GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2009-01 > 1231175580


From: "Ian Logan" <>
Subject: Re: [DNA] mtDNA sequences from Tunisian centenarians !
Date: Mon, 5 Jan 2009 17:16:28 -0000
References: <010520090031.17832.496154CC000593F7000045A82215551724CE050C0E9D080C9C0D@comcast.net>


Bonnie / List

I have re-drawn my Haplogroup I chart
- see http://www.ianlogan.co.uk/discussion/hap_N.htm

to take into account the comments from Bonnie (thank you).

Overall I think the sequencing for the recently tested samples is probably accurate
- but the older sequencing from Finland and the USA is perhaps not fully accurate.

So what is needed now is for more Haplogroup I sequences to be sent into GenBank.
Is there anybody with an 'I' sequence that has not so far been sent in ?
I am always happy to make up submission files for complete sequences.

Ian
www.ianlogan.co.uk
............

Ian wrote:

> I have found the I sequence unusual as it has a 'twig' all to itself.

Well, if you like, but it looks to me as though it simply had no further mutations beyond those that
normally define I1a, and all the other I1a samples you've included did have more mutations.

But your I1a tree is quite different from the way I would arrange it. You have had to put those
three Herrnstadt I1a samples, 27, 36, and 37, on a separate branch because they didn't include
Control Region data, and you defined the rest of your I1a by their having 203, 16172, and 16311. If
you hadn't used those HVR1 & 2 mutations to define that branch, you could have put the Tunisian and
Portuguese samples on the same level. Also, you've used the 455 insertion to define the branch
where you've separated the Tunisian and Portuguese samples. I think the Finnish papers didn't even
report that mutation, or Herrnstadt. I'm sure they all would have shown that mutation had they been
tested for it, as it is found in every member of I1, not only I1a, who has been tested for it.

I respect your work very much, but we have different philosophies for constructing phylogenetic
trees. In defining branches, I would not use mutations which only a portion of the samples included
have been tested for. If it's necessary to use samples like Herrnstadt's that omit HVR1 & 2, I
would assume that, like the others with those Coding Region mutations, they possess the 203, 16172,
and 16311 mutations found in all I1a. For example, I share the uncommon 14182 mutation with sample
37, and I have those typical I1a HVR1 & 2 mutations.

I'm sure I won't change your method, but I thought I would offer this analysis in case anyone is
interested.

Bonnie

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