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Archiver > GENEALOGY-DNA > 2006-11 > 1163945404


From: "Alfred A. Aburto Jr." <>
Subject: Re: [DNA] mtDNA Haplogroup C exact HVR1 match.
Date: Sun, 19 Nov 2006 06:10:04 -0800
References: <3f7.dc3370c.32912a87@aol.com>
In-Reply-To: <3f7.dc3370c.32912a87@aol.com>


Ann!
Thank you once again for guiding me correctly! With mtDNA we are talking
mostly about base pair matches and rare mismatches! It would be 569/569
in our case in HVR1.

If I use the mtDNA control region mutation rate of 10^(-5) that you give
in your book I get a TMRCA of (less than or equal to) 7900 years at 95%
probability and 1800 years at 50% --- still ancient, even with a 569/569
match in HVR1.

Charles Kerchner at http://www.kerchner.com/mtdnatmrcacalculations.htm
indicates a mutation rate of 0.00003. Here I get a TMRCA of less than or
equal to 2600 years at 95% probability and 600 years at 50%.

If we test HVR1 & HVR2 we test 1050 base pairs and if we match there at
1050/1050 again, then the TMRCA would be less than or equal to 1400
years at 95% and less than or equal to 330 years at 50%.

And, wandering off here a bit, if we tested the full sequence mtDNA
(16500 base pairs) then a 16500/16500 match would be 3 generations (90
years) at 95% probability. So testing the full sequence could be *very
important* and informative and necessary.

Ian, you're right.
Al


> wrote:

>In a message dated 11/18/2006 2:56:15 PM Pacific Standard Time,
> writes:
>
>
>
>>Thanks. I thought however that your point about the number of
>>polymorphisms in the HVR1 was important! I am wondering if it was still
>>52 generations if one had a 10 out 10 match in the HVR1 region (matching
>>haoplogroups too), instead of, for example 3 out of 3 plus haplogroup,
>>or 6 out of 6 plus haplogroup?...
>>
>>
>
>Actually, you are a 569/569 match -- the two of you match all bases in HVR1,
>16001-16569.
>
>The number of polymorphisms is a function of how closely you are related to
>an arbitrary reference sequence, the Cambridge Reference Sequence. The CRS is
>in haplogroup H2b, so C is quite distant. See Whit Athey's phylogenetic diagram
>at
>
>http://www.worldfamilies.net/mtDNA.htm
>
>Ann Turner
>
>


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