating of trees, and more affordable SNP testing are offered elsewhere. But the NextGen sequencing (that has to be run on million-dollar machines) has to be done at FTDNA -- or sent to another place (they are not thick on the ground) that makes that level of equipment available to consumers. I don't believe any other such place also has public projects with several thousand more or less related haplotypes with which one may compare oneself.

I do think DF27 has some special problems, that make it a little more resistant to panel testing than some other large haplogroups. One is being invisible. Others would include several high level, watershed-creating SNPs that nobody (including the nimble, and usually responsive, YSEQ team) wants to test. And we know perfectly well that there are a good few branches of DF27 still undiscovered; their members aren't going to discover their own "terminal" SNP by spending good money on a panel designed prior to its discovery.

By now, those who have found nothing below DF27 are a small minority; and I'd agree with Earl that the updated, current version of the YSEQ panel (or set of panels) is probably good enough, for most members of our DF27 project. So Thomas does deserve our congratulations; he also has requested updates we may offer, and a few have been proposed. But the DF27+, Z195- members who buy it, and still don't learn anything, will not in retrospect share that majority viewpoint. At the moment, the group I'd consider most relevant is the last column to the right on Alex's Big Tree:

5857

MJost
09-11-2015, 02:02 AM
... At the moment, the group I'd consider most relevant is the last column to the right on Alex's Big Tree:

5857
Wow, was that a INDel situation? With that many people today, maybe there had been another SNP or two that occurred in a bottle neck and got deleted and pass down to a son, and this man then had many sons and their sons made many branches each over a century that passed it on with no common SNP other than each new branch's SNPs with these 15 men.

How else would that happen?

MJost

razyn
09-11-2015, 02:43 AM
Wow, was that a INDel situation?

No, those are the samples with NextGen (or 1000 kG, lower resolution) sequencing results, that still have no matches -- so Alex has them grouped together as the sort of orphan collection. And I have established group Ea for them -- as a replacement for the former Aaa (tested everything we could think of, so they must be DF27**). We probably have a few more of these to find -- some people with NextGen results don't know they are DF27 and haven't joined this project; and others may be members, but haven't uploaded their data for comparison with the rest (so we don't yet realize that they have no matches).

On the other hand, every now and then a new test comes in and matches somebody from this group. Then we get a new DF27 branch. And every time it happens -- although it is a good thing -- the most current possible DF27 panel test becomes obsolete by one SNP.

Mikewww
09-11-2015, 11:55 AM
Earl and I are not an alliance, AFAIK. We are customers at FTDNA, and have at no charge carried some tons of their organic fertilizer for them. We aren't stupid, so I assume that we agree that more informed analysis, more nimble updating of trees, and more affordable SNP testing are offered elsewhere. But the NextGen sequencing (that has to be run on million-dollar machines) has to be done at FTDNA -- or sent to another place (they are not thick on the ground) that makes that level of equipment available to consumers. I don't believe any other such place also has public projects with several thousand more or less related haplotypes with which one may compare oneself.

I do think DF27 has some special problems, that make it a little more resistant to panel testing than some other large haplogroups. One is being invisible. Others would include several high level, watershed-creating SNPs that nobody (including the nimble, and usually responsive, YSEQ team) wants to test. And we know perfectly well that there are a good few branches of DF27 still undiscovered; their members aren't going to discover their own "terminal" SNP by spending good money on a panel designed prior to its discovery.

By now, those who have found nothing below DF27 are a small minority; and I'd agree with Earl that the updated, current version of the YSEQ panel (or set of panels) is probably good enough, for most members of our DF27 project. So Thomas does deserve our congratulations; he also has requested updates we may offer, and a few have been proposed. But the DF27+, Z195- members who buy it, and still don't learn anything, will not in retrospect share that majority viewpoint. At the moment, the group I'd consider most relevant is the last column to the right on Alex's Big Tree:
...
I think YSEQ is fine and they are clearly more nimble as you say, where as FTDNA is slow as molasses. Thomas has done a great job. No argument at all from me. I just question the consistency in positions taken here.

I recommend people wait and see the DF27 pack from FTDNA. It will have more SNPs than the YSEQ panel. I assume our true interest is in the genetic genealogy community, the project members, the hobbyists ourselves. If so, you would probably agree that it is good to follow suit with the U106 project admin's team approach.
- wait, then ready, set, go!

