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: <><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.

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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