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From: "Ken Nordtvedt" <>
Subject: Re: [DNA] Applicability of Kens method to mtDNA. Was Re: S21/S28Split+m223 stuff
Date: Tue, 20 May 2008 07:55:08 -0600
References: <018701c8b9dc$c8cbeb10$6400a8c0@Ken1><ea3bd9560805191258n7d57e52an52752fc51f79edc4@mail.gmail.com><01f301c8b9ed$119eb2e0$6400a8c0@Ken1><ea3bd9560805191336u212d50bxda454d1c27958f9f@mail.gmail.com><024001c8b9f5$b85eb640$6400a8c0@Ken1><ea3bd9560805191457j17fda021nd57964e0743a802d@mail.gmail.com><026301c8b9fd$d86792b0$6400a8c0@Ken1><00d601c8ba05$6159b150$0100a8c0@john><031b01c8ba08$bbd348f0$6400a8c0@Ken1> <002101c8ba27$5c3f6ad0$0100a8c0@john><001601c8ba2e$6337ea90$6400a8c0@Ken1><4832CE60.8060504@comcast.net>


I'd have to think about any special factors relevant to mtdna, but in
principle don't see why such approaches would not work for mtdna haplotypes.
My programmed excel spreadsheet is in some sense hard wired for the specific
ydna application with columns spelled out for specific STRs. But I will
send it later today so you might get ideas how you might rebuild it for
mtdna. Ken



----- Original Message -----
From: "J. J. (Jim) Logan" <>
To: <>
Sent: Tuesday, May 20, 2008 7:13 AM
Subject: [DNA] Applicability of Kens method to mtDNA. Was Re: S21/S28
Split+m223 stuff


> Ken:
>
> Since my work has been primarily mtDNA, rather that Y-DNA, I started
> seriously following your discussion rather late and have not been able
> to decipher the symbols and assemble all the formulas. I've now reached
> the point that I would like to really understand your approach and
> hopefully apply it to my research.
>
> You see, my research it mtDNA. I have mined GenBank and developed a new
> phylogeny for mtDNA haplogroup J (See Spring 2008 issue of JOGG). More
> recently, using simple average number of coding-region polymorphisms
> for a clade and a coding region mutation rate estimated from the
> chimp-human split, I have done an estimate of ages. I am now working to
> refine these estimates based on additional data and using only
> synonymous mutations. I am also looking at alternative approaches and
> would like to develop confidence intervals for my estimates.
>
> First do you see any reason your mathematics would not be applicable to
> full sequence mtDNA data, with possible tweaking.
>
> Second, can you provide me a copy of you Excel software and any
> instructions you might have so that I can try it.
>
> Thanks.
>
> ====
> J. J. (Jim) Logan
> Group Administrator, J1mtDNA, FxGS, and Logan DNA Projects
> Owner/Moderator, J-mtDNA discussion group on Yahoo
> FxGS SIG Leader, Surname Projects and Genetic Genealogy
> ===================================================
>
> Ken Nordtvedt wrote:
>> There is a confidence interval for the formula. It, incidently, is so
>> straightforward and intuitive (the one for age to MRCA for two different
>> clade populations), it must be used widely in journal papers. I think it
>> has never been applied before to the S21 and S28 populations. If anyone
>> has, it should be straightforward to compare calculations and results.
>>
>> I have not yet worked out the confidence interval for the interclade
>> formula, but I'd guess it is something like
>>
>> delta G / G = 1/squareroot(2MG) times 1 / square root(effective N) with
>> effective N the number of effectively independent paths from a haplotype
>> in
>> clade A to a a haplotype in clade B. N would have nothing to do with
>> sample
>> population size and could be close to 1 for two clades connected mainly
>> by
>> long pre-MRCA single branch lines. But the 2MG values are typically of
>> order 16 or so, so deltaG/G of 25 percent or less would not be
>> unreasonable. Our S21/S28 application has essentially no appreciable
>> branch lines before their two MRCAs, so we might get some effective N > 1
>>
>> Yes, it assumes selection neutrality of the ydna mutations. But we can't
>> throw in selection for one application and leave it out for other
>> applications.
>>
>> Remember what the basic counting is all about for the S21/S28 MRCA. We
>> are
>> just averaging the squared distance version of genetic distance between
>> pairs of haplotypes, one of the pair being a present day S21+ and the
>> other
>> of the pair being a S28+. If G is the distance back to the MRCA for S21
>> and
>> S28 clades, each pair is precisely separated by 2G generations. The
>> expected variance produced in 2G generations is 2MG for every pair. This
>> is
>> not rocket science, although my round about derivation sort of was. This
>> problem of interclade MRCA age estimate does not have the complication of
>> path length differences between different pairs of haplotypes that you
>> raise
>> and which modifies the self variance for a single clade's MRCA age.
>>
>> My excel software is available to anyone who wants to check it out for
>> validity and mistakes, or for use.
>>
>> Ken
>>
>>
>> ----- Original Message -----
>> From: "Alister John Marsh" <>
>> To: <>
>> Sent: Monday, May 19, 2008 9:12 PM
>> Subject: Re: [DNA] S21/S28 Split+m223 stuff
>>
>>
>>> Ken,
>>>
>>> I admit my posting was based on assumptions. I was putting forward a
>>> way
>>> of
>>> looking at the issue. I don't think the assumptions can be considered
>>> disproven just yet.
>>>
>>> I think that an Ockham's razor approach would find the assumption that
>>> S116+
>>> was in Ireland and other places 8,000 years ago would be one of the
>>> simpler
>>> ways of explaining the present day distribution of S116+. However, I
>>> have
>>> an open mind, and it will be interesting if 8,000 year old Y-DNA is ever
>>> recovered to prove this matter one way or the other.
>>>
>>> If S28+ is not long after the common ancestor of S21+ and S28+, an
>>> explanation could be that S28+ is older than 8,000 years. Could it be
>>> that
>>> "if" S28+ is 8000+ years old, that your formula would need a "fudge
>>> factor"
>>> added?
>>>
>>> Your formula is probably reliant on assumptions, such as assumptions
>>> that
>>> no
>>> Y-STR mutations are detrimental to the long term survival of a Y-line.
>>> Your
>>> formula may give misleading results by having large numbers of survivors
>>> of
>>> recent branches, and none or very few survivors from very old thin
>>> branches
>>> from antiquity, or none from extinct branch lines. Perhaps what your
>>> formula is showing is the time of large expansion of S28+, rather than
>>> the
>>> age of S28+?
>>>
>>> Do you have "statistical confidence intervals" for your formula? Is the
>>> 95%
>>> confidence interval 2000 to 8000 years?
>>>
>>> John.
>>
>>
>>
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