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Author Topic: R1b-DF27 - keeping the phylogenetic tree updated  (Read 3819 times)
Mike Walsh
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« on: July 31, 2012, 04:24:38 PM »

I'm just looking for help keeping track of the positioning of new SNPs.

ISOGG is way ahead of FTDNA, which is expected to some extent, on recognizing SNPs that can be placed on the Y DNA phylogenetic tree.
http://isogg.org/tree/ISOGG_HapgrpR.html

Here is Thomas Krahn's draft version of the tree for DF27.
http://ytree.ftdna.com/index.php?name=Draft&parent=99813460

Below is a representation of what I use in the P312xL21 Haplotype spreadsheet for DF27. Do I have it right?  Am I missing SNPs? The below is actually represented in formulas in a spreadsheet so it is important that I get it right to display haplogroup labels correctly. I also try to use the asterisk and double asterisk to help denote immediate downstream SNP results.

DF27+  >>> R-DF27; * = Z196-  ** = Z196- L617- L86.2-

Z196+  >>> R-DF27/Z196; * = L176.2-  ** = Z209- DF17- L176.2-
Z274+  >>> R-DF27/Z196/Z274; * = Z209-  ** = Z209- DF17-
Z209+  >>> R-DF27/Z196/Z274/Z209; * = Z220-  ** = Z220-
Z220+  >>> R-DF27/Z196/Z274/Z209/Z220; * = Z216-
Z216+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216; * = Z278-
Z278+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278; * = Z214-  ** = Z214- L629-
Z214+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214; * = M153-
M153+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214/M153; Terminal
L629+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/L629; Terminal
DF17+  >>> R-DF27/Z196/Z274/DF17; Terminal
L176.2+  >>> R-DF27/Z196/L176; * = Z262-  ** = Z262- L165-
Z262+  >>> R-DF27/Z196/L176/Z262; * = SRY2627-
SRY2627+  >>> R-DF27/Z196/L176/Z262/SRY2627; Terminal
L165+  >>> R-DF27/Z196/L176/L165; Terminal

L617+  >>> R-DF27/L617; Terminal

L86.2+  >>> R-DF27/L86.2; Terminal

Z225+  >>> R-DF27/Z225; Terminal

L1231+ >>> Unpositioned under DF27
L1245+ >>> Unpositioned under DF27
L1246+ >>> Unpositioned under DF27
Z229+ >>> Unpositioned under DF27
L586+ >>> Unpositioned under Z196
L587+ >>> Unpositioned under Z196
L588+ >>> Unpositioned under Z196
Z198+ >>> Unpositioned under L176.2
L276+ >>> Unpositioned under SRY2627
L628+ >>> Unpositioned under SRY2627
L659+ >>> Unpositioned under SRY2627
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Mike Walsh
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« Reply #1 on: August 06, 2012, 11:40:00 PM »

I've updated the P312xL21 file after reworking the DF27 varieties (STR signature based speculative clusters.)
https://dl.dropbox.com/u/17907527/R1b-P312xL21_Haplotypes.zip

I did work in L484 under Z220 as a special manual case as L484.NS.

DF27+  >>> R-DF27; * = Z196-  ** = Z196- L617- L86.2-

Z196+  >>> R-DF27/Z196; * = L176.2- Z209-  ** = L176.2- Z209- DF17-

L176.2+  >>> R-DF27/Z196/L176; * = Z262-  ** = Z262- L165-
Z262+  >>> R-DF27/Z196/L176/Z262; * = SRY2627-

SRY2627+  >>> R-DF27/Z196/L176/Z262/SRY2627; Terminal

L165+  >>> R-DF27/Z196/L176/L165; Terminal

Z274+  >>> R-DF27/Z196/Z274; * = Z209-  ** = Z209- DF17-
Z209+  >>> R-DF27/Z196/Z274/Z209; * = Z220-  ** = Z220-
Z220+  >>> R-DF27/Z196/Z274/Z209/Z220; * = Z216-  ** = Z216- L484-
Z216+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216; * = Z278-
Z278+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278; * = Z214-  ** = Z214- L629-
Z214+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214; * = M153-
M153+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214/M153; Terminal
L629+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/L629; Terminal
L484.NS+  >>> R-DF27/Z196/Z274/Z209/Z220/L484.NS; Terminal

