Dear Bill, As a biological scientist I find it distressing that you and others are trying to convince us that it doesn't really matter if your SNP test does or does not show that you are M222+, you can still be included in the M222 project on the basis of your STR haplotype. Data based on such an assumption would not be acceptable in a rigorous scientific journal. It would seem to me that the benchmark of the M222 project should be the presence of M222+. At some stage in our background two brothers may have had an identical or nearly identical STR haplotype, but brother one had a de novo mutation that created the M222 SNP and brother two did not. The descendants of brother one would be M222+ and the descendants of brother two would be M222-. This de novo mutation occurred at a specific date and we would all be very interested in that date. However, if the samples used to measure that date are a mixture of = and - SNPs, then you can't measure the date of appearance of M222 accurately because common STR haplotypes would predate the appearance of the M222 SNP. Let's focus on the rigor of the analysis, not the cost of SNP testing. David -- Dr. David H. MacLennan, Banting and Best Department of Medical Research, University of Toronto, Charles H. Best Institute, 112 College St., Toronto, Ontario, Canada M5G1L6 Tel:1-416-978-5008 Fax:1-416-978-8528 http://www.utoronto.ca/maclennan > From: Bill Howard <weh8@verizon.net> > Reply-To: <dna-r1b1c7@rootsweb.com> > Date: Fri, 08 Jul 2011 14:00:22 -0400 > To: <dna-r1b1c7@rootsweb.com> > Subject: Re: [R-M222] There is no practical difference between M222+ and M222- > > Hi, Paul, > Sorry about the "Pat" -- someone else used Pat along the way and I failed to > check it. My apologies. > I only wanted to make the point that the so-called plusses and minuses for > M222 are inextricably mixed so it doesn't matter if you use both in studies > related to the M222 group. > Indeed, the RCC time scale does not depend on M222 membership at all. It will > estimate the TMRCAs of any pair of haplotypes, and when it is looking at a > surname cluster, or any other cluster that has many members, the estimate goes > from about 180 years (SD) for a pair, downwards by a factor of the square root > of (n-1) where n is the number of haplogroups in the cluster. The junction > points on the phylogenetic tree are also pretty well-defined in time using the > same reasoning. > Whether or not it is a SNP is a red-herring. They only have to be haplotypes. > - Bye from Bill Howard > > On Jul 8, 2011, at 12:52 PM, Paul Conroy wrote: > >> Bill, >> >> First of all my name is Paul Conroy, not "Pat" - he's the writer, I'm the >> hacker! >> >> Second, what I said was the R-L21 M222+ and R-L21 M222- are mostly not >> significantly different in STR values. So in areas where they both occur, a >> NPE would likely go largely unnoticed based solely on STR values. However >> any calculations that date the TMRCA or possible Location of said ancestor, >> based on Non-SNP tested data, are liable to be erroneous. That is as true a >> statement now as ever before. >> >> However, I don't think anyone should be pressured into getting SNP tested - >> although they should be encouraged to do so. But any investigator who is >> carrying out calculations based on Non-SNP tested data, should state that >> upfront, and add the caveat that results are thus likely to be erroneous - >> simple as that. The alternative of course would be just to stick to SNP >> tested data, and avoid the confusion altogether?! >> >> I have no more to say on this - as IMO it should be obvious that you can't >> predict dates for clusters defined by certain SNP's, when some of the data >> don't actually have those SNP's. >> >> Cheers, >> Paul >> >> On Fri, Jul 8, 2011 at 12:34 PM, Bill Howard <weh8@verizon.net> wrote: >> >>> My primary interest in replying to Paul Conroy was to state that there is >>> little if any difference between what he calls the M222+ and M222 - groups. >>> I am glad to see that John McLaughlin and apparently David Wilson agree with >>> me. This is crucial to what I am trying to do because the M222 group I am >>> working on consists of both Conroy's groups and I find them >>> indistinguishable. I appreciate the remarks of John and others about the >>> history of what