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Author Topic: R-L21: DF41 another new subclade to watch - it is old!  (Read 40832 times)
Larry Walker
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« Reply #375 on: November 28, 2012, 02:38:56 PM »

Opinions wanted - Possible R-DF41 Project supplement:

Keeper or Cul?
 https://www.dropbox.com/s/diz3ea981wuwnz9/DF41Supp.xlsx


I like it, especially the tree at the bottom. Thanks!

The tables remind me of McGee's Utility, which I used to mess with a few years ago. Such things seem more useful now that we are getting greater SNP resolution.
The tables ARE from McGee's utility Beta which now handles Y111. The tree is calculated using PHYLIP and charted using MEGAS. I looked at Fluxus Network, but the learning curve looked too steep for this OLD dog. Besides, this combination handles mixed size tests, which I'm not sure Fluxus does, and there is no point in duplicating what Mark is already doing.
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Mark Jost
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« Reply #376 on: November 28, 2012, 03:37:55 PM »


The tables ARE from McGee's utility Beta which now handles Y111. The tree is calculated using PHYLIP and charted using MEGAS. I looked at Fluxus Network, but the learning curve looked too steep for this OLD dog. Besides, this combination handles mixed size tests, which I'm not sure Fluxus does, and there is no point in duplicating what Mark is already doing.
Larry,

No Fluxus can not handle mixed length haplotype. I think Phylip should either due to GD's. But a few probably wont affect it to much.

By the way, I posted this DF41 diagram on Yahoo L21 the other day.

 DF41_67Marker.pdf
Nov 24
DF41- 67Marker TMRCA & Fluxus View 

http://f1.grp.yahoofs.com/v1/MF-2UOry5gHRgd61-4jOV8iwlajqECYAkhnakaFgbl_u0TWm6KSRr78gPX-NwlHuZWgiBLCxP-XBUynDuIOjXbcYyRbS8w/DF41_67Marker.pdf

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Larry Walker
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« Reply #377 on: November 28, 2012, 06:46:27 PM »


The tables ARE from McGee's utility Beta which now handles Y111. The tree is calculated using PHYLIP and charted using MEGAS. I looked at Fluxus Network, but the learning curve looked too steep for this OLD dog. Besides, this combination handles mixed size tests, which I'm not sure Fluxus does, and there is no point in duplicating what Mark is already doing.
Larry,

No Fluxus can not handle mixed length haplotype. I think Phylip should either due to GD's. But a few probably wont affect it to much.

By the way, I posted this DF41 diagram on Yahoo L21 the other day.

 DF41_67Marker.pdf
Nov 24
DF41- 67Marker TMRCA & Fluxus View 

http://f1.grp.yahoofs.com/v1/MF-2UOry5gHRgd61-4jOV8iwlajqECYAkhnakaFgbl_u0TWm6KSRr78gPX-NwlHuZWgiBLCxP-XBUynDuIOjXbcYyRbS8w/DF41_67Marker.pdf

MJost

Mark,

I love your DF41 tree, but I wasn't aware of it until a day after I had learned to drive the McGee Utility/PHYLIP/MEGAS route and posted my initial results to the DF41 Facebook group.

Your point about mixing lengths is well taken from a technical viewpoint, but I think that I am looking at a different audience.

A lot of folks join the projects who could probably care less about the genetics except as a means to better understand how they relate to other people. I believe that, to them, being included may be more important than technical accuracy even if they are only tested to Y12 as long as what they see is not too far out of the ballpark. If it is, then it provides a pretty strong argument why they should upgrade their tests for their own personal interests.

So, I think that there is room for both. I may be wrong, which is why I am seeking opinions. I had hoped to also get some from the L21 Yahoo group, but my post was interpreted as a possible virus, got pulled, and I got bounced from the group.

Oh well, such is life.

Thanks again for all of the good work you do.

Larry DF41+ L563-, L744/746-
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rms2
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« Reply #378 on: November 29, 2012, 08:50:41 PM »

DF41 seems to be moving kind of slowly lately. I guess that is what you get when your SNP resolution gets good enough to place you in a subclade that only amounts to about 5% or so of the DF13+ guys (which is still a lot of people).

I would be pleased if we got some new blood in our group: you know, someone in a cluster not yet known to be DF41+.
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Larry Walker
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« Reply #379 on: November 29, 2012, 09:32:41 PM »

DF41 seems to be moving kind of slowly lately. I guess that is what you get when your SNP resolution gets good enough to place you in a subclade that only amounts to about 5% or so of the DF13+ guys (which is still a lot of people).

I would be pleased if we got some new blood in our group: you know, someone in a cluster not yet known to be DF41+.
252650 Akers is ordering, but he is 41-1426.
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rms2
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« Reply #380 on: November 29, 2012, 09:56:17 PM »

DF41 seems to be moving kind of slowly lately. I guess that is what you get when your SNP resolution gets good enough to place you in a subclade that only amounts to about 5% or so of the DF13+ guys (which is still a lot of people).