There is no reason* to hurry when FTDNA's pack support is just around the corner. YSEQ won't raise their price and might even lower it when FTDNA enters this niche of the market. YSEQ has done this before. I should show you some of the early prices of the panels over in L21.

Plus, since FTDNA will have more SNPs there might be advantages for some people and haplogroup assignments will be updated which helps on FTDNA's project and matching displays.

If your sole argument is testing the SNP DF27 itself and someone isn't sure, by all means get it tested at YSEQ for $17.50.

* The exception is Lawrence's concern where we have people near death, but think about it. Some may purely be in this for self-edification and knowledge, but I submit many of us our in this for posterity, for our families and descendants, and general public knowledge. If that is the case, you want your results available easily accessible on-line on project web pages and the like - by a self-sustaining enterprise that can afford those million dollar testing machines, computer server farms, cybersecurity, database systems, etc.


At the moment, the group I'd consider most relevant is the last column to the right on Alex's Big Tree:
...
This is a generic statement that may be important for research and/or project priorities, but the most important column to any tester is the one they are in, or will be in.

You might ask yourself if I'm doing the genetic genealogy community any good? I'm disagreed with often (which doesn't bother me). The scenario has played out before and will again. You are seeing it in mid-stream on U106 and a slightly earlier stage on DF27. YSEQ hears of FTDNA's plans and moves quickly to try to get some tests before FTDNA's products hit. The competition is all good for the community unless there is mudslinging. Mudslinging is the equivalent of negative political campaigns. It really works but the final result is that voter turnout declines. Positive competition creates more pressure on the vendors to produce better products and lower their prices. (Egads! I am the consumer advocate here and have empathy for Ralph Nader.):)

Still, the best way is Next Generation Sequencing as all of this of other stuff is a bit of chasing the wind (as far as genetic genealogy purposes.)

Earl Davis
09-13-2015, 11:58 AM
Earl, from the surface it seems strange that you start this post and Razyn refers to it from Facebook.... then less than two weeks later your or someone using your name on the DF27 yahoo group is saying.
"Thomas thanks for making these improvements to your DF27 panel. This version appears to be a very inclusive and well rounded test.

Earl." https://groups.yahoo.com/neo/groups/R1b-DF27-Project/conversations/messages/3029;_ylc=X3oDMTJxMGttNWpxBF9TAzk3MzU5NzE0BGdycElk Azg4OTExOTYwBGdycHNwSWQDMTcwNTE4Nzk4MgRtc2dJZAMzMD I5BHNlYwNmdHIEc2xrA3JwbHkEc3RpbWUDMTQ0MTg5MDUyMA--?act=reply&messageNum=3029

Can you comment? I may totally misunderstand, but the purpose of this thread does not seem be what it is portrayed as. I admit I just may be confused, but help me understand.

On one hand, we think FTDNA takes decades to do things while at the same time we are afraid they may be too quick and rash. Meanwhile YSEQ has had a product for some time and now we think their update yesterday is "very inclusive" and "well rounded". ?????

The YSEQ product is excellent. I'm glad they had one in the spring and glad they have a good update now. I just don't understand the positions taken.

Hi Mike.

Yes that's me on Facebook. I will explain.

When YSEQ launched their DF27 panel I was not very impressed. It focussed on a lot of well known branches that are well tested already and to me offered little in the way of hope to about 50% of DF27. I thought there was a good chance that significant numbers of people who took the test would learn little or nothing new. The update is much more comprehensive than the original offering and is more inclusive as it includes many snips from the largely ignored Z196- part of the tree.

Indeed it was YEQ's first DF27 panel that caused be to have concerns about an FTDNA panel coming out too early.

In summary it's a big improvement over version 1.

I have also been impressed at the flexibility shown in improving the test.

I don't know where this leaves people who already purchased a version 1 test. As there are still many gaps in the early DF27 tree branching I also don't know where those people will be in 5 months time when a version 3 will probably be needed.

I still think it's too early for a really top quality DF27 panel that can find at least something for everyone but I still see a reason to cheer when a weaker first offering is superseded by a significantly improved second offering.

