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Archiver > GENEALOGY-DNA > 2010-02 > 1266102370


From: Sasson Margaliot <>
Subject: Re: [DNA] Y Tree SNPs can not be counted
Date: Sun, 14 Feb 2010 01:06:10 +0200
References: <mailman.4572.1266045490.2099.genealogy-dna@rootsweb.com><6A16FA701F2F4350A90C379D3AA5DC21@anatoldesktop>
In-Reply-To: <6A16FA701F2F4350A90C379D3AA5DC21@anatoldesktop>


Anatole,

Why is it that you do not simply use tandard terminology?

1) There are 500 samples. 14 samples are identical,
they all belong to the same haplotype.
You say they are "14 haplotypes.". Standardly,
there is just one "base" haplotype, and
14 samples are said to belong to it.

2) The other 486 samples have
1788 differences from the base haplotype.
You call these differences "mutations".
People naturally think you count the number of mutation events,
because this is what you appear to be saying.
You probably can estimate the number of mutation events,
but of course this is not what you count.

3) When a cluster has a prominent sub-cluster,
you usually say that it "has two common ancestors".
This is not a standard way to describe the situation.


4) For confidence intervals, other writers give
theoretical upper limits for a GENERAL CASE,
and they know their intervals are correct..
You are eliminating all the suspicious sub-clusters,
so you are not dealing with the most general case.
Naturally, your intervals are shorter, since you
only accept well behaved clusters.
But people simply think you give wrong intervals,
because they are different.

Much of the discussion is concentrated on
misunderstandings about terminology.

Sasson


> If we have, say, 500 of 67-marker haplotypes,
> and 14 haplotypes among them
> are identical to each other (base haplotypes),
> and the other 486 mutated haplotypes have
> (collectively) 1788 mutations from the base,
> then those 1788 mutations are those
> that we count"


> >> (Anatole) I suspect that by "counting mutations" you mean something VERY
> >> different compared with, e.g., what I mean.
>
> >Indeed!
>
>


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