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Archiver > GENEALOGY-DNA > 2011-11 > 1320655564


From: "Sandy Paterson" <>
Subject: Re: [DNA] Any feedback on the RCC method of TMRCA estimates?
Date: Mon, 7 Nov 2011 08:46:04 -0000
References: <mailman.1080.1320605197.10215.genealogy-dna@rootsweb.com><20111106152808.L0KW2.1830091.imail@fed1rmwml4201>
In-Reply-To: <20111106152808.L0KW2.1830091.imail@fed1rmwml4201>


Hi Richard

Here is an Excel spreadsheet, in both .xlsx and .xls format :


http://dl.dropbox.com/u/2733445/RYBURN.xlsx


http://dl.dropbox.com/u/2733445/RYBURN.xls


It's set up to calculate the 'correlation coeficient' and the RCC for two
37-marker haplotypes.

Column A and column B each contain an M222+ haplotype.

The 'correlation coeficient' is in cell C41 and the RCC in cell D41.

The RCC is 102.0561.

Now change cell B34 from 34 to 33.

The RCC changes from 102.06 to 131.31, a change of 29.25. Multiply that by
43 and we have a jump of 43 x 29.25 = 1258 years in the estimate for a
pairwise TMRCA for a single mutation in CDYa.

Play around with it. Change marker values at random. You'll soon see how
erratic the TMRCA estimates are.

I haven't set out the calculations from first principals but I'm happy to do
so if that will help.


Sandy



-----Original Message-----
From:
[mailto:] On Behalf Of RThrift
Sent: 06 November 2011 20:28
To:
Subject: Re: [DNA] Any feedback on the RCC method of TMRCA estimates?

Sandy, please do, that's the point here.

FYI, part 2 of Howard's pair of papers is at
http://www.jogg.info/52/files/Howard2.pdf

Ken, just read it (part 1).

Once a matrix of pairwise correlation coefficients is set up (some details
seem to be obscured in the paper), as Sandy mentioned each value is scaled:
Take the reciprocal of the 'correlation coefficient' so calculated. Subtract
1. Multiply by 10,000. =RCC

But that's just the starting point. He in effect comes up with an overall
mutation rate ("time scale") from known pedigree /haplotype data using the
Hodges-Lehmann estimator and pairwise TMRCAs. 1 RCC = 43.3 years, SD ~ 8%.

He argues that the average RCC of a cluster is a good proxy for the MRCA of
the cluster. Time to the common ancestor = 52.7 x (the average RCC of the
cluster) (just read the paper!)

Richard Thrift


From: "Sandy Paterson" <alexanderpatterson@
...I could also easily show how the paper uses (abuses?) the concept in
trying to apply it to two haplotypes.

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