Sandy, ISOGG uses this terminology too. I think the correct full term is "phylogenetically equivalent" and this is used for situations where two physically different SNPs marked the same branch on the Y DNA tree. http://www.isogg.org/tree/ISOGG_Glossary.html This is different from what ISOGG calls a synonym. That would be a case where two different SNP labels identify the exact same physical SNP. In these cases, on their tree they use a slash ("/") between SNP labels that are synonyms. Regards, Mike W On Wed, Nov 27, 2013 at 11:34 AM, Alexander Paterson < [email protected]> wrote: > Hi Iain, > > Could you try and clarify something, namely the word 'equivalent'. > > Jim's original tree was titled 'M222 and ~ 24 equivalents'. As a > mathematician, I have to say that 'equivalent' means 'is the same as'. So > S675 is equivalent to DF85. To say that M222 is equivalent to for example > S675 seems like a non-sequitur to me. Perhaps we need to know what > 'phylogenically equivalent' means? > > Best, > > Sandy > > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Iain Kennedy > Sent: 19 November 2013 18:21 > To: [email protected] > Subject: [R-M222] Revised M222 tree > > > > > > > > > > > > > > > > > List > > I have several updates to the M222 tree this evening. Jim Wilson has > provided a list of SNPs which he considers phylogenetically equivalent to > M222 and are (mostly) on the Chromo2 chip. As the list is now too long to > force into a personal name in my tree I have also posted the raw tree > diagram he sent me which primarily shows the top level above and below, so > it is not a replacement for the whole earlier diagram. > > There are three features in his new diagram: > 1. What appears to be a new hg between S474/DF49 and S193/DF23 called S476 > which is not on the ISOGG tree. > 2. The new list of M222 equivalents > 3. A new SNP below M222 called S7073. > > I have moved everything at the root of M222 below S7073 but having not seen > Steve Lominac's raw file yet I can't confirm that he is positive for it. I > am as is Rob McBride too of course. > > The other change to the diagram, which Rob McBride spotted and neither Jim > nor I did is that he is positive for F3952, one of the SNPs we got off Geno > 2.0 which previously only a Mitchell was positive for. I have double > checked > with Jim and he reviewed the raw genotype and agrees with this placement. > My > checking procedures have been amended accordingly and I have added Mitchell > to the diagram too. > > Upper tree update: > > http://www.kennedydna.com/S474.jpg > > Main tree from M222: > > http://www.kennedydna.com/M222.pdf > > Iain > > > > > > > > > > > > ------------------------------- > 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 Mike, Thanks. That makes some sense, but I would re-phrase slightly. My guess is that 'phylogenetically equivalent' means that they are part of the same tree, but further downstream'. So the boss man is M222 and the rest are also M222, but with other mutations downstream of M222. Best, Sandy -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Mike W Sent: 27 November 2013 17:43 To: M222 Rootsweb Subject: Re: [R-M222] Revised M222 tree Sandy, ISOGG uses this terminology too. I think the correct full term is "phylogenetically equivalent" and this is used for situations where two physically different SNPs marked the same branch on the Y DNA tree. http://www.isogg.org/tree/ISOGG_Glossary.html This is different from what ISOGG calls a synonym. That would be a case where two different SNP labels identify the exact same physical SNP. In these cases, on their tree they use a slash ("/") between SNP labels that are synonyms. Regards, Mike W On Wed, Nov 27, 2013 at 11:34 AM, Alexander Paterson < [email protected]> wrote: > Hi Iain, > > Could you try and clarify something, namely the word 'equivalent'. > > Jim's original tree was titled 'M222 and ~ 24 equivalents'. As a > mathematician, I have to say that 'equivalent' means 'is the same as'. > So > S675 is equivalent to DF85. To say that M222 is equivalent to for > example > S675 seems like a non-sequitur to me. Perhaps we need to know what > 'phylogenically equivalent' means? > > Best, > > Sandy > > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Iain Kennedy > Sent: 19 November 2013 18:21 > To: [email protected] > Subject: [R-M222] Revised M222 tree > > > > > > > > > > > > > > > > > List > > I have several updates to the M222 tree this evening. Jim Wilson has > provided a list of SNPs which he considers phylogenetically equivalent > to > M222 and are (mostly) on the Chromo2 chip. As the list is now too long > to force into a personal name in my tree I have also posted the raw > tree diagram he sent me which primarily shows the top level above and > below, so it is not a replacement for the whole earlier diagram. > > There are three features in his new diagram: > 1. What appears to be a new hg between S474/DF49 and S193/DF23 called > S476 which is not on the ISOGG tree. > 2. The new list of M222 equivalents > 3. A new SNP below M222 called S7073. > > I have moved everything at the root of M222 below S7073 but having not > seen Steve Lominac's raw file yet I can't confirm that he is positive > for it. I am as is Rob McBride too of course. > > The other change to the diagram, which Rob McBride spotted and neither > Jim nor I did is that he is positive for F3952, one of the SNPs we got > off Geno > 2.0 which previously only a Mitchell was positive for. I have double > checked with Jim and he reviewed the raw genotype and agrees with this > placement. > My > checking procedures have been amended accordingly and I have added > Mitchell to the diagram too. > > Upper tree update: > > http://www.kennedydna.com/S474.jpg > > Main tree from M222: > > http://www.kennedydna.com/M222.pdf > > Iain > > > > > > > > > > > > ------------------------------- > 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