What I don't understanding is the testing strategy the testing companies are expecting customers to take with these tests. Do they expect to keep expanding the panel every year and then people pay to test all the newly added stuff each time round?

When I am dreaming up what might be included in a DF27 panel my thoughts were very much about trying to identity all the early branching points in the tree. There are probably going to end up being more than 200 in the first four levels after DF27. So I would not have included SRY2627 in a DF27 panel as that's at least 5 levels below DF27. Instead as the R1b panel detects SRY2627 I assumed most people would take the R1b panel and then jump to some SRY2627 panel and bypass a DF27 panel altogether. What Thomas has done is not only include SRY2627 but 8 more levels below it down to A7080. That's at least 13 levels under DF27. There are probably more than 10,000 snips at that level under DF27.

What I am getting at there is thinking about the long term design of the panel and where it's going in the future.

Earl.

Earl Davis
09-13-2015, 12:26 PM
I just wonder why an imminent FTDNA panel is "rash" and is recommended to be "deferred 3 to 6 months" while a YSEQ panel is "very inclusive and well rounded" ?

If the answer is along the lines of I don't like FTDNA and I like YSEQ or I think YSEQ's tests are more reliable, that's all fair. Everyone has a right to an opinion. Let's just be plain about it so folks listening and just look at the facts and make their minds based on an open display of the data.

I'm being a little harsh. I apologize, but the purpose of the thread is hard to understand and I'm not sure if it is what is best for the community. As far as that goes, I'll defer back to let's get all of the companies working in our areas and have a good free for all. This has worked well for L21 for some time. It is about to work for U106 although they are of the wait until the ready, set, go mindset. It's not a bad way to go. I give them credit.

Just for clarity here I am a FTDNA customer. I have never used YSEQ and have no current plans to do so. I am considering using FGC but have been waiting to see if FTDNA launches some sort of BigY+ test that covers regions not included in BigY itself.

My motivation for this thread was a concern at significant amount people would take a panel and learn very little or nothing at all. When I started this thread about 17 or 18 people on Alex's tree matched no one else at all. That's already down to 11 people in just a few days so the high level branching is still fleshing out at pace.

If a panel launched today that included everything on Alex tree in the first four blocks under DF27 itself about 75% of people would get to four levels under DF27 (including palindromes). IF next week that improved to 76% and to 77% the week after and so on is it worth waiting to perfect the test a little? From a testers point of view I would say yes. From FTDNA's commercial point of view now that YSEQ has an improved DF27 offering I can absolutely understand a need for them to get in the DF27 game.

gotten
09-13-2015, 03:04 PM
What I don't understanding is the testing strategy the testing companies are expecting customers to take with these tests. Do they expect to keep expanding the panel every year and then people pay to test all the newly added stuff each time round?


I think it is just like the electronics industry. We know computers/phones get better every year, some people buy a new one every few years, others wait until the previous one falls apart or is totally obsolete. You can have an up-to-date computer/phone right now which will be outdated within a year. But without the regular updates people wouldn't have any choice. People now have the freedom to choose themselves if they want to upgrade right now, or wait a few years for an even better product.

The companies need to sell products in order to pay the bills and recover the enormous investments they made (the sequencing machines are extremely expensive). With multiple companies offering similar tests we can get a bit of competition which will be better for the customers.

Ofcourse the most economic for the customer would be wait until Full Genome Sequencing is in the price range of these SNP panels but that development will only happen when there is a healthy market for DNA tests.

razyn
09-14-2015, 02:10 AM
those are the samples with NextGen (or 1000 kG, lower resolution) sequencing results, that still have no matches -- so Alex has them grouped together as the sort of orphan collection...


every now and then a new test comes in and matches somebody from this group. Then we get a new DF27 branch.

So, for example, that Sept. 10th screen shot had four guys listed who are not there tonight, Sept. 13th. [HG01241, 113701, N112478, 92432.] They are under a new SNP, ZZ41 -- located in the P5 palindrome region. Its position is ambiguous, so it's hard to read. And it's directly under ZZ12, similarly ambiguous (though it covers slightly over half of Alex's DF27 sample). Nevertheless, ZZ41 appears to define a new subclade (four out of 317 sequenced DF27 genomes), that won't be detected by a pack or panel that builds in a refusal to look for it. Some people think that's a good thing -- gives the tree more integrity, stability, permanence or something. The people who (because of all that integrity) won't find their own terminal SNP, after being tested with a brand new panel, may disagree.

