Comparing all the Chromo2 “positive” snps declared for a L161 Isles-D2 person against two other L161 Isles people, I came up with two snps, S7703 and S7725, which look like solid positives unique to the D2 line This is not definitive because of lack of the actual raw data file. See “Tree for L161” Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net

I see that I had the positions of the mismatches between the HUGO reference X and Y sequences slightly off. The mismatch points are 22 bases upstream and 32 bases downstream of the PF3514 site. Also, I looked at several I2a samples (HG00360, HG01344, and HG01197) from the 1000 Genomes project and they all show C at the site of PF3514, so I have yet to see a next-generation-sequencing sample with G at this site. On Sat, Jan 4, 2014 at 3:36 AM, G. Magoon <[email protected]> wrote: > Hi Wayne, > You should be able to find results for PF3514 in the genotyping ("gtype") > report. > > Nice analysis, Obed! > Greg > On Jan 4, 2014 3:50 AM, "Wayne R. Roberts" <[email protected]> > wrote: > > > Obed, my samples went to UCLA and unfortunately UCLA results were not > > satisfactory. I have sent new samples off to Full Genomes so will have to > > wait longer for results. > > > > Do you know what result Adam Waalkes received for PF3514? Ken, Aaron and > I > > have all his results data but I'm not so sure how to read the raw data > > files. > > > > > > On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> wrote: > > > > > Thanks, Wayne. Are you still waiting for your Full Genomes results? If > > so, > > > please let us know your result at the site of PF3514 when you receive > > them. > > > > > > > > > On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts > > > <[email protected]>wrote: > > > > > > > Obed, my question to Thomas was: > > > > > > > > One of our I-M223 Project members just received his Geno 2.0 results. > > He > > > is > > > > from the Project's Continental 2a group CTS6433+. When his raw data > is > > > > compared with that of other members he shows PF3514 with A A. All > > others > > > > show A G. Ybrowse has PF3514 mutation as A to G. How should I > interpret > > > his > > > > result? Is he derived and ancestral is actually G or is he ancestral > > > (back > > > > mutation) and everyone else is derived? Thanks for any advise, Wayne. > > > > > > > > He did not indicate it should be A to C and Ybrowse has A to G. > > > > > > > > > > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> > wrote: > > > > > > > > > Wayne, > > > > > > > > > > Did Thomas explicitly say that the derived value for PF3514 is G, > or > > > > could > > > > > it be C? My Full Genomes result clearly shows that I have C at this > > > > > location. I looked at the X and Y sequences in this region and they > > are > > > > > indeed very similar, but they do differ at points 17 bases upstream > > and > > > > 37 > > > > > bases downstream of the PF3514 site, which must be enough for Full > > > > Genomes > > > > > to separate the Y and X sequences. Full Genomes shows my X sequence > > to > > > be > > > > > identical to the HUGO reference, with A at the PF3514-homologous > > site. > > > So > > > > > Geno 2.0 was clearly in error when they reported me as AG instead > of > > > AC. > > > > > > > > > > Although I cannot see their raw data, Full Genomes also reports > > > several > > > > > other I1 people to have C at this position. These include another > > > > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be > > interesting > > > to > > > > > hear what your Full Genomes test showed at the PF3514 site. In > > > particular > > > > > I'm wondering if Full Genomes has shown anyone to have G at the > > PF3514 > > > > > site. I suppose it's possible that those of us who have C have had > a > > > > second > > > > > mutation at this site, from G to C. > > > > > > > > > > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > > > > <[email protected]>wrote: > > > > > > > > > > > This is what Thomas had to say about PF3514: > > > > > > > > > > > > Everyone in IJ is supposed to be derived. Actually all others > have > > an > > > > A. > > > > > It > > > > > > seems like the region around PF3514 is very similar to > > > > > > ChrX:91846733..91846902. > > > > > > > > > > > > I've made a comparison here: > > > > > > > > > > > > > > > > > > > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > > > > hope this link works for you). > > > > > > > > > > > > The X chromosome has also a "A" at this position and the probe on > > the > > > > > Geno2 > > > > > > chip picks them up both. What likely happened is that his > ancestors > > > > were > > > > > > derived for PF3514, but some X-Y recombination event has wiped > that > > > > > > mutation out at a later time so that it shows the ancestral "A" > > again > > > > at > > > > > > this location. > > > > > > > > > > > > ------------------------------- > > > > > > To unsubscribe from the list, please send an email to > > > > > > [email protected] with the word > > 'unsubscribe' > > > > > > without the quotes in the subject and the body of the message > > > > > > > > > > > > > > > > ------------------------------- > > > > > To unsubscribe from the list, please send an email to > > > > > [email protected] with the word > 'unsubscribe' > > > > > without the quotes in the subject and the body of the message > > > > > > > > > > > > > ------------------------------- > > > > To unsubscribe from the list, please send an email to > > > > [email protected] with the word 'unsubscribe' > > > > without the quotes in the subject and the body of the message > > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

