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Archiver > GENEALOGY-DNA > 2010-02 > 1266335124


From: Robert Stafford <>
Subject: Re: [DNA] Variance Assessment wrt back and parallel mutations
Date: Tue, 16 Feb 2010 09:45:24 -0600
References: <mailman.5086.1266274228.2099.genealogy-dna@rootsweb.com><C73CADC1F38E4147A484F459509F2474@anatoldesktop>
In-Reply-To: <C73CADC1F38E4147A484F459509F2474@anatoldesktop>


Anatole, \

Are you using the term ancestral haplotype in the specific sense that
genetic genealogists use it? This is the Y-STR haplotype deduced by testing
descendants of two or more sons until matches are found on all markers. We
distinguish between it and the modal.

http://www.kerchner.com/deducedancestralhaplotype.htm

How do you count mutations? Do you count all that differ from the ancestral
or just those that are unique?

Bob Stafford



On Mon, Feb 15, 2010 at 10:45 PM, Anatole Klyosov <>wrote:

>
>
> Dear John,
>
>
>
> Now, to the ancestral haplotype. There are nine of "35", one "34" and
> one"36" in the allele row. Which one is the ancestral one?
>
> In the next column there are eight of "39", one "38" and two of "37", but
> the latter belong to a different branch. Which one is the ancestral one in
> the main branch?
>
> Generally speaking, a mistake can be made in anything. A mistake can be
> made
> in assigning of a wrong haplotype as an ancestral one, particularly in
> small
> datasets like yours . That is why I avoid the word "ancestral" and call it
> "base". However, in your case the situation with the base haplotype is very
> clear.
>
> You repeatedly use a phrase that by picking a wrong base haplotype I can
> miss the boat by 2 times. Big deal. Tell Lev Zhivotovsky about it, he
> constantly miss the boat by 3 times. Everyone in "academic" world following
> the Zhivotovsky "procedure" missed it by 3 times. So with 2 times it does
> not look too bad on that background. Of course it can happen. However, I
> very seldom work with 11-haplotype datasets. I prefer hundreds of them, and
> for those it is very unlikely to make a mistake with a base haplotype.
>
> I suggest you to reconsider your family dataset, unless you have a solid
> proof with family records. However, who can guarantee that the family
> records do reflect the reality?
>
> Regards,
>
> Anatole
>
> *******************************
>
> (John)
> He appears to have
> simplistically assumed the modal haplotype, distorted by having over
> representation of one branch of a 2 branch family tested, was the ancestral
> haplotype. If he had recognized parallel mutations as impacting on his
> system, he could have looked deeper, and found in my view what is more
> likely to have been the ancestral haplotype. Or at the very least, he
> could
> have recognized the ancestral haplotype was ambiguous, and the alternatives
> might give results differing by a factor of 2. He could have qualified his
> results, by stating that if the alternative ancestral haplotype applied,
> which had perhaps 50% chance of applying, his calculation may be out by a
> factor of 2.
>
> To be fair to Anatole, I was aware of some partial genealogical,
> historical,
> and geographical information concerning the example I put to him. I have
> been studying this family for decades. This gave me a considerable
> advantage over him. However, it showed I think that by simplistically
> looking at the raw DNA data, without the contextual genealogical,
> historical, and geographical data, and considering the potential affect of
> back mutations, it was possibly to be out by of the order of a factor of 2.
>
> Anatole's system in my view might work tolerably well if the ancestral
> haplotype can be correctly identified. But if parallel mutations are
> lightly dismissed as just as well being "vertical" mutations, then Anatole
> is missing an opportunity to improve the outcomes of his system.
>
> Sometimes ancestral haplotype can be inferred by considering parallel
> mutations. But probably more often, parallel mutations make things very
> ambiguous, and then selecting the ancestral haplotype becomes a lottery and
> picking the wrong haplotype might change the mutation count by a factor of
> 2.
>
> Anatole says if the logarithmic method agrees with the mutation count
> method, all is well. I can't comment on that, the maths is well outside of
> my comfort zone. But "I think" in the genealogical time frame
> (particularly
> with less than a dozen random mutations) , the play of feral mutations
> might
> cause the logarithmic and mutation count method to sometimes randomly match
> even if both are wrong. But I expect Anatole to remind me that what "I
> think" has no place in mathematics. He is probably right, and I take no
> offence if he should remind me of that.
>
> John.
>
>
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