Earl Davis
09-14-2015, 01:21 PM
As this panel looks to be going ahead I don't know if it's useful to mention any early new branches that come to light for possible late inclusion on the panel.

This week so far as well as the discovery of ZZ41 the SNP FGC23071 has emerged from a large block of snips and now appears as the lead in a small block at level 2 under DF27. FGC23066 now seems less significant than it did in the early branching and now leads a much larger block under FGC23071.


Earl.

Mikewww
09-14-2015, 02:23 PM
As this panel looks to be going ahead I don't know if it's useful to mention any early new branches that come to light for possible late inclusion on the panel. ...
I think it is very timely to dig around and bring up any potential branch defining SNPs within DF27. YSEQ can add them quickly. FTDNA is not so quick so feeding them new news is important.

I apologize if for some of the pressure I put on in terms of questions. I agree with your general thrust and the problematic nature of fixed SNP testing. Panels/Packs are the fixed SNP low cost way to go. However, they are doomed to always be out of date. In fact, we want them to be out of date as we are long a way from the DF27 tree being fully discovered. If a fixed set of SNPs was current that means NGS testing has dried up... and that's what we really need. NGS (Big Y or FGC) discovery testing. It's the feeder system for the lower cost fixed SNP Panels/Packs.

From a genetic genealogy perspective, the U106 guys were the first to say this that I'm aware of but it is quite right - Known SNP testing is testing somebody else's SNPs while NGS testing is discovering your own.

Earl Davis
09-23-2015, 07:37 AM
The block under CTS4188 has broken up nicely in the last few weeks. S14445 has now been identified as an older and more significant SNP than all the other snps in its former block. S14445 now sits 4 levels under DF27. The block lead by S11121 now drops to 5 levels under DF27.

Earl.

razyn
09-28-2015, 05:11 PM
that Sept. 10th screen shot had four guys listed who are not there tonight, Sept. 13th. [HG01241, 113701, N112478, 92432.] They are under a new SNP, ZZ41 -- located in the P5 palindrome region.

I didn't make a ZZ41 subgroup when Alex put it on the Big Tree, because only two of the identified samples were in the DF27 project. Today we got a third BigY test (278732) who has several "shared novel variants" uniquely in common with one of our ZZ41 guys (113701); so I am assuming he's also ZZ41+, and went ahead and created the subgroup (Pc). Having done so, I also raided the P312 project for 92432, who hadn't gotten around to joining DF27 yet.

Mikewww
09-28-2015, 08:53 PM
I didn't make a ZZ41 subgroup when Alex put it on the Big Tree, because only two of the identified samples were in the DF27 project. Today we got a third BigY test (278732) who has several "shared novel variants" uniquely in common with one of our ZZ41 guys (113701); so I am assuming he's also ZZ41+, and went ahead and created the subgroup (Pc). Having done so, I also raided the P312 project for 92432, who hadn't gotten around to joining DF27 yet.
Thank you, Razyn. We all appreciate that you are staying on top of DF27 analysis.

Earl Davis
10-01-2015, 07:15 AM
Someone else has had moved out of the ZZ12* group after matching a new sample at position 22024379C-T. 22024379C-T appears to be at level two under DF27.

Earl.

Earl Davis
10-02-2015, 09:12 AM
22293687-G-A seems to be the key 'regular' SNP under the ZZ41 group so far.

razyn
10-04-2015, 12:57 AM
Someone else has moved out of the ZZ12* group after matching a new sample at position 22024379C-T.
Neither one of those guys was a member of the R1b-DF27 and Subclades project when you posted that, but Alex passed along my invitation and both have joined. So now they are subgroup Pd, and if anybody else shows up with that mutation I'll tell him where to go.

Pd used to be L194, but that is basically one tested guy and two of his relatives so I thought they should stay at the end of the line, and changed their category to Pe. I think I'll post my longer comment about that on the "Why doesn't FTDNA fix their haplotree" thread, assuming I can still find it.