DF17+  >>> R-DF27/Z196/Z274/DF17; Terminal
L617+  >>> R-DF27/L617; Terminal

L86.2+  >>> R-DF27/L86.2; Terminal

Z225+  >>> R-DF27/Z225; Terminal

L1231+ >>> Unpositioned under DF27
L1245+ >>> Unpositioned under DF27
L1246+ >>> Unpositioned under DF27
Z229+ >>> Unpositioned under DF27
L586+ >>> Unpositioned under Z196
L587+ >>> Unpositioned under Z196
L588+ >>> Unpositioned under Z196
Z198+ >>> Unpositioned under L176.2
L276+ >>> Unpositioned under SRY2627
L628+ >>> Unpositioned under SRY2627
L659+ >>> Unpositioned under SRY2627
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razyn
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« Reply #2 on: August 07, 2012, 12:20:04 AM »

I did work in L484 under Z220 as a special manual case as L484.NS.

Thanks.

And also, woo hoo!  Squeaky wheel got greased.  We're awaiting the final 8 markers for Hall's upgrade to 111; and we're hoping a Richert will be moved to test L484, and/or upgrade beyond 37.  But any time you feel moved to run some of the magic Nordtvedt numbers on our variance, feel free.  I'm curious to see how our node compares with one of the more Iberian looking subclades of DF27, which occur on both main limbs of Z196 (with and without L176.2) -- as well as in some DF27* that's none of the above, I guess.

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Mike Walsh
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« Reply #3 on: August 13, 2012, 11:33:08 AM »

What about L881?

Here's what I see from Y DNA SNP reports:

L881- people:

f51865   John McFarlane, b.1801, Islington, Middlesex, England   P312+ M65- U152- DF27- L459- DF19- L238- Z245- L881- Z229-
f27045   John White, b.1804, Drumcliff, Co. Sligo, Ireland    L644+ L1200- L881-
f90959   John Bowker, b.1790, Battersea, Surrey, South East, England  DF27+ Z196- L617- Z225- L147.3- L719- L881- L1231- Z229-
f24201   Edward Swann, b. Eagleton Plantation, England   DF27+ Z196- L617- L881- L1231-
f212887   George Henry Parker (Les), b.c.1860, USA   DF27+ L881-
f93184   Thomas Ranney, b.1616, Scotland   DF19+ L1063+ Z302- L881-


L881+ people:

f37812   Alan de Halsall, liv.1202, Halsall, Lancashire, North West, England   P312+ L881+ M65- U152-
f221355   Ronald Jester   P312+ L881+
fH1295   Henry Sutton, b.1839, UK   P312+ L881+
f26020   Benjamin Tucker Howland, b.1778, North Carolina, USA (England)   DF27+ L881+ L875+ Z196-


There are DF27+ people that are L881- and since there are also L881+ people that are DF27+ we can infer that L881 is downstream of DF27.  We see that an L881+ person is Z196- so we can infer L881 is parallel to Z196.

Looks like an L617+ person and an L86.2+ person should test for L881 but it appears to be a nice nice peer for Z196.

Am I missing anything?
« Last Edit: August 13, 2012, 11:35:11 AM by Mikewww » Logged

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« Reply #4 on: August 13, 2012, 06:01:42 PM »

I went ahead and updated the P312xL21 file at the Yahoo group with the latest data. Here is the direct link.
https://dl.dropbox.com/u/17907527/R1b-P312xL21_Haplotypes.zip

Here us the direct link to the P312 Descandancy chart I used for the spreadsheet haplogroup assignment purposes.
https://dl.dropbox.com/u/17907527/R1b-P312_Descendancy_Tree.jpg

Below is what's in the Clades table and hopefully matches the graphic I drew. I included L881 as a peer to Z196 under DF27. More testing is need though to formalize that.

