RootsWeb: GENEALOGY-DNA-L Re: [DNA] Is H2a2 the same thing as ... H*?

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Archiver > GENEALOGY-DNA > 2007-07 > 1185730339

From: "Dora Smith" <>
Subject: Re: [DNA] Is H2a2 the same thing as ... H*?
Date: Sun, 29 Jul 2007 12:32:19 -0500
References: <bc6.15c96850.33ddf44a@aol.com><01a001c7d1fb$e74d0750$640fa8c0@Villandra2>

Kathy just cleared it up for me. The CRS's values are the rare values of the CRS. The CRS has all five values as A. Along the path of H2a2 toward H*, the A's gradually turn into G's. Actually the A's are the mutations, but our annotation expresses mutations in terms of mutations from the CRS. ON the direct path leading to the CRS the result is confusion. I knew it could as easily be that I was missing something glaring as that the scientists are. It's confusing because the phylogenetic order is backwards. I guess I'm not H2a2 - but if I'm H*, I'm not going to know what to make of it. Or maybe I am H2 - keep reading. I don't know if a tool like GenSnip will be of much use with a sequence that has chunks missing. (The sequence is not yet complete - though I don't see anything important that is specifically missing.) I have preliminary raw output. I created a spreadsheet, and aligned my raw output against teh CRS, each letter in its own cell, which I then sorted together, line by line. I then color coded the cells by letter value, and drew lines around the pairs of cells. In theory it is now easy to spot mutations. Actually I missed two of them until I specifically looked for them once I knew they should be there. The thing is, though, that only one of them is specifically marked with its letter value. The other four markers are all marked "R" instead of with a letter value. There are also two "M"'s, at places that don't correspond to previously reported mutations, and I'm allowing that they could be among the aspects of the sequence that will eventually clear up as the output becomes less preliminary. There's also an odd blank where there shouldn't be a mutation, that is different from the odd blanks that often appear next to the strings of n's that indicate missing data. I checked HVR1 and HVR2 twice as carefully as the rest of it because easier to do for the short sections of data, and mutations more likely to be there - and no mutations are there. So here's what I actually have for the five markers. 15326 G 8860 R 1438 R 4769 R 750 R I also have 574 blank, which happened because no value exists for that spot and I left it blank; 1174 M, and 4763 M. If that means nothing to anybody I'm not worried about it because they may not actually mean anything. I don't want to bother my company that was nice enough to send me the preliminary data with questions, but I think a very logical thing to do would be to ask what "R" and "M" mean - simple question, simple answer, the answer could conceivably make my life easier, LOL! Unless someone here has seen this before and happens to know what R and M mean. One possibility is that I appear to have a mutation at 15326 and not at teh other four markers and the program is programmed to flag this as a possible sign of an error. Is it possible to have a mutation at 15326 and not at 8860? Logically I suppose so, but I wonder if I did, that would be a reason to submit it to Genbank, LOL! Now we know in which order those two mutations historically happened. Do I correctly understand that if I am NOT H2 or H*, then the mutation or mutations that defines some other branch of H or some branch leading away from H, WILL appear in the output, so I just need to identify those values and specifically look for them? I suppose it's possible that mutations will eventually appear where they don't now exist and this is part of what is taking so long. Sigh. Yours, Dora Smith Austin, TX ----- Original Message ----- From: "Dora Smith" <> To: <> Sent: Sunday, July 29, 2007 11:17 AM Subject: Re: [DNA] Is H2a2 the same thing as ... H*? > Ann, you've addressed a question I asked last night - is H2a2 the same > thing > as H*, and if not, what is actually the difference? But you haven't > explained why the same markers used to arrive at H2a2 are also used just > as > logically to arrive at H* > > If you look at Roostalu's phylogeny, then those five mutations clearly > lead > in a stepwise fashion to H2b2. Yet they are also used to discern H*, and > everyone who is H* has all five mutations and no more. > > Your chart shows how 1438 leads to H2, 4769 leads to H2a, 750 leads to > H2a2, > and then - here's a new wrinkle. You've honestly thought of different > directionality than everyone else did. > > Roostalu's charts have 8860 and 15326 leading from the CRS to H. Then > 1438 > leads to H2, 4769 leads to H2a, 750 leads to H2a2. > > You have, from H, however we got to H, 1438 leads to H2. 