According to the M223 Project results page the vast majority of members have 439=11 or 12. DYS439=10 in combination with some other markers like DYS392=13, seems to be a characteristic of this Z161* Vella-McMillan group. On Sat, Jan 4, 2014 at 11:20 AM, Kenneth Nordtvedt <[email protected]>wrote: > Almost the whole population has 10 at 439. So that marker does not help > say whether Jesatko is member of a specific subgroup of the population. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Wayne R. Roberts > Sent: Friday, January 03, 2014 6:09 PM > To: y-dna-haplogroup-i > Subject: Re: [yDNAhgI] Believable > > Jesatko has the DYS439=10 > > > On Sat, Jan 4, 2014 at 2:34 AM, Scott E. Stewart > <[email protected]>wrote: > > > Jesatko has a high DYS 385a for Z161*, more like that of the L701 Sector, > > but 37 markers should tell: > > > > -----Original Message----- > > From: [email protected] > > [mailto:[email protected]] On Behalf Of Wayne R. > > Roberts > > Sent: Friday, January 3, 2014 5:39 AM > > To: y-dna-haplogroup-i > > Subject: Re: [yDNAhgI] Believable > > > > Waiting on 37 marker upgrade for Jesatko. What about the others in this > > Z161 cluster? Do they separate into three subgroups? > > > > > > On Fri, Jan 3, 2014 at 3:44 PM, Kenneth Nordtvedt > > <[email protected]>wrote: > > > > > Probably too early to say who Jesatko belongs with. > > > > > > > > > > > > Kenneth Nordtvedt > > > > > > Haplogroup I Clade Modalities and Trees at: > > > http://knordtvedt.home.bresnan.net > > > > > > -----Original Message----- > > > From: Wayne R. Roberts > > > Sent: Thursday, January 02, 2014 10:16 PM > > > To: y-dna-haplogroup-i > > > Subject: Re: [yDNAhgI] Believable > > > > > > Do you see Vella, Membrana & Micallef as a Mediterranean subgroup, > > > then Jesatko, Perkins & Rogers as another subgroup and then Macmillan, > > > McMillan, Tanner, McPhee and Cameron as a Scottish subgroup? > > > > > > What age estimates do you have for this cluster's founder and subgroup > > > founders? > > > > > > > > > On Fri, Jan 3, 2014 at 10:23 AM, Kenneth Nordtvedt > > > <[email protected]>wrote: > > > > > > > Vella peels off 1800 years b.p. from rest of the McMillan group in > > > > M223 Tree. > > > > > > > > Kenneth Nordtvedt > > > > > > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without > > > the quotes in the subject and the body of the message > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without > > the quotes in the subject and the body of the message > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Ken- Is your explanation below, then, the reason that the GENO 2.0 derived reading on L380 is not reported by FTDNA in their conversion process? If not, have you found other GENO 2.0 readings not reported in the FTDNA conversion? JB McCrummen -------- Original Message -------- Subject: Re: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion From: "Kenneth Nordtvedt" <[1][email protected]> Date: Fri, January 03, 2014 3:33 pm To: <[2][email protected]> I'm afraid everyone is AA for L380. Whether that is technically ancestral or derived is of secondary importance it seems; it could have mutated somewhere upstream in the tree rendering IJK as well as R haplogroups as derived AA. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: [3]http://knordtvedt.home.bresnan.net -----Original Message----- From: JB MCCRUMMEN Sent: Friday, January 03, 2014 12:53 PM To: YDNA I_ROOTSWEB LIST Subject: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion In previous post, Diana mentioned a missing derived GENO 2.0 result (L380+) in the Project I conversion by FTDNA. I checked the FTDNA GENO 2.0 conversion for my results and L380+ is also missing in the FTDNA conversion table. My GENO 2.0 L380 reading is derived ( AA and ISOGG/Krahn Browser confirms this is derived). Two Questions: 1- Are there other GENO 2.0 participants whose readings (L380 and other SNPs) missing and/or not accurately converted? 2- Are there other GENO 2.0 SNP readings missing and/or not accurately converted? JB MCCRUMMEN FTDNA KIT: 75432 --------------- Previous posting from Diana: From: "Diana Gale Matthiesen" <[4][email protected]> Subject: [yDNAhgI] Rasey I2 Date: Fri, 3 Jan 2014 10:04:28 -0500 Well, duhhh. I could just go look at the ISOGG tree, so I did. Given that he's Z78-, it does surprise me that he's also CTS6433-. But I guess what does surprise me is that his L380+ is still not on the page, even at the bottom as a private SNP. My first impulse is to order CTS1977 and L1290, but I'm wondering if I shouldn't just pop for the BigY, instead of this drip, drip, drip ordering of a la carte SNPs. Diana ----------------- ------------------------------- To unsubscribe from the list, please send an email to [5][email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message References 1. mailto:[email protected] 2. mailto:[email protected] 3. http://knordtvedt.home.bresnan.net/ 4. mailto:[email protected] 5. mailto:[email protected]