defines the M222 group. >>> >>> In John's note he cites a URL where the marker modals are found. It is at: >>> <http://clanmaclochlainn.com/R1b1c7/M222repeat.htm> >>> >>> There MUST be a mistake of transcription there, because there are two >>> entries in the clanmaclochlainn.com file that disagree significantly with >>> my modal list. Before we go further, my modal file is identical when I >>> derive them from the O'Cathain group that John McLaughlin sent me AND with >>> two larger files of M222, one of which contains 320 haplotypes and the other >>> contains 683 haplotypes. My conclusion is that the clanmaclochlainn.comfile >>> MUST be wrong for the following DYS values: >>> >>> DYS My Value clanmaclochlainn.com Value >>> 426 12 13 >>> 454 11 12 >>> >>> On the website that gives modal values for M222, located at < >>> http://www.littlescottishcluster.com/RL21/Files/R-L21%20Tree%2020110531.pdf>>>> , >>> the values for these markers agree with mine, not the posting on >>> clanmaclochlainn.com. >>> Let values on the latter site are wrong. They are crucial since they are >>> very slow mutators, hence are valuable for analysis of the phylogenetic tree >>> at high values of RCC. I think someone needs to look into the details of >>> how the clanmaclochlainn values were done. It surely needs correction for >>> those two markers. >>> >>> - Bye from Bill >>> >>> >>> >>> On Jul 7, 2011, at 10:16 PM, Lochlan@aol.com wrote: >>> >>>> In a message dated 7/7/2011 7:00:26 A.M. Central Daylight Time, >>>> weh8@verizon.net writes: >>>> >>>> There has been considerable discussion both on- and off-line about how >>> the >>>> M222 SNP is defined. >>>> First, I understand that its early definition depended on the first 12 >>>> markers. >>>> Next, we have the deep clade test of FTDNA with a proprietary approach >>> we >>>> know little about. >>>> Next, there are discussions of how the markers agree or disagree with >>> the >>>> modal values of the deep clade test, but only with respect to the first >>> 12 >>>> markers of the FTDNA string. >>>> >>>> Bill, a few others have chimed in on various aspects of these >>> assumptions >>>> but I have to add myself they are wrong. >>>> >>>> <First, I understand that its early definition depended on the first 12 >>>> markers. >>>> >>>> 25 markers was the norm at FTDNA when David Wilson first announced his >>>> discovery of what he called the NW Irish cluster. He was soon followed >>> by the >>>> Trinity team with 17 markers who called the same cluster the Irish Modal >>>> Haplotype (IMH). >>>> >>>> <Next, we have the deep clade test of FTDNA with a proprietary approach >>> we >>>> know little about. >>>> >>>> >>>> This has already been covered. It's not proprietory and details are >>>> readily available. >>>> >>>> <Next, there are discussions of how the markers agree or disagree with >>> the >>>> modal values of the deep clade test, but only with respect to the first >>> 12 >>>> markers of the FTDNA string. >>>> >>>> This has never been true anywhere that I know of and never in the M222 >>>> project. David Wilson has had a full modal haplotype online at Ysearch >>> as >>>> long as I can remember. It is true that FTDNA awards their Nial icon >>> based >>>> on an exact match at 12 markers. Perhaps this is what you're thinking >>> of. >>>> >>>> David's M222 modal is M5UKQ on Ysearch. >>>> >>>> < I include now a table that shows the percentage of M222 testees that >>>> have mutations at the various points in the haplotype. For example, those >>> with >>>> 454 had a constant value of the modal for 454, and less than 50% of the >>>> testees had the modal for the two CDYs. >>>> >>>> That's already been done. >>>> >>>> _http://clanmaclochlainn.com/R1b1c7/M222repeat.htm_ >>>> (http://clanmaclochlainn.com/R1b1c7/M222repeat.htm) >>>> >>>> >>>> If this thread continues much longer I'll attempt to get David Wilson >>> back >>>> on board. He no longer is a member of the list but he surely will have >>>> some strong opinions on some of the statements made lately. He began >>> the >>>> M222 project and was the one who made the decision that SNP testing was >>> not >>>> necessary for inclusion in the project. Why? Because membership in >>> the >>>> clade was easily detected via STRs alone. >>>> >>>> Pat Conroy threw out the Wilson sample as an