I feel like I'm missing Z198's position. Any new news?

DF27+  >>> R-DF27;  * = Z196-  ** = Z196- L617- L881- L86.2-

Z196+  >>> R-DF27/Z196;  * = L176.2- Z209-  ** = L176.2- Z209- DF17-,  Equivalents: Z195
L176.2+  >>> R-DF27/Z196/L176;  * = Z262-  ** = Z262- L165-,  Equivalents: Z198
Z262+  >>> R-DF27/Z196/L176/Z262;  * = SRY2627-  ** = n/a
SRY2627+  >>> R-DF27/Z196/L176/Z262/SRY2627; Terminal,  Equivalents: M167
L165+  >>> R-DF27/Z196/L176/L165; Terminal,  Equivalents: S68
Z274+  >>> R-DF27/Z196/Z274;  * = Z209-  ** = Z209- DF17-
Z209+  >>> R-DF27/Z196/Z274/Z209;  * = Z220-  ** = Z220-
Z220+  >>> R-DF27/Z196/Z274/Z209/Z220;  * = Z216-  ** = Z216- L484-
Z216+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216;  * = Z278-  ** = n/a
Z278+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278;  * = Z214-  ** = Z214- L629-,  Equivalents: rs1469371
Z214+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214;  * = M153-  ** = n/a
M153+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214/M153; Terminal
L629+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/L629; Terminal
L484.NS+  >>> R-DF27/Z196/Z274/Z209/Z220/L484.NS; Terminal
DF17+  >>> R-DF27/Z196/Z274/DF17; Terminal

L617+  >>> R-DF27/L617; Terminal

L881+  >>> R-DF27/L881; Terminal

L86.2+  >>> R-DF27/L86.2; Terminal

Z225+  >>> R-DF27/Z225; Terminal


L1231+ >>> Unpositioned under DF27
L1245+ >>> Unpositioned under DF27
L1246+ >>> Unpositioned under DF27
L194+ >>> Unpositioned under DF27
Z229+ >>> Unpositioned under DF27
L586+ >>> Unpositioned under Z196
L587+ >>> Unpositioned under Z196
L588+ >>> Unpositioned under Z196
Z198+ >>> Unpositioned under L176.2
L276+ >>> Unpositioned under SRY2627
L628+ >>> Unpositioned under SRY2627
L659+ >>> Unpositioned under SRY2627
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razyn
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« Reply #5 on: August 13, 2012, 07:22:52 PM »

I appreciate the effort that has gone into this, and I really like your colorful descendancy charts.  But I wonder why L881 got onto the latest revision, and L484.NS didn't.  Can't be the lack of ISOGG recognition -- L881 doesn't have that, either.
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Mike Walsh
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« Reply #6 on: August 13, 2012, 07:30:14 PM »

I appreciate the effort that has gone into this, and I really like your colorful descendancy charts.  But I wonder why L881 got onto the latest revision, and L484.NS didn't.  Can't be the lack of ISOGG recognition -- L881 doesn't have that, either.

That's what I get for going out on the limb, but I'm betting L881 will get ISOGG recognition. L881 appears to be stable and I can see it will have GD's that will break through private status.

On the other hand, L484.NS is just a representation I created on a spreadsheet. We don't really know how many instances of L484 there are.  Did you get anything out of Thomas Krahn?
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razyn
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« Reply #7 on: August 13, 2012, 07:45:38 PM »


On the other hand, L484.NS is just a representation I created on a spreadsheet.

Well, that, and a SNP for which at least three and probably four minor lineages from England, France and Poland, unrelated to each other for over a thousand years, are positive.  And one that is positioned to demonstrate that its nephew clade Z278 went to Iberia, and did not come from there.  And that will annoy so many people, on so many levels.  (I've been reading Celtic from the West, this week.)

Quote
We don't really know how many instances of L484 there are.  Did you get anything out of Thomas Krahn?

Nope, assuming you mean an answer to my email request for a discovery sequence number.  I've gotten several SNP tests out of him, since May 2011; and I'm not really complaining, because I think things are actually moving along pretty well, considering the complexity of the process.