Jesatko has the DYS439=10 On Sat, Jan 4, 2014 at 2:34 AM, Scott E. Stewart <[email protected]>wrote: > Jesatko has a high DYS 385a for Z161*, more like that of the L701 Sector, > but 37 markers should tell: > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Wayne R. > Roberts > Sent: Friday, January 3, 2014 5:39 AM > To: y-dna-haplogroup-i > Subject: Re: [yDNAhgI] Believable > > Waiting on 37 marker upgrade for Jesatko. What about the others in this > Z161 cluster? Do they separate into three subgroups? > > > On Fri, Jan 3, 2014 at 3:44 PM, Kenneth Nordtvedt > <[email protected]>wrote: > > > Probably too early to say who Jesatko belongs with. > > > > > > > > Kenneth Nordtvedt > > > > Haplogroup I Clade Modalities and Trees at: > > http://knordtvedt.home.bresnan.net > > > > -----Original Message----- > > From: Wayne R. Roberts > > Sent: Thursday, January 02, 2014 10:16 PM > > To: y-dna-haplogroup-i > > Subject: Re: [yDNAhgI] Believable > > > > Do you see Vella, Membrana & Micallef as a Mediterranean subgroup, > > then Jesatko, Perkins & Rogers as another subgroup and then Macmillan, > > McMillan, Tanner, McPhee and Cameron as a Scottish subgroup? > > > > What age estimates do you have for this cluster's founder and subgroup > > founders? > > > > > > On Fri, Jan 3, 2014 at 10:23 AM, Kenneth Nordtvedt > > <[email protected]>wrote: > > > > > Vella peels off 1800 years b.p. from rest of the McMillan group in > > > M223 Tree. > > > > > > Kenneth Nordtvedt > > > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without > > the quotes in the subject and the body of the message > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without > the quotes in the subject and the body of the message > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

This is what Thomas had to say about PF3514: Everyone in IJ is supposed to be derived. Actually all others have an A. It seems like the region around PF3514 is very similar to ChrX:91846733..91846902. I've made a comparison here: http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I hope this link works for you). The X chromosome has also a "A" at this position and the probe on the Geno2 chip picks them up both. What likely happened is that his ancestors were derived for PF3514, but some X-Y recombination event has wiped that mutation out at a later time so that it shows the ancestral "A" again at this location.

Ken, Are there some subclades of Haplogroup I where Chromo2 is especially useful? In particular do you think there is much more to be learned from more I-L161 Chromo2 results? It looks good so far. I know that we have no Chromo2 results at all for I-M26, I-L233 etc so hard to say anything about these clades yet. Bernie

Of the 23 I-M223 members that tested individually for L380 with FTDNA, all were reported as ancestral (-). Only Rasey is reported as L380 derived (+) from WTY test. Diana, I have noticed today that your two Rasey members in the I-M223 Project along with their whole clade have been moved by Aaron to the Cont2b sector of the Project's results page. On Sat, Jan 4, 2014 at 9:33 AM, Kenneth Nordtvedt <[email protected]>wrote: > I'm afraid everyone is AA for L380. Whether that is technically ancestral > or derived is of secondary importance it seems; it could have mutated > somewhere upstream in the tree rendering IJK as well as R haplogroups as > derived AA. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: JB MCCRUMMEN > Sent: Friday, January 03, 2014 12:53 PM > To: YDNA I_ROOTSWEB LIST > Subject: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > In previous post, Diana mentioned a missing derived GENO 2.0 result > (L380+) in the Project I conversion by FTDNA. I checked the FTDNA GENO > 2.0 conversion for my results and L380+ is also missing in the FTDNA > conversion table. > > My GENO 2.0 L380 reading is derived ( AA and ISOGG/Krahn Browser > confirms this is derived). > > Two Questions: > 1- Are there other GENO 2.0 participants whose readings (L380 and other > SNPs) missing and/or not accurately converted? > 2- Are there other GENO 2.0 SNP readings missing and/or not accurately > converted? > > > JB MCCRUMMEN > > FTDNA KIT: 75432 > > --------------- > Previous posting from Diana: > > From: "Diana Gale Matthiesen" <[email protected]> > Subject: [yDNAhgI] Rasey I2 > Date: Fri, 3 Jan 2014 10:04:28 -0500 > > > Well, duhhh. I could just go look at the ISOGG tree, so I did. > > Given that he's Z78-, it does surprise me that he's also CTS6433-. But I > guess > what does surprise me is that his L380+ is still not on the page, even > at the > bottom as a private SNP. > > My first impulse is to order CTS1977 and L1290, but I'm wondering if I > shouldn't > just pop for the BigY, instead of this drip, drip, drip ordering of a la > carte > SNPs. > > Diana > > ----------------- > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

