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From:
Subject: Re: [DNA] Re: Halotype Analysis Cautions (and Some SNP Considerations)
Date: Sun, 20 Mar 2005 23:38:06 -0800
References: <200503210351.j2L3pFJC019806@lists5.rootsweb.com> <6.2.0.14.0.20050321005341.02868ee8@mail.blairgenealogy.com>
In-Reply-To: <6.2.0.14.0.20050321005341.02868ee8@mail.blairgenealogy.com>


One thing that I have noticed about the heated discussions on this list is that they are very much like the heated discussions of siblings, & they stir memories of my youth. We all share a passion for this research & that generates passionate debate, which has always been the hallmark of emerging disciplines of science, so it seems fitting. Since this is an open forum, there are inevitably interactions between all levels of understanding. Ultimately, our common goal is to push this nascent research in a direction which will be of the most benefit to all of us, from the most accomplished & brilliant researchers, to the total novices who are doing their utmost to grasp the basics. All of us want to get the most bang for our buck, & nobody wants to look back thinking that they just threw away money that could have been better used examining a different angle. When I first considered Y-STR testing, I was completely alone, with very little to guide me in choosing the test or know!
ing what to expect. When I received my first results, I spent countless hours examining them & comparing them to any results that were approximately close to my own. The timing was such that within a few months I chanced upon Trace Genetics initial offering to test the SNPs of the customer's choice, so I had them test all of the SNPs downstream of P25, which had previously been tested positive by FTDNA. I didn't really understand at the time that those downstream SNPs had been derived from a very small sampling, but I don't think it would have changed my approach, which was (& still is), to leave no stone unturned. Trace Genetics obviously had some problems following up on their offering this sort of testing, & dropped out fairly quickly (which is as unfortunate for us as it is for them). So like Ken, I am one of the few that have had "extensive" SNP testing. David has correctly interpreted the meaning of my previous post to mean SNP testing of those markers which are curren!
tly used to define haplogroups using the YCC 2005 nomenclature. I think that those of you who understand that this is of little value in connection with recent genealogical history are correct to a degree, but I believe that this type of testing is of more than just anthropological value. I recently posted to the list a comparison of haplotypes that are fairly close to my own on a fairly large spread of markers. All of the surname project administrators have constructed similar databases with clusters of individuals who are matches & near matches. These are usually correlated to documentation that proves that those tested individuals who share a common surname & match in these clusters are descended from a man known in history by the "paper trail" he left behind. What a lot of us notice very soon after testing is that we have a lot of near (sometimes even exact) matches with different men of different surnames & no known paper trail connections. Initially the retail testing !
companies discouraged us from pursuing those matches, attributing them to genetic drift, or possibly just because they realized that without any historic documentation connecting them, nothing could ever come from such investigations, which might discourage potential new customers from accepting the legitimacy & usefulness of the science. Then as the availability of new & more informative markers expanded, people realized that they were finally seeing matches at very high resolution, again without a common surname or documented connection, but often with a history of a shared ethnic culture &/or most probable geographic origin. In my case, I have found that many of my near matches have Scottish surnames &/or they are descendants of American communities with a strong Scotch-Irish identity. I think that matches of this nature are worth investigating & I certainly don't plan on ignoring them because they don't fit in the narrow context of my original purpose. This is at the hea!
rt of how we will use genetic genealogy. If we only use it in the context of identifying those who share our surname in the past 300-500 years, we are going to miss a grand opportunity to find the source of our ethnicities. We are all aware that surnames have only entered common usage in the past 15-20 generations. That means that all of us who share common ancestors from a more distant past will ultimately find matches & near matches with surnames different from our own. When most novices find matches with different surnames, the imagination is piqued, & all sorts of ideas run amok. We now know that many of us will find many such matches & near matches as time passes & more people are tested. For those who have haplotypes that don't fit the haplogroup predictors with any very strong margins, SNP testing is absolutely essential, & I don't think anybody is arguing that point. I would take it a step further. When I got my extended SNP test results, I created a benchmark for my!
haplotype & then gathered a group of very similar haplotypes with a common cultural identity, & suspected (if not proven) common geographic origin. My suspicion is that everyone of that haplotype is P25+/M269+ & negative for all of the downstream markers available for testing within the current hierarchy - we are probably all R1b1c*. I would rest a little more assured if someone else from my little database was also SNP tested. It's true that with this example, there is a very high probability that we are all R1b1c*, but for other haplotypes, that may be considerably less probable. By definitively proving the haplogroup for any given haplotype, we will be creating a catalogue of haplotypes within each haplogroup & effectively define the STR variability within each haplogroup. It's a start. Just as the NASA space program resulted in a flurry of spin-off technologies in the 60s, the repetitive SNP testing on a commercial scale could results in improvements in the technology, !
with the hopeful development of improved SNP discovery techniques. Medical SNP discovery research continues as we speak, so the issue at hand is funding. As genetic genealogist, we all have a vested interest in this approach. I can envision a time in the future when a 50+ marker haplotype is accompanied by SNP testing, so that when results are returned to the customer, he will know that he is a descendant of an genetically successful man who lived in X geographic area, perhaps one or two thousand years ago, & that he is related in his direct paternal line to a group of men who share a common genetic & cultural heritage. I know that there are some that believe that culture/ethnicity should not be linked to genetic testing, but I don't understand why you would be tested if you didn't want to make that link. Three or four hundred years (or 15-20 generations) is but the blink of an eye in historic or genetic terms. Genealogy is a good start, but I don't think I want to give up t!
here. I favor the idea of banding together to generate funding for SNP discovery. Admittedly, there are not enough of us dedicated to this at present to make a very large impact, but every journey starts with a first step. Happy hunting, Pat Tagert



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