4769 leads to > H2a. 750 leads to H2a2, and then, voila - 8860 and 15326 leads to - the > CRS! > > Now, wait a minute. If I had teh CRS I wouldn't have five mutations that > are different from the CRS. This does not all END at teh CRS. Well, > maybe in actuality it does, but I want to know my actual subclade, which > is > not the CRS. > > Now, what I had noticed is that alot of people, including it seems Ian > Logan, are going in the opposite direction. They start at the CRS, and > then if you have the five mutations, 1438, 4769, 750, 8860, and 16326, you > are H* - which makes a sort of good logical sense given the truth of what > you have said below. It looks as if teh entire rest of the mtdna world > is > descended from some clade defined by 1438, 4769, 750, 8860, and 16326. > One > schematic chart even shows 1438, 4769, 750, 8860, and 16326, leading from > the CRS to H, and defining haplogroup H. > > It is necessary to ascertain for one thing, if some people in the chain of > mutatoins between the CRS and H don't have all five mutations, and if > anyone > has less than four of them. > > But if you have all five mutations, are you really a subclade of H known > as > H2a2, H*, or - both? > > Ann, it just occurred to me. Some people who have 1438 do not have 4769. > Does everyone who has 1438 have 8860 and 15326? If so, then 8860 cannot > lead on the phylogenetic chart from 750 to the CRS. > > Does everyone who has 1438 in fact have 8860, 15326, and 750, and some of > those have 4769? > > Yours, > Dora Smith > Austin, TX > > > ----- Original Message ----- > From: <> > To: <> > Sent: Sunday, July 29, 2007 8:46 AM > Subject: Re: [DNA] Is H2a2 the same thing as H2b? > > >> In a message dated 7/28/2007 7:20:56 AM Pacific Daylight Time, >> writes: >> >>> Was the CRS really once H2b and now it's H2a2, do Roostalu and someone >>> else >>> >>> disagree, or do the markers 4769G, 1438G, and 8860G among others >>> differentiate H2a from H2b? >> >> I tried to diagram the situation in a text message, but I really needed >> to >> do >> it in a graphic format, so I uploaded a file to the RootsWeb Companion at >> DNA >> Heritage. It remains to be seen whether new papers will use Roostalu's >> nomenclature, which was just formally published early this year. There is >> a lot of >> literature that refers to H2b. >> >> http://www.dnaheritage.com/files/rootswebupload/H2b_or_H2a2_CRS.GIF >> >> Most people in the world will have five "mutations" at 750G, 1438G, >> 4769G, >> 8860G, and 15326G, including most people in haplogroup H. I put >> "mutations" in >> quotes, because the actual mutations occurred between the clan mother of >> haplogroup H and the CRS, which is just a tiny twig branching off of H. >> The CRS has >> the rare values and others have the ancestral values, but everything is >> reported in terms of *differences* from the CRS. The closer you are to >> the >> CRS, the >> fewer differences you will see on your report. I haven't seen anyone yet >> who >> actually matches the CRS completely. >> >> Ann Turner >> >> >> >> >> ************************************** >> Get a sneak peek of the all-new AOL at >> http://discover.aol.com/memed/aolcom30tour >> >> ------------------------------- >> To unsubscribe from the list, please send an email to >> with the word 'unsubscribe' without >> the >> quotes in the subject and the body of the message >> > > > > -- > Internal Virus Database is out-of-date. > Checked by AVG. > Version: 7.5.476 / Virus Database: 269.10.4/897 - Release Date: 7/11/2007 > 9:57 PM > > > ------------------------------- > To unsubscribe from the list, please send an email to > with the word 'unsubscribe' without the > quotes in the subject and the body of the message > -- Internal Virus Database is out-of-date. Checked by AVG. Version: 7.5.476 / Virus Database: 269.10.4/897 - Release Date: 7/11/2007 9:57 PM