There has not been a chromo2 result which has been unproductive so far, and I mean they've been really productive. That's the good news. The bad news is that hardly anyone is bringing their results forward to be intercompared with others, and that's the only way to position the many ysnps on the tree. I have In haplogroup I only 7 sets of Chromo2 raw data plus two renditions of a customer's positives. That total has hardly changed in several weeks. The two who have shared just their renditions seem to be saying that even they have not received their raw data yet. If the people at BritainsDNA don't figure out a way to get more of the hundreds of folks who have results for these Chromo2 tests to share them for intercomparisons, I think in a month or so everyone will be turning their attention to BigY and will forget about Chromo2. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Bernie Cullen Sent: Saturday, January 04, 2014 8:51 AM To: y-dna-haplogroup-i Subject: Re: [yDNAhgI] Another L161 Chromo2 Helps the Tree Ken, Are there some subclades of Haplogroup I where Chromo2 is especially useful? In particular do you think there is much more to be learned from more I-L161 Chromo2 results? It looks good so far. I know that we have no Chromo2 results at all for I-M26, I-L233 etc so hard to say anything about these clades yet. Bernie ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

thanks BobDNA Projects I2*, ISOGG new I2b, I2c HG & Tyler Surname and ISOGG YTree > From: [email protected] > To: [email protected] > Date: Fri, 3 Jan 2014 08:25:47 -0700 > Subject: Re: [yDNAhgI] Generations111T > > Yes; all those outputs are in generations. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Robert May > Sent: Thursday, January 02, 2014 11:01 PM > To: [email protected] > Subject: [yDNAhgI] Generations111T > > > > > Ken > Just to confirm that GA Goal, GB Goal, GA and GB are in generations? > > BobDNA Projects I2*, ISOGG new I2b, I2c HG & Tyler Surname and ISOGG YTree > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Hi Wayne, You should be able to find results for PF3514 in the genotyping ("gtype") report. Nice analysis, Obed! Greg On Jan 4, 2014 3:50 AM, "Wayne R. Roberts" <[email protected]> wrote: > Obed, my samples went to UCLA and unfortunately UCLA results were not > satisfactory. I have sent new samples off to Full Genomes so will have to > wait longer for results. > > Do you know what result Adam Waalkes received for PF3514? Ken, Aaron and I > have all his results data but I'm not so sure how to read the raw data > files. > > > On Sat, Jan 4, 2014 at 4:12 PM, Obed W Odom <[email protected]> wrote: > > > Thanks, Wayne. Are you still waiting for your Full Genomes results? If > so, > > please let us know your result at the site of PF3514 when you receive > them. > > > > > > On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts > > <[email protected]>wrote: > > > > > Obed, my question to Thomas was: > > > > > > One of our I-M223 Project members just received his Geno 2.0 results. > He > > is > > > from the Project's Continental 2a group CTS6433+. When his raw data is > > > compared with that of other members he shows PF3514 with A A. All > others > > > show A G. Ybrowse has PF3514 mutation as A to G. How should I interpret > > his > > > result? Is he derived and ancestral is actually G or is he ancestral > > (back > > > mutation) and everyone else is derived? Thanks for any advise, Wayne. > > > > > > He did not indicate it should be A to C and Ybrowse has A to G. > > > > > > > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> wrote: > > > > > > > Wayne, > > > > > > > > Did Thomas explicitly say that the derived value for PF3514 is G, or > > > could > > > > it be C? My Full Genomes result clearly shows that I have C at this > > > > location. I looked at the X and Y sequences in this region and they > are > > > > indeed very similar, but they do differ at points 17 bases upstream > and > > > 37 > > > > bases downstream of the PF3514 site, which must be enough for Full > > > Genomes > > > > to separate the Y and X sequences. Full Genomes shows my X sequence > to > > be > > > > identical to the HUGO reference, with A at the PF3514-homologous > site. > > So > > > > Geno 2.0 was clearly in error when they reported me as AG instead of > > AC. > > > > > > > > Although I cannot see their raw data, Full Genomes also reports > > several > > > > other I1 people to have C at this position. These include another > > > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be > interesting > > to > > > > hear what your Full Genomes test showed at the PF3514 site. In > > particular > > > > I'm wondering if Full Genomes has shown anyone to have G at the > PF3514 > > > > site. I suppose it's possible that those of us who have C have had a > > > second > > > > mutation at this site, from G to C. > > > > > > > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > > > <[email protected]>wrote: > > > > > > > > > This is what Thomas had to say about PF3514: > > > > > > > > > > Everyone in IJ is supposed to be derived. Actually all others have > an > > > A. > > > > It > > > > > seems like the region around PF3514 is very similar to > > > > > ChrX:91846733..91846902. > > > > > > > > > > I've made a comparison here: > > > > > > > > > > > > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > > > hope this link works for you). > > > > > > > > > > The X chromosome has also a "A" at this position and the probe on > the > > > > Geno2 > > > > > chip picks them up both. What likely happened is that his ancestors > > > were > > > > > derived for PF3514, but some X-Y recombination event has wiped that > > > > > mutation out at a later time so that it shows the ancestral "A" > again > > > at > > > > > this location. > > > > > > > > > > ------------------------------- > > > > > To unsubscribe from the list, please send an email to > > > > > [email protected] with the word > 'unsubscribe' > > > > > without the quotes in the subject and the body of the message > > > > > > > > > > > > > ------------------------------- > > > > To unsubscribe from the list, please send an email to > > > > [email protected] with the word 'unsubscribe' > > > > without the quotes in the subject and the body of the message > > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

