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From: "Lancaster-Boon" <>
Subject: [DNA] Variance Assessment of R:U106 DYS425Null Cluster
Date: Sun, 7 Feb 2010 19:51:52 +0100


Dear Anatole

Thanks for your extended answer. The first thing I need to point out in
order to avoid misunderstanding is that you have used my words about
"shooting in the dark" a lot, as if people are calling everything you do and
say "shooting in the dark". Then you went through a long explanation of what
is easiest to follow in your method, and asked rhetorically where the
shooting in the dark is - implying unfortunately that I had been very
unclear.

In fact I was not quite that unclear. I specified where I thought I saw
shooting in the dark, and for the people who read through the first section
of your response you do eventually come to it. Some parts of your post:-

---
Anatole: It was absurd in a way how Ken switched the subject. There is
nothing absurd in the haplotypes themselves, it is was just an improper and
incorrect selection (or, rather made up serious of haplotypes). Those
haplotypes did not represent a one lineage. When we have discussed U106, it
was one lineage. Absurd was in a manner of discussion. "Fuzziness" was a
lack of focusing on a subject of the preceding discussion.

Andrew: I presume this is because it implies no clear ancestral modal and no
clear family tree structure? Is this correct?

Anatole: "Not quite. It was deliberately made that it does not have one
ancestral haplotype. It was deliberately made in such a way to justify that
a margin of error can be high. Of course it can be high, but not in a case
of 284 of 25-marker haplotypes that we have discussed earlier. If there is
just one mutation in a dataset, margin of error will be 100%. So what?"

---

This still seems to me to be where people are talking past each other. You
are pointing out correct your maths is, but I think what people are asking
about is whether Ken really changed the subject. All haplotypes have common
ancestry, and the question with any set of them is always how they descend
via a "family tree"; which sub-sets share common ancestors. Your answers
repeatedly imply that this question is not even one you think worth worrying
about. You seem to be claiming that your data sets show none of the
difficulties that Ken's example shows?

More from your post:-

---

Andrew: To me Ken's example looks like something we see all the time even
within solidly defined family groups, or SNP defined clades.

Anatole: It means that there is something very wrong with your approach.
First, the Ken's "example" can be approximately described with TMRCA of more
than 10,,000 ybp. This is just cannot be in your family studies. Either you
give now a huge exaggeration, or you just actually saying "we do not know
what we are doing". You boil water on top of a mountain, figuratively
speaking, without realizing that you operate in a wrong context. Or you take
two haplotypes, look at five mutations between them and scratching your
head.

---

Let me make my point a different way and see if it still sounds crazy. I
very rarely see datasets which have only one likely family tree. Most of
them have many. Your approach seems to rely on the assumption that even with
big sets of data the family tree structure can be stated with zero doubt?

Best Regards
Andrew


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