I would be pleased if we got some new blood in our group: you know, someone in a cluster not yet known to be DF41+.
252650 Akers is ordering, but he is 41-1426.

Well, at least we'll get a new positive result, if not a new DF41+ cluster.
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rms2
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« Reply #381 on: December 07, 2012, 10:24:18 PM »

A few days ago we got a couple of new members who are French and from the island of Corsica. What is interesting is that their surname is Stuart, they are L745+, and they match the other royal Stewarts/Stuarts. They descend from a Stuart who went to Corsica from Belfast in the 1700s. I am reading a pdf in English that one of them sent me. It's interesting and involves some intrigue and mystery in the wake of the Jacobite Rebellion. At one point one of their ancestors or relatives (I haven't had time to sort it all out) hispanized the surname to Estuarte.

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Jdean
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« Reply #382 on: December 09, 2012, 05:36:15 AM »

A few days ago we got a couple of new members who are French and from the island of Corsica. What is interesting is that their surname is Stuart, they are L745+, and they match the other royal Stewarts/Stuarts. They descend from a Stuart who went to Corsica from Belfast in the 1700s. I am reading a pdf in English that one of them sent me. It's interesting and involves some intrigue and mystery in the wake of the Jacobite Rebellion. At one point one of their ancestors or relatives (I haven't had time to sort it all out) hispanized the surname to Estuarte.



Scottish & Corsican !! that sounds like a heady mixture :)

Great result though, and I would say a very good example to give of DNA contributing to a family's genealogy research.
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rms2
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« Reply #383 on: December 09, 2012, 09:57:28 PM »

It's pretty cool. It puts me in mind of one of my favorite novels of all time: Kidnapped, by Robert Louis Stevenson. Great book. I've read it several times. I may have to dust it off and read it again soon.
« Last Edit: December 09, 2012, 09:57:48 PM by rms2 » Logged

Larry Walker
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« Reply #384 on: December 10, 2012, 09:03:22 PM »

Well, I see that GENO 2.0 results are hitting the streets without a codebook to decipher them. Confusion until Christmas when Santa is expected to drop down the chimney with codebooks galore apparently. Maybe its just as well that DF41 missed the cut.
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rms2
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« Reply #385 on: December 11, 2012, 04:59:52 AM »

Well, I see that GENO 2.0 results are hitting the streets without a codebook to decipher them. Confusion until Christmas when Santa is expected to drop down the chimney with codebooks galore apparently. Maybe its just as well that DF41 missed the cut.

That will take some sorting out for sure.

In the meantime, our recruiting has taken an upturn the last couple of days. :-)
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rms2
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« Reply #386 on: December 12, 2012, 07:46:13 AM »

Good news this morning for us DF41+ types: MacKenzie, kit 71100, got a DF41+ result. His mdka came from Applecross, Ross and Cromarty (modern Wester Ross), Scotland.
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Larry Walker
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« Reply #387 on: December 13, 2012, 06:06:19 PM »

I think that maybe I'm glad that DF41 didn't make the cut for GENO 2.0. There's an example of the kinds of things they are getting below, and it is going to take more than a day or two to sort those worms from the spagetti. Sometimes I guess that less is more.

-------------

Now after uploading my Geno data to FTDNA, my terminal SNP's are not in agreement - as follows:
1. FTDNA - M222
2. Geno - DF23


Let's hope this gets resolved soon. One possibility is that a new SNP was found between DF23 and M222, as well as other SNP's below M222?


If David Wilson or Paul Burns are reading this, are there any other M222+ people who have results to share from Geno 2.0.


My full list of SNP's - for anyone interested is:


CTS10168+, CTS10362+, CTS10834+, CTS109+, CTS11358+, CTS11468+, CTS11575+, CTS11726+, CTS11985+, CTS12478+, CTS125+, CTS12632+, CTS1996+, CTS2134+, CTS2664+, CTS3063+, CTS3135+, CTS3331+, CTS3358+, CTS3431+, CTS3536+, CTS3575+, CTS3654+, CTS3662+, CTS3868+, CTS3996+, CTS4244+, CTS4364+, CTS4368+, CTS4437+, CTS4443+, CTS4740+, CTS5318+, CTS5457+, CTS5532+, CTS5577+, CTS5884+, CTS6135+, CTS623+, CTS6383+, CTS6800+, CTS6907+, CTS7400+, CTS7659+, CTS7922+, CTS7933+, CTS8243+, CTS8591+, CTS8665+, CTS8728+, CTS8980+, CTS9828+, DF23+, F1046+, F115+, F1209+, F1302+, F1320+, F1329+, F1704+, F1714+, F1753+, F1767+, F1794+, F180+, F2048+, F2075+, F211+, F212+, F2142+, F2155+, F2402+, F2587+, F2688+, F2710+, F2837+, F29+, F295+, F2985+, F2993+, F3111+, F313+, F3136+, F33+, F332+, F3335+, F344+, F3556+, F356+, F359+, F3692+, F378+, F4+, F47+, F506+, F556+, F63+, F640+, F647+, F652+, F671+, F719+, F82+, F83+, F93+, L11+, L132+, L15+, L150+, L151+, L16+, L23+, L265+, L278+, L350+, L388+, L389+, L407+, L468+, L470+, L471+, L478+, L482+, L483+, L498+, L500+, L502+, L506+, L51+, L52+, L566+, L585+, L721+, L747+, L752+, L754+, L761+, L768+, L773+, L774+, L779+, L781+, L82+, M126-, M139+, M153-, M160-, M168+, M173+, M18-, M207+, M222+, M235+, M269+, M294+, M343+, M37-, M415+, M42+, M45+, M526+, M65-, M73-, M89+, M94+, P128+, P131+, P132+, P135+, P136+, P138+, P14+, P141+, P145+, P146+, P148+, P151+, P158+, P159+, P160+, P166+, P187+, P207+, P225+, P226+, P228+, P229+, P230+, P232+, P233+, P235+, P236+, P237+, P238+, P240+, P242+, P243+, P244+, P245+, P25+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P295+, P297+, P310+, P66-, PAGES00083+, PF1016+, PF1029+, PF1031+, PF1040+, PF1046+, PF1061+, PF1092+, PF1097+, PF110+, PF1169+, PF1203+, PF1269+, PF1276+, PF15+, PF192+, PF210+, PF212+, PF223+, PF234+, PF258+, PF2591+, PF2593+, PF2599+, PF2600+, PF2608+, PF2611+, PF2615+, PF2624+, PF263+, PF2631+, PF2643+, PF272+, PF2745+, PF2747+, PF2748+, PF2749+, PF2770+, PF278+, PF292+, PF316+, PF325+, PF342+, PF500+, PF5465+, PF5466+, PF5468+, PF5471+, PF5851+, PF5853+, PF5854+, PF5865+, PF5869+, PF5871+, PF5882+, PF5886+, PF5887+, PF5888+, PF5953+, PF5956+, PF5957+, PF5964+, PF5965+, PF5982+, PF6007+, PF601+, PF6063+, PF6091+, PF6145+, PF6246+, PF6249+, PF6250+, PF6263+, PF6265+, PF6270+, PF6271+, PF6272+, PF6404+, PF6409+, PF6411+, PF6424+, PF6425+, PF6430+, PF6432+, PF6434+, PF6438+, PF6443+, PF6463+, PF6494+, PF6495+, PF6498+, PF6500+, PF6506+, PF6507+, PF6509+, PF6524+, PF667+, PF719+, PF720+, PF725+, PF779+, PF796+, PF803+, PF815+, PF821+, PF840+, PF844+, PF892+, PF937+, PF951+, PF954+, PF970+, s10+, s3+, SRY2627-, V186+, V189+, V205+, V52+, V9+, YSC0000067+, YSC0000072+, YSC0000075+, YSC0000082+, YSC0000166+, YSC0000176+, YSC0000179+, YSC0000182+, YSC0000186+, YSC0000191+, YSC0000194+, YSC0000201+, YSC0000203+, YSC0000205+, YSC0000207+, YSC0000213+, YSC0000219+, YSC0000224+, YSC0000225+, YSC0000227+, YSC0000230+, YSC0000232+, YSC0000233+, YSC0000251+, YSC0000269+, YSC0000270+, YSC0000279+, YSC0000288+, YSC0000294+, Z290+

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rms2
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« Reply #388 on: December 13, 2012, 08:38:32 PM »

I noticed that, too. Data overload!

I remember when most of us were stuck at R-M269 (called "R1b1c" back then) and a certain poster on Rootsweb was claiming that the downstream SNPs that had been discovered - U106, U152, M222, SRY2627, and maybe a couple of others - were it.

Funny to think of that.
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Larry Walker
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« Reply #389 on: December 14, 2012, 06:41:02 PM »

IF DF13 did make it into GENO 2.0 hidden in that mass of information overload, maybe there is just a sprig of hope for DF41 or a subclade after all.

see http://tech.groups.yahoo.com/group/R1b-L21-Project/message/12864
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seferhabahir
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« Reply #390 on: December 14, 2012, 07:54:26 PM »

IF DF13 did make it into GENO 2.0 hidden in that mass of information overload, maybe there is just a sprig of hope for DF41 or a subclade after all.

see http://tech.groups.yahoo.com/group/R1b-L21-Project/message/12864

Well, I can't find those two CTS SNPs in any list of Geno 2.0 tested SNPs...
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Jdean
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« Reply #391 on: December 14, 2012, 08:58:18 PM »

IF DF13 did make it into GENO 2.0 hidden in that mass of information overload, maybe there is just a sprig of hope for DF41 or a subclade after all.

see http://tech.groups.yahoo.com/group/R1b-L21-Project/message/12864

Well, I can't find those two CTS SNPs in any list of Geno 2.0 tested SNPs...