By itself, no. Add the information supplied by Thomas Krahn at the time: "This is a fairly confusing marker because it is close to the Yp pseudoautosomal region and it probably recombines with the Xchromosome more often than we like it." Regards, H. Styri > From: Kenneth Nordtvedt [[email protected]] > Sent: 2014-01-04 00:23:01 CET > To: [email protected] > Subject: Re: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > What you say below BY ITSELF does not make L380 unreliable; simply having > mutated in the known Tree at least twice --- which is no big deal. > > I will check all Geno2 results from haplogroup I and get back to you > shortly. I think I did so for I1 earlier today and it was monolithic > whatever it was in the raw data. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Haakon Styri > Sent: Friday, January 03, 2014 4:15 PM > To: [email protected] > Subject: Re: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > In case some of you have forgotten, L380 is an unreliable SNP. If I remember > correct, it showed up in I1 at about the same time as it showed up in I2. > That was in 2011. Some time before that, in 2010 i think it was, it showed > up somewhere in haplogroup R1b. > > Regards, > H. Styri > > > > From: Diana Gale Matthiesen [[email protected]] > > Sent: 2014-01-03 21:22:56 CET > > To: [email protected] > > Subject: Re: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > > > I'm afraid I wasn't talking about it missing from a Geno 2.0 conversion, I > > said > > it was missing from the ISOGG Hg I Haplotree page. > > > > L380+ was found on a WTY and, so far, it appears to be Private for my > > RASEY > > #69631. It's negative for my RAZEE #70816: > > > > #70816 RAZEE I2-L801+ > Z78+ > L1198+ [L380-] > > > > #69631 RASEY I2-L801+ > L380+ [Z78-] > > > > http://dgmweb.net/DNA/Rasey/RaseyDNA-results.html > > > > Diana > > > > > -----Original Message----- > > > From: [email protected] > > > [mailto:y-dna-haplogroup-i- > > > [email protected]] On Behalf Of JB MCCRUMMEN > > > Sent: Friday, January 03, 2014 2:53 PM > > > To: YDNA I_ROOTSWEB LIST > > > Subject: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > > > > > In previous post, Diana mentioned a missing derived GENO 2.0 result > > > (L380+) in the Project I conversion by FTDNA. I checked the FTDNA GENO > > > 2.0 conversion for my results and L380+ is also missing in the FTDNA > > > conversion table. > > > > > > My GENO 2.0 L380 reading is derived ( AA and ISOGG/Krahn Browser > > > confirms this is derived). > > > > > > Two Questions: > > > 1- Are there other GENO 2.0 participants whose readings (L380 and other > > > SNPs) missing and/or not accurately converted? > > > 2- Are there other GENO 2.0 SNP readings missing and/or not accurately > > > converted? > > > > > > > > > JB MCCRUMMEN > > > > > > FTDNA KIT: 75432 > > > > > > --------------- > > > Previous posting from Diana: > > > > > > From: "Diana Gale Matthiesen" <[email protected]> > > > Subject: [yDNAhgI] Rasey I2 > > > Date: Fri, 3 Jan 2014 10:04:28 -0500 > > > > > > > > > Well, duhhh. I could just go look at the ISOGG tree, so I did. > > > > > > Given that he's Z78-, it does surprise me that he's also CTS6433-. But I > > > guess > > > what does surprise me is that his L380+ is still not on the page, even > > > at the > > > bottom as a private SNP. > > > > > > My first impulse is to order CTS1977 and L1290, but I'm wondering if I > > > shouldn't > > > just pop for the BigY, instead of this drip, drip, drip ordering of a la > > > carte > > > SNPs. > > > > > > Diana > > > > > > ----------------- > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > Y-DNA-HAPLOGROUP-I- > > > [email protected] with the word 'unsubscribe' without the quotes in > > > the > > > subject and the body of the message > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