example of a false M222 >>> based >>>> on STRS. I'm glad someone else mentioned that. I have five times in >>> the >>>> last month to no response. The Clark sample in the M222 negative >>> section >>>> is almost identical. David Wilson listed these two as possibly pre >>>> M222. There is one other similar sample (Hannan) listed in the M222 >>> negative >>>> section. He probably should go into the pre M222 section as well. >>>> >>>> The Wilson sample has an interesting history. David Wilson who was >>> also >>>> the admin. of the Wilson DNA project. He assumed this sample was M222+ >>>> and was shocked to learn it was M222- by SNP test. At David's urging, >>>> FTDNA retested the sample several times. It came back negative every >>> time. >>>> >>>> There are a few suspicious parts of both the Clark and Wilson samples. >>>> Both have 385 = 12-14 which is unusual in M222. The Clark sample at 464 >>> has >>>> 15-15-16-17 at 464. That is highly unusual in M222. I see nothing >>> unusual >>>> in the Hannan sample at all. None of these samples stand out as unusual >>>> in terms of genetic distance. Each has matchers within the project at >>>> 6,7-20 GDS which is no different from most other cluster members. >>> That's no >>>> different from the Conroy sample. >>>> >>>> If I were presented with any of these samples and had to chose whether to >>>> admit them to the project based on STRS alone I probably would without an >>>> SNP test. I think David Wilson would do the same. >>>> >>>> So I will be the first to admit there could be some samples in the >>>> project which appear to be M222 but are not. The question is how many? >>>> >>>> What Bill has not mentioned to the list is a theory that the bi-modality >>> he >>>> mentioned is caused by M222 project samples that are M222-. The twin >>>> humps his graph shows seems to be equally large on each side. That >>> would seem >>>> to indicate there are roughly as many M222- in the project as M222+. >>> Is >>>> that possible? >>>> >>>> Not long ago the count of project members with SNP tests was 334. >>> That's >>>> out of 668 or about half the project. I can't guess how many of the >>> non >>>> tested members might be M222-. Not too many is my guess. >>>> >>>> The way the project is currently organized shouldn't cause any >>> confusion. >>>> FTDNA clearly indicates those with SNP tests. Those who only want to >>>> include them in analysis can do so easily. Dropping half the project >>> without >>>> SNP tests would greatly reduce the surname diversity available. Is that >>> a >>>> wise thing to do? >>>> >>>> I for one have no interest in getting an SNP test. I belong to a >>>> cluster of McLaughlins, four or five of whom have been SNP tested and >>> are M222+. >>>> As far as I'm concerned an SNP test for me would be a waste of money. >>> I >>>> won't spend the extra money just to keep the purists happy. >>>> >>>> On the other hand there could be a few samples in the project who are not >>>> M222 positive. It would be interesting to find out for sure. Right >>> now >>>> we can only guess. >>>> >>>> >>>> That is a conundrum. >>>> >>>> >>>> John >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> R1b1c7 Research and Links: >>>> >>>> http://clanmaclochlainn.com/R1b1c7/ >>>> ------------------------------- >>>> To unsubscribe from the list, please send an email to >>> DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the >>> quotes in the subject and the body of the message >>> >>> >>> R1b1c7 Research and Links: >>> >>> http://clanmaclochlainn.com/R1b1c7/ >>> ------------------------------- >>> To unsubscribe from the list, please send an email to >>> DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the >>> quotes in the subject and the body of the message >>> >> R1b1c7 Research and Links: >> >> http://clanmaclochlainn.com/R1b1c7/ >> ------------------------------- >> To unsubscribe from the list, please send an email to >> DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the >> quotes in the subject and the body of the message > > > R1b1c7 Research and Links: > > http://clanmaclochlainn.com/R1b1c7/ > ------------------------------- > To unsubscribe from the list, please send an email to > DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the quotes > in the subject and the body of the message