I'm refreshing my request to Thomas today, and will copy that email to the several people (apart from us bearers of the L484 SNP) who might seem to have some reason to care.
« Last Edit: August 14, 2012, 12:24:00 PM by razyn » Logged

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« Reply #8 on: August 19, 2012, 10:45:16 AM »

For purposes of discussion or correction I'd like to paste in a few ballpark estimates of the date at which these SNPs happened.  My additions, based on some pairwise mismatch data that Spanjool posted today to the Yahoo R-P312 group, are the red numbers preceding some of the SNPs in Mike's table.  I repeat, the red stuff is not from Mike; don't be misled by the graphic framing of a "quotation," which is done to give him credit for the basic sequence, which I have annotated (or perhaps desecrated).

Obviously there is a margin of error, for any of the dates -- but it isn't infinite, and is proportional to the dating error (or accuracy) for other closely related SNPs.  Any of these may be perceived as a WAG, if that makes you happy; I'm neither qualified nor inclined to argue with grad students in statistics, or others who will willfully miss the point.  The point is that these events are binary, and a later one did not happen prior to the birth of its grandparent.  Nor, perhaps, to the west of a place to which its unborn grandson had not yet dreamed of migrating from the east.  Or, vice versa.

And even if these estimates are completely wrong, it's an interesting exercise for some more sophisticated person to go through.  I think of it as supplementary captioning for those phylogenetic descendancy charts Mike has been preparing, lately.

1175 BC  DF27+  >>> R-DF27;  * = Z196-  ** = Z196- L617- L881- L86.2-

875 BC  Z196+  >>> R-DF27/Z196;  * = L176.2- Z209-  ** = L176.2- Z209- DF17-,  Equivalents: Z195
L176.2+  >>> R-DF27/Z196/L176;  * = Z262-  ** = Z262- L165-,  Equivalents: Z198
Z262+  >>> R-DF27/Z196/L176/Z262;  * = SRY2627-  ** = n/a
SRY2627+  >>> R-DF27/Z196/L176/Z262/SRY2627; Terminal,  Equivalents: M167
475 BC  L165+  >>> R-DF27/Z196/L176/L165; Terminal,  Equivalents: S68
Z274+  >>> R-DF27/Z196/Z274;  * = Z209-  ** = Z209- DF17-
Z209+  >>> R-DF27/Z196/Z274/Z209;  * = Z220-  ** = Z220-
850 BC  Z220+  >>> R-DF27/Z196/Z274/Z209/Z220;  * = Z216-  ** = Z216- L484-
Z216+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216;  * = Z278-  ** = n/a
625 BC  Z278+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278;  * = Z214-  ** = Z214- L629-,  Equivalents: rs1469371
Z214+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214;  * = M153-  ** = n/a
215 AD  M153+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/Z214/M153; Terminal
L629+  >>> R-DF27/Z196/Z274/Z209/Z220/Z216/Z278/L629; Terminal
400 AD  L484.NS+  >>> R-DF27/Z196/Z274/Z209/Z220/L484.NS; Terminal
DF17+  >>> R-DF27/Z196/Z274/DF17; Terminal

L617+  >>> R-DF27/L617; Terminal

L881+  >>> R-DF27/L881; Terminal

L86.2+  >>> R-DF27/L86.2; Terminal

Z225+  >>> R-DF27/Z225; Terminal

One other detail I'll throw in, not part of Mike's table but somewhat relevant:  L238 (which isn't under DF27) would date from about 275 AD proportionately to these other estimates.
« Last Edit: August 20, 2012, 12:08:29 PM by razyn » Logged

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« Reply #9 on: September 10, 2012, 09:11:50 AM »

For purposes of discussion or correction I'd like to paste in a few ballpark estimates of the date at which these SNPs happened.