In case some of you have forgotten, L380 is an unreliable SNP. If I remember correct, it showed up in I1 at about the same time as it showed up in I2. That was in 2011. Some time before that, in 2010 i think it was, it showed up somewhere in haplogroup R1b. Regards, H. Styri > From: Diana Gale Matthiesen [[email protected]] > Sent: 2014-01-03 21:22:56 CET > To: [email protected] > Subject: Re: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > I'm afraid I wasn't talking about it missing from a Geno 2.0 conversion, I said > it was missing from the ISOGG Hg I Haplotree page. > > L380+ was found on a WTY and, so far, it appears to be Private for my RASEY > #69631. It's negative for my RAZEE #70816: > > #70816 RAZEE I2-L801+ > Z78+ > L1198+ [L380-] > > #69631 RASEY I2-L801+ > L380+ [Z78-] > > http://dgmweb.net/DNA/Rasey/RaseyDNA-results.html > > Diana > > > -----Original Message----- > > From: [email protected] [mailto:y-dna-haplogroup-i- > > [email protected]] On Behalf Of JB MCCRUMMEN > > Sent: Friday, January 03, 2014 2:53 PM > > To: YDNA I_ROOTSWEB LIST > > Subject: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > > > In previous post, Diana mentioned a missing derived GENO 2.0 result > > (L380+) in the Project I conversion by FTDNA. I checked the FTDNA GENO > > 2.0 conversion for my results and L380+ is also missing in the FTDNA > > conversion table. > > > > My GENO 2.0 L380 reading is derived ( AA and ISOGG/Krahn Browser > > confirms this is derived). > > > > Two Questions: > > 1- Are there other GENO 2.0 participants whose readings (L380 and other > > SNPs) missing and/or not accurately converted? > > 2- Are there other GENO 2.0 SNP readings missing and/or not accurately > > converted? > > > > > > JB MCCRUMMEN > > > > FTDNA KIT: 75432 > > > > --------------- > > Previous posting from Diana: > > > > From: "Diana Gale Matthiesen" <[email protected]> > > Subject: [yDNAhgI] Rasey I2 > > Date: Fri, 3 Jan 2014 10:04:28 -0500 > > > > > > Well, duhhh. I could just go look at the ISOGG tree, so I did. > > > > Given that he's Z78-, it does surprise me that he's also CTS6433-. But I > > guess > > what does surprise me is that his L380+ is still not on the page, even > > at the > > bottom as a private SNP. > > > > My first impulse is to order CTS1977 and L1290, but I'm wondering if I > > shouldn't > > just pop for the BigY, instead of this drip, drip, drip ordering of a la > > carte > > SNPs. > > > > Diana > > > > ----------------- > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to Y-DNA-HAPLOGROUP-I- > > [email protected] with the word 'unsubscribe' without the quotes in the > > subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message >