Somebody's tested positive for CTS6581 though according to Ymap

http://ymap.ftdna.com/cgi-bin/gb2/gbrowse_details/hs_chrY?ref=ChrY;start=15501996;end=15501996;name=CTS6581;class=Sequence

which is apparently the same as DF41 so maybe it did make it onto the chip ?

Fingers crossed !!
« Last Edit: December 14, 2012, 09:01:10 PM by Jdean » Logged

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Larry Walker
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« Reply #392 on: December 14, 2012, 09:31:41 PM »

IF DF13 did make it into GENO 2.0 hidden in that mass of information overload, maybe there is just a sprig of hope for DF41 or a subclade after all.

see http://tech.groups.yahoo.com/group/R1b-L21-Project/message/12864

Well, I can't find those two CTS SNPs in any list of Geno 2.0 tested SNPs...

Somebody's tested positive for CTS6581 though according to Ymap

http://ymap.ftdna.com/cgi-bin/gb2/gbrowse_details/hs_chrY?ref=ChrY;start=15501996;end=15501996;name=CTS6581;class=Sequence

which is apparently the same as DF41 so maybe it did make it onto the chip ?

Fingers crossed !!
I think maybe you can uncross them. There is 1 positive out of 5 tests shown on Ymap, but it does not specify that those were GENO 2.0 tests. The CTS synonyms for DF63, DF13, and DF41 all have a comment of "Extracted from 1000 genomes data. Not qualified." at Ymap. Speculation: "Not qualified" = not on GENO 2.0 chip?
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rms2
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« Reply #393 on: December 14, 2012, 10:30:33 PM »

IF DF13 did make it into GENO 2.0 hidden in that mass of information overload, maybe there is just a sprig of hope for DF41 or a subclade after all.

see http://tech.groups.yahoo.com/group/R1b-L21-Project/message/12864

Well, I can't find those two CTS SNPs in any list of Geno 2.0 tested SNPs...

Somebody's tested positive for CTS6581 though according to Ymap

http://ymap.ftdna.com/cgi-bin/gb2/gbrowse_details/hs_chrY?ref=ChrY;start=15501996;end=15501996;name=CTS6581;class=Sequence

which is apparently the same as DF41 so maybe it did make it onto the chip ?

Fingers crossed !!

Where is that list of "Chris Tyler Smith" (CTS) SNPs that are included in the Geno 2.0? I saw it somewhere.

Was CTS6581 on it?

That would be a real boon to us, if it were.
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rms2
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« Reply #394 on: December 15, 2012, 10:00:51 AM »

I heard from David Reynolds that CTS6581 is not included in the Geno 2.0.

So, I guess my verdict on the Geno 2.0 from a DF41+ perspective still stands: it's a dud.
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Larry Walker
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« Reply #395 on: December 17, 2012, 09:01:01 PM »

I heard from David Reynolds that CTS6581 is not included in the Geno 2.0.

So, I guess my verdict on the Geno 2.0 from a DF41+ perspective still stands: it's a dud.
Mayibe we'll pick up a few through the back door. I've been noticing a few GENO 2.0 strike outs that haven't tested DF41, so I posted them a reminder on L21 Yahoo.
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rms2
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« Reply #396 on: December 21, 2012, 10:02:14 AM »

Well, we have our first continental DF41+ result: Bontron-Major, kit N67581, whose ancestor came from Montussaint in Franche Comte in eastern France, between Basel, Switzerland, and Dijon.
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eochaidh
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« Reply #397 on: December 21, 2012, 12:54:57 PM »

Well, we have our first continental DF41+ result: Bontron-Major, kit N67581, whose ancestor came from Montussaint in Franche Comte in eastern France, between Basel, Switzerland, and Dijon.

By Alan's calculations, that would be equal to 100 French results for DF41. One result could be explained away as migrating from The Isles, but not 100. This would seem to make France the origin of DF41. The same thing has happened with DF23, M222 and other subclades of L21.
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Jdean
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« Reply #398 on: December 21, 2012, 01:19:08 PM »

dam I really miss that 'Roll Eyes' emoticon they had on DNA-Forums.
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Mark Jost
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« Reply #399 on: December 21, 2012, 02:07:35 PM »

dam I really miss that 'Roll Eyes' emoticon they had on DNA-Forums.




Here is how you could show one.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
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