In that there has been zero discussion or correction of this (in the three weeks since I posted it), I think I'll link to the TMRCA calculations thread, on which Spanjool has posted revised estimates today (similarly adjusted on the basis of pairwise mismatches) for the TMRCA of several of the same SNPs:

http://www.worldfamilies.net/forum/index.php?topic=10575.msg138524#msg138524
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Mike Walsh
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« Reply #10 on: October 23, 2012, 03:22:49 AM »

I've just updated the spreadsheet of all the confirmed R1b-P312+ (except L21)
people that I can find.

It's out under the "links" section of this Yahoo Group at
http://groups.yahoo.com/group/R1b-P312-Project/links
(which gets you to https://dl.dropbox.com/u/17907527/R1b-P312xL21_Haplotypes.zip
- please bookmark)

It is very evident that DF27's ranks are swelling. Everyone who is P312+ should
make sure to test for all U152, L21 and DF27. If you have not tested for DF27,
make sure to.

I can count 601 DF27+ people overall, of which 49 are DF27* (DF27+ Z196-)
people.

Of the DF27* people
21 are from the British Isles
7 are from the Iberian Peninsula
4 are from Poland, Hungary and the Ukraine
9 are from Western Continental Europe (France, Germany, Switzerland)
0 from Nordic countries

Regards,
Mike W

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RickA
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« Reply #11 on: October 28, 2012, 08:16:43 PM »

.......I can count 601 DF27+ people overall, of which 49 are DF27* (DF27+ Z196-)
people.

Of the DF27* people
21 are from the British Isles
7 are from the Iberian Peninsula
4 are from Poland, Hungary and the Ukraine
9 are from Western Continental Europe (France, Germany, Switzerland)
0 from Nordic countries

Regards,
Mike W



DF27* now at an even 50.  Got my Z196- a few days ago. Unfortunately I can't help much in the origins column, as I'm stuck in Southside Virginia c 1730.  BI seems a reasonable guess of course.

« Last Edit: October 28, 2012, 08:22:02 PM by RickA » Logged

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« Reply #12 on: October 29, 2012, 10:03:03 AM »

.......I can count 601 DF27+ people overall, of which 49 are DF27* (DF27+ Z196-)
people.

Of the DF27* people
21 are from the British Isles
7 are from the Iberian Peninsula
4 are from Poland, Hungary and the Ukraine
9 are from Western Continental Europe (France, Germany, Switzerland)
0 from Nordic countries

Regards,
Mike W



DF27* now at an even 50.  Got my Z196- a few days ago. Unfortunately I can't help much in the origins column, as I'm stuck in Southside Virginia c 1730.  BI seems a reasonable guess of course.



BI makes the most sense, I think. Are you going to go for the Geno 2.0 thing?
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« Reply #13 on: October 29, 2012, 07:05:05 PM »


BI makes the most sense, I think. Are you going to go for the Geno 2.0 thing?

Not sure. I'm still getting my bearings, having been away so long.  I think I read somewhere (probably here) that the SNPs on the geno 2.0 chip were set in somehing like Dec 2011. So I wonder if that wil help me drill down below DF27.  I've already got my Z196- . So, doesn't that leave only L881, L617, L86.2, and L225 left to test?  Any idea which if any of these SNPs are on the G2 chip?  Are there other reasons?
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« Reply #14 on: October 30, 2012, 08:07:52 AM »


BI makes the most sense, I think. Are you going to go for the Geno 2.0 thing?

Not sure. I'm still getting my bearings, having been away so long.  I think I read somewhere (probably here) that the SNPs on the geno 2.0 chip were set in somehing like Dec 2011. So I wonder if that wil help me drill down below DF27.  I've already got my Z196- . So, doesn't that leave only L881, L617, L86.2, and L225 left to test?  Any idea which if any of these SNPs are on the G2 chip?  Are there other reasons?

I heard the same thing, but then Bennett Greenspan said things like, "There are three new SNPs under M222 that nobody knew about" (I'm paraphrasing), so perhaps not everything was made public that was discovered prior to Dec 2011.
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« Reply #15 on: October 30, 2012, 08:41:08 AM »


BI makes the most sense, I think. Are you going to go for the Geno 2.0 thing?