Thanks, Wayne. Are you still waiting for your Full Genomes results? If so, please let us know your result at the site of PF3514 when you receive them. On Fri, Jan 3, 2014 at 9:32 PM, Wayne R. Roberts <[email protected]>wrote: > Obed, my question to Thomas was: > > One of our I-M223 Project members just received his Geno 2.0 results. He is > from the Project's Continental 2a group CTS6433+. When his raw data is > compared with that of other members he shows PF3514 with A A. All others > show A G. Ybrowse has PF3514 mutation as A to G. How should I interpret his > result? Is he derived and ancestral is actually G or is he ancestral (back > mutation) and everyone else is derived? Thanks for any advise, Wayne. > > He did not indicate it should be A to C and Ybrowse has A to G. > > > On Sat, Jan 4, 2014 at 1:10 PM, Obed W Odom <[email protected]> wrote: > > > Wayne, > > > > Did Thomas explicitly say that the derived value for PF3514 is G, or > could > > it be C? My Full Genomes result clearly shows that I have C at this > > location. I looked at the X and Y sequences in this region and they are > > indeed very similar, but they do differ at points 17 bases upstream and > 37 > > bases downstream of the PF3514 site, which must be enough for Full > Genomes > > to separate the Y and X sequences. Full Genomes shows my X sequence to be > > identical to the HUGO reference, with A at the PF3514-homologous site. So > > Geno 2.0 was clearly in error when they reported me as AG instead of AC. > > > > Although I cannot see their raw data, Full Genomes also reports several > > other I1 people to have C at this position. These include another > > I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting to > > hear what your Full Genomes test showed at the PF3514 site. In particular > > I'm wondering if Full Genomes has shown anyone to have G at the PF3514 > > site. I suppose it's possible that those of us who have C have had a > second > > mutation at this site, from G to C. > > > > > > On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts > > <[email protected]>wrote: > > > > > This is what Thomas had to say about PF3514: > > > > > > Everyone in IJ is supposed to be derived. Actually all others have an > A. > > It > > > seems like the region around PF3514 is very similar to > > > ChrX:91846733..91846902. > > > > > > I've made a comparison here: > > > > > > > > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > > > hope this link works for you). > > > > > > The X chromosome has also a "A" at this position and the probe on the > > Geno2 > > > chip picks them up both. What likely happened is that his ancestors > were > > > derived for PF3514, but some X-Y recombination event has wiped that > > > mutation out at a later time so that it shows the ancestral "A" again > at > > > this location. > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without the quotes in the subject and the body of the message > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Diana, what has me surprised is his CTS6433 ancestral result. In some ways I am not surprised as he does not seem to fit that grouping but still thought he would be derived. Perhaps Kenneth can offer some advice. Is he CTS1977 or L1290 or some unknown SNP? On Fri, Jan 3, 2014 at 9:30 PM, Diana Gale Matthiesen <[email protected]>wrote: > Thanks for the added info, Wayne. > > My I2 RASEY's result has just come in, so now we have double proof: as > expected, he, too, is L1439-. > > This was another fast SNP test return. I ordered the test on December > 15th and > it returned January 2nd. > > Diana > > > > From: Wayne R. Roberts > > Sent: Thursday, January 02, 2014 7:02 PM > > To: y-dna-haplogroup-i > > Subject: Re: [yDNAhgI] Unbelievable > > > > L1439 is ancestral in I2-M223 (I2a2a, old I2b1) for Kit 69631. > > > > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Waiting on 37 marker upgrade for Jesatko. What about the others in this Z161 cluster? Do they separate into three subgroups? On Fri, Jan 3, 2014 at 3:44 PM, Kenneth Nordtvedt <[email protected]>wrote: > Probably too early to say who Jesatko belongs with. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > -----Original Message----- > From: Wayne R. Roberts > Sent: Thursday, January 02, 2014 10:16 PM > To: y-dna-haplogroup-i > Subject: Re: [yDNAhgI] Believable > > Do you see Vella, Membrana & Micallef as a Mediterranean subgroup, then > Jesatko, Perkins & Rogers as another subgroup and then Macmillan, McMillan, > Tanner, McPhee and Cameron as a Scottish subgroup? > > What age estimates do you have for this cluster's founder and subgroup > founders? > > > On Fri, Jan 3, 2014 at 10:23 AM, Kenneth Nordtvedt > <[email protected]>wrote: > > > Vella peels off 1800 years b.p. from rest of the McMillan group in M223 > > Tree. > > > > Kenneth Nordtvedt > > > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without > the quotes in the subject and the body of the message > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

> My Geno 2.0 result for PF3514 also shows > AG, but this probably means nothing since my C would not have been > detectable by the Geno 2.0 chip if it is looking for A or G. I think it is > possible that PF3514 was erroneously reported by Paolo Francalacci as A to > G instead of A to C, especially since both PF3514 and Y1850 (FGC2408) are > shown by the ISOGG Y Browser to be located at the IJ level in the Y tree. So does this mean that all the Geno 2.0 results for PF3514+ might be mistaken and are reading AG when they should be reading CC and that the few anomalous AA results for I1 people are also mistaken and should be reading CC in that location? Matthew Simonds > Date: Fri, 3 Jan 2014 14:13:11 -0600 > From: [email protected] > To: [email protected] > Subject: Re: [yDNAhgI] PF3514 > > My Full Genomes result also shows me to be FGC2408+; i.e, A to C at > location 5578819 of the Y. All 76 of my reads at this location show C, so > the result seems quite reliable. My Geno 2.0 result for PF3514 also shows > AG, but this probably means nothing since my C would not have been > detectable by the Geno 2.0 chip if it is looking for A or G. I think it is > possible that PF3514 was erroneously reported by Paolo Francalacci as A to > G instead of A to C, especially since both PF3514 and Y1850 (FGC2408) are > shown by the ISOGG Y Browser to be located at the IJ level in the Y tree. > > > On Fri, Jan 3, 2014 at 11:35 AM, John O'Grady <[email protected]>wrote: > > > There are two SNPs at the same position. PF3514 is A to G. Y1850 is A to C. > > Geno 2.0 shows me as AG. Full Genomes shows me as CC, and calls the SNP > > FGC2408, which is the same as Y1850. > > Anyone who has AG in Geno 2.0 is probably actually CC and Y1850/FGC2408. > > John O'Grady > > > > > > > > There is something erratic about the behavior of PF3514. I show 5 I1 > > plus > > > one I2 with AA, while many dozens of others are all AG. But those 5 > > > anomalies in I1 are from very different parts of the I1 tree; their > > results > > > can not be due to an inherited common mutation in their ancestral lines. > > > > > > Kenneth Nordtvedt > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