Earl Davis
10-09-2015, 11:58 AM
22293687-G-A seems to be the key 'regular' SNP under the ZZ41 group so far.

This has now been joined by a small 'brother' block lead by S7432.

Earl.

razyn
10-09-2015, 03:10 PM
I'll move the new guy 284255 to group Pc, he's been below my radar for a long time. The Big Tree is very helpful in that regard, among others.

Earl Davis
10-17-2015, 12:21 PM
The block formerly lead by FGC23066 has recently been broken up. FGC23066 drops to being at level 3 under DF27 and is replaced by FGC23071 at the second level under DF27. An unnamed snp at 6704205G-A appears to be a brother of FGC23066 at level 3.

Earl.

razyn
10-29-2015, 04:39 PM
Speaking of the original premise here, with which I suppose I have reluctantly come to disagree (probably, more people are offended by FTDNA's not offering a test they than by their offering one that should include their terminal SNP but doesn't, because we haven't found it yet) -- this morning (EDT) two things that illustrate that debatable premise happened more or less simultaneously.

(1) I was compiling the SNP data (Shared Novel Variants discovered when a new BigY test came in and matched older ones) to inform several guys that they are in a newly discovered subclade of Z295; and

(2) FTDNA released a new SNP pack for Z209 -- which should include this new subclade, but can't, since I haven't reported it yet to anybody but the people who have the mutations.

So is that good news, or bad? Rash, premature panel testing -- or a snail's pace for discovery, that might have accelerated sooner if we had some basic sorting of larger groups, so we'd know where the BigY dollars really need to be spent?

Not for me to say. Opinions vary. Even my own opinions vary. First steps are harder for babies than running is for teenagers, and so on.

Mikewww
10-30-2015, 01:14 AM
....(2) FTDNA released a new SNP pack for Z209 -- which should include this new subclade, but can't, since I haven't reported it yet to anybody but the people who have the mutations.
Let's keep trying as Yogi Berra says, "It ain't over 'till its over." What's the subclade? I'll submit it. We've seen other SNPs included at the last second.


....So is that good news, or bad? Rash, premature panel testing -- or a snail's pace for discovery, that might have accelerated sooner if we had some basic sorting of larger groups, so we'd know where the BigY dollars really need to be spent?
There is truly a challenge that any fixed SNP package type of test faces. This extends into single SNP chasing too. It's never really over until someone from your genealogical timeframe family does an NGS test. ... so it's dollars and knowledge of your lineage upfront versus distributing the dollars over time and deferring the knowledge and hoping someone else goes first (with NGS testing.) You know what I think since I'm a old reformed SNP chaser, but we should respect the individual's choice.

razyn
10-30-2015, 01:46 AM
What's the subclade? I'll submit it. We've seen other SNPs included at the last second.

I called it Bc* for the purpose of grouping it more obviously near Z295+, w/o going downstream of M153 and its immediate forebears. Too many lower-case letters were eaten up by that line, they need some hierarchy. Anyway, Bc* now is nominally 7010864, T to C. But there are eleven more at the same level... and maybe a new one above it, that's on a palindrome; so it will take the wisdom of Solomon and the patience of Job to get it accepted, by anybody but Alex (if it turns out to be real). Which is one of the things I like about his tree.

Earl Davis
11-01-2015, 06:48 PM
Congrats on the panels. Have we seen many orders so far?

Earl.

razyn
11-01-2015, 07:37 PM
Congrats on the panels. Have we seen many orders so far?

It won't always be easy to answer that; but at the moment (coincidentally, because the the lab batches orders on Wednesday and these panels were introduced on a Thursday) the "Pending shipment to lab" report tells me that in the first three days there have been 45 orders for the DF27 pack, 8 orders for the Z198, and 4 orders for the Z209... by members of the DF27 project. I don't get notifications of other such orders (from surname project members, etc.). I rather suspect that the older SRY2627 project gets more traffic about Z198, including orders for these new packs.

Earl Davis
11-01-2015, 08:16 PM
Thanks. That's pretty impressive for week one.

