**GENEALOGY-DNA-L Archives**

From:"Ken Nordtvedt" <>Subject:Re: [DNA] Question for John ChandlerDate:Tue, 16 Feb 2010 19:43:51 -0700References:<mailman.4572.1266045490.2099.genealogy-dna@rootsweb.com> <A597BD8569E24290A10B37465204E6B5@anatoldesktop> <525460709C6A493EBD3D6BECD514B319@john><REME20100214190716@alum.mit.edu><000601caaeef$640b0120$2c210360$@com><REME20100216194750@alum.mit.edu><D9854FFD8A924EB9A9295845122C981C@john>----- Original Message -----

From: "Alister John Marsh" <>

> I have been concerned about this imbalance for a long time. I wondered if

> it would impact at all on the "variance of variance' calculations to

> determine TMRCA, but I was unable to understand the maths enough to check

> myself. I had presumed that Ken and others had allowed for individual

> mutation rates of individual markers in the variance calculation, rather

> than just doing the calculations based on all markers having average

> mutation rates. Is that assumption correct? [[[ Yes, of course; the

> mixture of STR mutation rates has been taken into account. I have strived

> for over 5 years to never use the dreadful formulation or slang "average

> mutation rate". It corrupts one's frame of mind. Each STR is doing its

> own thing, and the different independent clocks are only combined when a

> best single time estimate is desired. Ken ]]]

Or does having a mixed set of

> fast and slow markers not affect the variance calculation? [[ If STRs are

> mutating in the simple text book manner, each with their own rate, each

> STR grows the expected value of its variance in proportion to its mutation

> rate. But its variance of variance grows non-linearly (faster) than in

> proportion to its mutation rate.

<Variance> = mG

Variance of Variance = mG ( 1 + 4mG)

This latter variance of variance non-linear m-dependence canalter the

optimum strength with which to combine all the STR variances, especially for

large G cases; it implies downweighting the fast STRs more and more as one's

clade is getting older (higher G)

Ken ]]

>

> In Tim's series of TMRCA calculations using variance, he consistently

> seemed

> to get different results for faster markers than slower markers. Could

> this

> be evidence that in mixed sets of fast/ slow markers, there is an effect

> from the mixture which is not being mathematically allowed for?

[[ There is growing evidence that the faster STRs are deviating from the

standard (simple) mutation rule, but instead have mutation rates, and up

versus down ratios, dependent on

repeat values, such that there repeat values tend to get confined to

sweetspots. But I don't think genealogical problems need worry much about

this. Ken]]

[[ <Variance> takes back mutations and repeated mutations in the same

direction into account automatically. No corrections are needed like GD

needs. There is no issue here if one is willing to do the necessary

corrections to <GD> versus G. These corrections are indeed dominated by the

fast markers as the correction scales as square of the STRs mutation rate.

Ken ]]

**This thread:**

- [DNA] Question for John Chandler by "Sandy Paterson" <>
- Re: [DNA] Question for John Chandler by (John Chandler)
- Re: [DNA] Question for John Chandler by "Alister John Marsh" <>
**Re: [DNA] Question for John Chandler by "Ken Nordtvedt" <>**

- Re: [DNA] Question for John Chandler by (John Chandler)

- Re: [DNA] Question for John Chandler by "Alister John Marsh" <>

- Re: [DNA] Question for John Chandler by (John Chandler)