> From: Wayne R. Roberts > Sent: Friday, January 03, 2014 7:25 PM > To: y-dna-haplogroup-i > Subject: Re: [yDNAhgI] Missing GENO 2.0 Results in FTDNA Conversion > > Of the 23 I-M223 members that tested individually for L380 with FTDNA, all > were reported as ancestral (-). Only Rasey is reported as L380 derived (+) > from WTY test. > > Diana, I have noticed today that your two Rasey members in the I-M223 > Project along with their whole clade have been moved by Aaron to the Cont2b > sector of the Project's results page. Yes, my site is out-of-date with regard to haplotype clusters. Updating them is on my "to do" list. Dina

Wayne, Did Thomas explicitly say that the derived value for PF3514 is G, or could it be C? My Full Genomes result clearly shows that I have C at this location. I looked at the X and Y sequences in this region and they are indeed very similar, but they do differ at points 17 bases upstream and 37 bases downstream of the PF3514 site, which must be enough for Full Genomes to separate the Y and X sequences. Full Genomes shows my X sequence to be identical to the HUGO reference, with A at the PF3514-homologous site. So Geno 2.0 was clearly in error when they reported me as AG instead of AC. Although I cannot see their raw data, Full Genomes also reports several other I1 people to have C at this position. These include another I1-Z138*, an I1-Z2541, and probably an I1-Z63. It would be interesting to hear what your Full Genomes test showed at the PF3514 site. In particular I'm wondering if Full Genomes has shown anyone to have G at the PF3514 site. I suppose it's possible that those of us who have C have had a second mutation at this site, from G to C. On Fri, Jan 3, 2014 at 7:06 PM, Wayne R. Roberts <[email protected]>wrote: > This is what Thomas had to say about PF3514: > > Everyone in IJ is supposed to be derived. Actually all others have an A. It > seems like the region around PF3514 is very similar to > ChrX:91846733..91846902. > > I've made a comparison here: > > http://genome.ucsc.edu/cgi-bin/hgc?o=91846732&g=htcUserAli&i=../trash/hgSs/hgSs_genome_49d7_4f0db0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_49d7_4f0db0.fa+ChrY:5578834..5579003&c=chrX&l=91846732&r=91846902&db=hg19&hgsid=357278251(I > hope this link works for you). > > The X chromosome has also a "A" at this position and the probe on the Geno2 > chip picks them up both. What likely happened is that his ancestors were > derived for PF3514, but some X-Y recombination event has wiped that > mutation out at a later time so that it shows the ancestral "A" again at > this location. > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

> both PF3514 and Y1850 (FGC2408) are shown by the ISOGG Y Browser to be located at the IJ level in the Y tree. In going over the Geno 2.0 results in the I1 group, they are all PF3514+ except for 8 kits although they should be PF3514+ if PF3514 is present at the IJ level: Espinoza Kit N116953Haken Kit N116628Hayes Kit N101637Howet Kit 252002Marlow Kit 203577Paine Kit 282760Simonds Kit 310372Wilmot Kit 247267 Matthew Simonds > Date: Fri, 3 Jan 2014 14:13:11 -0600 > From: [email protected] > To: [email protected] > Subject: Re: [yDNAhgI] PF3514 > > My Full Genomes result also shows me to be FGC2408+; i.e, A to C at > location 5578819 of the Y. All 76 of my reads at this location show C, so > the result seems quite reliable. My Geno 2.0 result for PF3514 also shows > AG, but this probably means nothing since my C would not have been > detectable by the Geno 2.0 chip if it is looking for A or G. I think it is > possible that PF3514 was erroneously reported by Paolo Francalacci as A to > G instead of A to C, especially since both PF3514 and Y1850 (FGC2408) are > shown by the ISOGG Y Browser to be located at the IJ level in the Y tree. > > > On Fri, Jan 3, 2014 at 11:35 AM, John O'Grady <[email protected]>wrote: > > > There are two SNPs at the same position. PF3514 is A to G. Y1850 is A to C. > > Geno 2.0 shows me as AG. Full Genomes shows me as CC, and calls the SNP > > FGC2408, which is the same as Y1850. > > Anyone who has AG in Geno 2.0 is probably actually CC and Y1850/FGC2408. > > John O'Grady > > > > > > > > There is something erratic about the behavior of PF3514. I show 5 I1 > > plus > > > one I2 with AA, while many dozens of others are all AG. But those 5 > > > anomalies in I1 are from very different parts of the I1 tree; their > > results > > > can not be due to an inherited common mutation in their ancestral lines. > > > > > > Kenneth Nordtvedt > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > ------------------------------- > To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message