Earl.

razyn
11-01-2015, 09:05 PM
Also in the same week, some more SNP discoveries (via new matches in recent BigY tests) have led me to create subgroups Bc* in the Z209 block; F7b and Pe (the latter name was formerly used by what is now group Pf) on the side that should be tested with the DF27 pack... only, it can't know about the very newest SNP discoveries. Which goes along with the "let's not be rash" theme.

I guess I agree with Mike, though -- it's time to make the discoveries (so far) more widely available, at a more reasonable price point that the cost of a Big Y (plus its thorough analysis elsewhere).

Mikewww
11-03-2015, 10:55 PM
Also in the same week, some more SNP discoveries (via new matches in recent BigY tests) have led me to create subgroups Bc* in the Z209 block; F7b and Pe (the latter name was formerly used by what is now group Pf) on the side that should be tested with the DF27 pack... only, it can't know about the very newest SNP discoveries. Which goes along with the "let's not be rash" theme.

I guess I agree with Mike, though -- it's time to make the discoveries (so far) more widely available, at a more reasonable price point that the cost of a Big Y (plus its thorough analysis elsewhere).
We have lift off. The Z209, Z198 and "rest of" DF27 SNP Packs are all updated and about to enter a test batch run at FTDNA. There have been changes made in just the last three business days so I think these things are about as current as you can get.

I changed my way of thinking on this as I'm now telling FTDNA to include all the phylogenetic equivalent SNPs they can and that this will save them money. Keep in mind, I'm in sales. :) I don't know if they believe me anyway.

How it saves them money is they will have less updates. I proved it to them on my L513 SNP Pack. Having a good number of equivalents for lightly tested blocks means no update is needed to the pack when a new individual Big Y result "busts" a phylogenetic equivalent block. Pack updates are needed for new terminal subclades, though. There is no getting around that.

Let me me re-iterate, I still think NGS SNP discovery testing is the way to go so you can invest in your own line of SNPs. However, the expense is what it is so fixed SNP bundles are going to be around.

If Razyn will take a well earned vacation, these packs will be current at least for that long.

ArmandoR1b
11-04-2015, 12:16 PM
Let me me re-iterate, I still think NGS SNP discovery testing is the way to go so you can invest in your own line of SNPs. However, the expense is what it is so fixed SNP bundles are going to be around.

I have mentioned in the past that there would be a lot of orders once an SNP Pack for DF27 was created. Based on the orders in the Z198 SNP pack thread I was right. There are too many people on a limited income, even in the U.S., and many others unwilling to spend more $575, or even $475, for a BigY test even if they have the money.

StationMaster
11-04-2015, 07:13 PM
I am one of the many who ordered the DF27 pack. This was not an easy decision for me. I had been thinking about taking Big Y in the next year or so. If I had believed that FTDNA would hold the price at $99, I probably would have waited a while, but I didn't want to waste $20 through indecision. I can afford Big Y, but I am young and in no big hurry. The DF27 pack will probably be the last money I spend on DNA testing for 5-10 years. I suspect that whole genome testing will be affordable by then and I will jump in.

Mikewww
11-04-2015, 07:28 PM
I am one of the many who ordered the DF27 pack. This was not an easy decision for me. I had been thinking about taking Big Y in the next year or so. If I had believed that FTDNA would hold the price at $99, I probably would have waited a while, but I didn't want to waste $20 through indecision. I can afford Big Y, but I am young and in no big hurry. The DF27 pack will probably be the last money I spend on DNA testing for 5-10 years. I suspect that whole genome testing will be affordable by then and I will jump in.
What's your kit # and I'll look it up to see if there are matches that have done deeper testing? What are your goals in DNA testing?

I see you are new to Anthrogenica. A lot of the data and details for DF27 are recorded at the R1b-DF27-project yahoo group. Please join there as well. Anthrogenica is a great place for in-depth discussions and we have some real experts on-line here. There are some good discussions on origins of DF27, R1b, etc. going on here that you might be interested in.

StationMaster
11-04-2015, 08:17 PM
Hi Mike,

We have been in touch by email before. I mostly lurk on Anthrogenica and I find the discussions fascinating. My primary goal is paternal line genealogy within the last 400 years. I am also quite interested in anthropology, but I have a limited budget for tests that won't directly help me with genealogy. I am already in your R1b spreadsheet and I have no close STR matches. As such, I am doing SNP testing out of curiosity, not to narrow down a long list of matches. I appreciate your offer to take a look at my kit, but I doubt you will learn anything new. I don't think I am allowed to send pms through this system, but I will send you an email. Thanks!

