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From: "Alister John Marsh" <>
Subject: Re: [DNA] TMRCA assessments
Date: Thu, 18 Feb 2010 05:40:08 +1300
References: <mailman.5283.1266379709.2099.genealogy-dna@rootsweb.com><23F3D18074D04F76AD3B53ED0AD6F7E9@anatoldesktop>
In-Reply-To: <23F3D18074D04F76AD3B53ED0AD6F7E9@anatoldesktop>


Anatole,

You say re parallel mutations...
>>>>>>>
This probably is a core of many of our mutual misunderstandings. I say "they

do not affect the TMRCA". You (and others) say "but they are useful for
family studies". That is fine and correct. However, there is no conflict
whatsoever between the two statements.
<<<<<<<

It is true that they can be useful for family studies, and on occasions they
can add to the confusion if they can't easily be identified as parallel
mutations.

But my main point concerning TMRCA, is that in some (many?) datasets, they
contribute to confusion about what the probably ancestral haplotype was. If
the ancestral haplotype is misidentified because of parallel mutations, then
the mutation count using your system can be significantly in error "because"
of their existence. If the parallel mutations cause the ancestral haplotype
to be misidentified, then in fact they have caused an affect on "estimated"
TMRCA.

I think with detailed study of context, "sometimes" the parallel and back
mutations can be identified, and if they are correctly allowed for, they
would not adversely affect estimates of TMRCA.

In my example which you examined, you still appear keen to equate the "modal
haplotype" to the "ancestral haplotype". By definition of these terms, a
modal and ancestral haplotype are not the same thing. I think that if you
recognized the importance of identifying parallel mutations, you would on
some occasions be able to get a better estimate of ancestral haplotype.

Regarding Back mutations, you seem to think that they might typically have
1% impact on TMRCA, I think they might typically have more. If they cause
misidentification of ancestral haplotype they could have a large affect on
mutation count. It they individually are not counted as mutations, they can
change the mutation count by 2. In an example where you count 13 mutations,
a difference of 2 is significant, particularly when compounded with any
errors caused by misidentification of ancestral haplotype.

I guess we are going to have to agree to disagree on some things, as both of
us for our various reasons seem to be bonded to our respective
interpretations of the evidence. If it makes you feel better, you are
better qualified in maths than me, so the problem may well be my ignorance.

John.




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