Not sure. I'm still getting my bearings, having been away so long.  I think I read somewhere (probably here) that the SNPs on the geno 2.0 chip were set in somehing like Dec 2011. So I wonder if that wil help me drill down below DF27.  I've already got my Z196- . So, doesn't that leave only L881, L617, L86.2, and L225 left to test?  Any idea which if any of these SNPs are on the G2 chip?  Are there other reasons?

I just don't think we can be sure of what's in Geno 2.0 until Spencer Wells puts out the paper. For the early consumers, this is a "you have to buy it to see what's in it" deal.

I think the paper is due out very soon, though.
I heard the same thing, but then Bennett Greenspan said things like, "There are three new SNPs under M222 that nobody knew about" (I'm paraphrasing), so perhaps not everything was made public that was discovered prior to Dec 2011.

P.S. - your area generally functional today, RMS2? It sounds like N. Virginia better get out their snow shoes.
« Last Edit: October 30, 2012, 08:43:26 AM by Mikewww » Logged

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« Reply #16 on: October 30, 2012, 09:39:39 AM »

P.S. - your area generally functional today, RMS2? It sounds like N. Virginia better get out their snow shoes.

I'm farther north in VA than rms2 is, and in fact have no power, wifi, etc.  These sad tidings are brought to you all from my neighborhood Starbucks.  Most people here have power, but I live in the woods, and there are two trees down across power lines on my street.  No houses or people hit.

And with regard to the actual subject of this thread, I think Thomas Krahn has previously said on the RootsWeb Genealogy DNA-L list that the Geno 2.0 chip doesn't include DF27, nor any of the Z SNPs under Z196.  It does have Z196.
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« Reply #17 on: October 30, 2012, 09:44:39 AM »

So far, we're still up and running. We've had a lot of rain and some wind, but not too bad. It's cold today, but when I look out my window, I still see just rain.

My youngest son, up near the West Virginia line, lost his power, though. He will probably see a lot of snow.
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« Reply #18 on: October 30, 2012, 03:26:16 PM »

I just got off the phone with my Dad who lives in Buckhannon, West Virginia and he was telling me that they currently have a foot of snow and no power. Said he was going to have to stay at work for most of the time because thats the only source of power at the moment due to the generators.
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« Reply #19 on: October 30, 2012, 07:18:51 PM »

Thanks to all who weighed in on my questions about geno 2.0. I'll probably wait to see what it offers. Hope all you east coasters fare well in the storm.
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« Reply #20 on: November 21, 2012, 10:37:18 AM »

We got a little sidetracked, about hurricanes and whatnot.  I thought it might be time to bring this forward in case the GenoChip starts regurgitating a lot of new SNP data, in the immediate future.  My assumption has been that the chip itself doesn't know there is such a thing as DF27 -- but it knows about some of the other SNPs that are under it; and it could be that new discoveries that are on the chip will turn out to have been DF27 subclades, as well.  Anyway, this link currently goes to the DF27 part of Thomas Krahn's Draft Tree.  Unless the url becomes obsolete, it should be one of the places to check for updates to the phylogeny -- whether from that source (GenoChip) or others:

http://ytree.ftdna.com/index.php?name=Draft&parent=99813460
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« Reply #21 on: November 25, 2012, 09:46:08 PM »

Has anyone noticed how the ages of a number of the DF27 subclades align pretty nicely with the beginning of the Hallstatt age, which began around 800 B.C.?
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William B. Webb
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« Reply #22 on: February 18, 2013, 03:49:42 PM »

Has geno 2.0 uncovered anything of interest under DF27? Any new prospects for Z196- folk?
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« Reply #23 on: February 18, 2013, 05:01:58 PM »

Has geno 2.0 uncovered anything of interest under DF27? Any new prospects for Z196- folk?

RickA, please check out the thread titled "O'Neill" just down from this one.  There are a number of Z196- testing four new snp's.
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« Reply #24 on: February 18, 2013, 10:30:51 PM »

Yes, I see them. DF83 looks promising. Thanks Webb.
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