Mikewww
11-05-2015, 03:10 AM
Hi Mike,

We have been in touch by email before. I mostly lurk on Anthrogenica and I find the discussions fascinating. My primary goal is paternal line genealogy within the last 400 years. I am also quite interested in anthropology, but I have a limited budget for tests that won't directly help me with genealogy.... !
Got it StationMaster. I just posted over on your "need education/enablement" thread. It is a trade-off of money versus time versus knowledge (vis a vis goals) and impact on others (seeding).
http://www.anthrogenica.com/showthread.php?5450-Better-arguments-education-needed-for-NGS
It's a good discussion to have but not really DF27 specific.

Krefter
11-06-2015, 05:50 AM
Anyone know of FTDNA coupons for DF27 package? All coupons I found are invalid.

lgmayka
11-06-2015, 09:44 AM
Anyone know of FTDNA coupons for DF27 package?
If you mean FTDNA's DF27 SNP Pack, the current introductory price of $99 is special and temporary. It will almost certainly rise to $119 by next Wednesday.

It is possible that the presumed upcoming holiday discount sale will include a discount or coupon applicable to SNP packs. But even if so, I doubt that it will reduce a $119 price much below $99.

Mikewww
11-06-2015, 01:21 PM
If you mean FTDNA's DF27 SNP Pack, the current introductory price of $99 is special and temporary. It will almost certainly rise to $119 by next Wednesday.

It is possible that the presumed upcoming holiday discount sale will include a discount or coupon applicable to SNP packs. But even if so, I doubt that it will reduce a $119 price much below $99.
I agree with Lawrence that this is probably the case. FTDNA will rerun tests no charge so I don't think there is a lot of risk in the $99 "beta" version of the pack.

I think we need to re-incorporate learnings from this back into the R1b-M343 Backbone Pack next.

I actually like the Z209 (North South cluster) and Z198 (for SRY2627 and L165) Packs better, though, so if you think you fit in better there I wouldn't be afraid to jump directly into those. The reason I like them is they are loaded with lightly tested phylogenetic equivalent blocks of SNPs so I think new branching will be discovered the packs.

razyn
11-06-2015, 05:08 PM
they are loaded with lightly tested phylogenetic equivalent blocks of SNPs so I think new branching will be discovered the packs.

I would agree more completely if I were more persuaded that equivalent blocks are likely to break down hierarchically. Some do; but the expectation that they will is largely based on experience, and that experience has until recently been based on very much shorter lists of equivalents. We don't really know that linear, sequential mutation events are the norm.

The more of these strings/lists of numerous equivalents I see, the more I tend to think it's pretty normal for a lot of SNPs to happen at once (one event, to one guy, in one place, at one time). It's also pretty normal for some lines to die out -- leaving an appearance of tree-like structure that's distorted because so many limbs have fallen off any older bush.

StationMaster
11-06-2015, 06:56 PM
Got it StationMaster. I just posted over on your "need education/enablement" thread. It is a trade-off of money versus time versus knowledge (vis a vis goals) and impact on others (seeding). ... It's a good discussion to have but not really DF27 specific.


Yes, as I said this was not an easy decision for me, but I have no regrets about ordering the DF27 pack. As a relative newcomer, I am reading as much as I can, including this entire thread. This is a bit of a "sausage-making" thread that is not geared towards people like me. I'm glad I read it though and I feel much better informed. There were clear warnings from Earl, razyn and you, which I interpreted to mean that some people might want to wait for a while for the next generation DF27 panel. Here are just a couple things that I read.


This is the constant problem of fixed SNP panels and packs of all sorts. The next Big Y test result could bring some valuable new information. Hence fixed SNP packages are doomed to be obsolete on the day they are released or soon thereafter.



That may be true theoretically; but in practice [noting that the practice is virtually limited to (a) FTDNA testers at the BigY level and (b) the heavily skewed sample of the 1000 Genomes project] a tree node that has two or three (or zero) subclades indicates a very small tested sample, like two to four guys. Whereas the Z195 side has a very large sample, many hundreds of guys (they don't have to have NGS testing if they tested the individual SNP in question, mainly with Sanger sequencing since 2011). Additionally, much of the apparent Z195+ "explosion" happened in the population toward which 1000 Genomes is skewed.

I think the ZZ12 side of the DF27 project -- or at least several specific, recently-discovered branches of it -- might be as bushy as the Z195 side. We lack the sample, so far, with which the rest of its bushiness can be discovered and differentiated. I don't for a moment believe that the fifty or so subsets of DF27+, ZZ12+ [my second illustration, plus the ones Alex includes but YSEQ doesn't test, plus over a dozen who have NextGen results or 1000 Genomes sequencing with no match yet found, plus some unknown number we have yet to discover at all] are "basal," or almost basal (DF27**) -- meaning they have had one or two mutations in 4900 years.

I think it's a sampling difference.

We don't know yet if ZZ12+ will prove as bushy as the Z195 or if it will continue to look like the comb that it is now. If it ends up being very bushy, then the test I am taking right now will be obsolete in short order. Hopefully though with all the SNPs that are being tested in this panel and all the people who have ordered the test, you guys will have a much better view of ZZ12+ after you have analyzed the results. If my $99 helps contribute to this effort, then it will be worth it.

The biggest reason that I held off on Big Y for now is probably my own paranoia, but it is a concern specific to DF27+>ZZ12+. I have been reading about Big Y's gold regions and about "SNP ascertainment bias". Since ZZ12 has not been tested as thoroughly as others, I began to wonder if some of our (my) novel SNPs lie outside of Big Y's testing regions. My fear is compounded by the fact that I have no close STR matches. Perhaps my SNPs are a bit unusual too. I don't mind spending $99 to test lots of SNPs, even if the test will be obsolete in a few months. I do mind spending $500 on a test that could miss some important SNPs.

I am glad that FTDNA (with help from razyn, you and others) made this test available and I am glad I decided to take it, but it is clear to me that the value of this test is limited by the quality of information that we have at this point. Some people will take it now. Others will wait. Both may be good decisions depending on the circumstances.

REWM
11-06-2015, 08:10 PM
The biggest reason that I held off on Big Y for now is probably my own paranoia, but it is a concern specific to DF27+>ZZ12+. I have been reading about Big Y's gold regions and about "SNP ascertainment bias". Since ZZ12 has not been tested as thoroughly as others, I began to wonder if some of our (my) novel SNPs lie outside of Big Y's testing regions. My fear is compounded by the fact that I have no close STR matches. Perhaps my SNPs are a bit unusual too. I don't mind spending $99 to test lots of SNPs, even if the test will be obsolete in a few months. I do mind spending $500 on a test that could miss some important SNPs.

StationMaster

I did the Big Y test and I am part of the ZZ12 side.
I did Big Y,
Big Y gave me no calls for important SNP's such as DF27, Z2573, Z29620, and A6104 which I had to test with YSEQ to find out that I was in deed positive for. So yes Big Y can miss important SNP's.

Kvenlander
11-07-2015, 08:04 AM
This is great news! I am especially waiting for those DF27 pack results. Maybe they reveal some new matches.

Kvenlander
11-27-2015, 02:12 PM
StationMaster

I did the Big Y test and I am part of the ZZ12 side.
I did Big Y,
Big Y gave me no calls for important SNP's such as DF27, Z2573, Z29620, and A6104 which I had to test with YSEQ to find out that I was in deed positive for. So yes Big Y can miss important SNP's.

I also did the Big Y and I am part of the ZZ12 side. I had no calls under DF27, so my terminal SNP was P312. However, thanks to R1b Project and Alex Williamson's Big tree I found my terminal SNP. And as I understand it, this will be part of DF27 SNP pack, so in a small part my Big Y test might have actually helped others along. Also, meanwhile my terminal SNP FGC17112 is designated as a known SNP in my Big Y results. Unfortunately MyFTDNA page still shows P312....

I am glad I did the Big Y, as now I just have to wait for new matches to come. There are 2000 years between me and my closest match in Big Y, so I am reasonably certain that one day someone will come there between and shed some light on my deep ancestry.