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Archiver > GENEALOGY-DNA > 2005-07 > 1121284605


From: "Ken Nordtvedt" <>
Subject: Re: [DNA] 25/1/14 and early Scots groups (WAS: R1b 37 STR cluster analysis e...
Date: Wed, 13 Jul 2005 13:56:45 -0600
References: <1e3.3fb42c42.300680c7@aol.com> <42D54382.1080402@scs.uiuc.edu> <001c01c587dd$a757d2c0$37c33442@ericpc>


1) There has been some papers which claim a correlation between how many
letters in the unit of repeat and the mutation rate of the STR.

2) Why do you expect a wider range of repeat values in 60,000 years? The
numbers don't suggest that. 60,000 years is 2000 generations. The random
walk formula (used throughout the physical and now biological sciences) says
basically ASD = w T with T being steps or generations in our case, w is
mutation rate and ASD is average squared difference. For w = 1/350 and 2000
generations one gets an ASD estimate of about 6; that is about 2.5 squared.
So we might expect a spread of repeat numbers to have developed from a
starting point with variance of plus or minus 2.5.

But why pick 60,000 years? I believe we share many of these STRs with
Neanderthal, Erectus perhaps, and even earlier hominids. So the time period
could go into the millions of years. Certainly other factors eventually
enter and limit the indefinite expansion of a purely random walk model into
the past. I suspect that STRs that don't have a feedback mechanism that
limits their length will "blow themselves apart" and cease to exist in the
genome. And other new STRs are at some slow rate coming into existence in
species.

Modal states arise because a founder, and individual with a unique
haplotype, begins a particularly prolific line of descendants. These
founders lived at a quite finite number of generations into the past. The
ASD from his repeat values will be less than the 6 I estimated above if the
founder lived 5000 years ago instead of 60,000 years. But the real reason
his modal haplotype stands out is because his founding haplotype started out
with a difference from the modal haplotype for the group in which he
existed. This will most of the time not be the case, but statistically will
occur sometimes. If a later founder in R1b happens to have the R1b modal
haplotype, and he strikes out to the next valley to start his own prolific
line, then we today interpret that simply as the expansion of the R1b modal
form into new territory.

Ken
----- Original Message -----
From: "Eric Olson" <>
To: <>
Sent: Wednesday, July 13, 2005 1:04 PM
Subject: Re: [DNA] 25/1/14 and early Scots groups (WAS: R1b 37 STR cluster
analysis e...


> What bothers me are that:
>
> 1) No one seems to be able to explain the "why" of the different observed
> mutation rates for various STRs. Why do some mutate faster than others?
> What are the underlying mechanisms or chemisms? It does not appear to be
> entirely at random.
>
> 2) The limited ranges of values observed for each allelic STR length needs
> explanation.
>
> Why does, say STR19, hover between 11 and 20, while STR 390 hovers
between
> 18 and 28? During the past 60,000 years or so, one might expect a much
> larger range of values than what is actually observed today if it's an
> entirely random phenomena , or a 2D random walk. Since there is
apparently
> no evolutionary advantage for any particular state (or is there?), then
how
> do we arrive at so called "modal" states as anything other than
mathematical
> artifacts? Where is the connection to physical, environmental reality?
>
> I know one does not have to physically understand a phenomena to model it
> mathematically, but without any real understanding of the "whys", we are
> just having fun with numbers. I suggest there is a limiter or other
> restorative biochemical force at work, constantly returning STRs towards a
> "modal" value , or lowest energy state, that would be more stable. Such a
> mechanism may account for the need to invoke a so-called "fudge factor"
used
> to bring recent and ancient mutation rates into concordance.
>
> An observed rate is usually a summation of many other contributing rates.
>
> Eric Olson
> Seattle
>
>
>
>
>
>
>
>
> ----- Original Message -----
> From: "Doug McDonald" <>
> To: <>
> Sent: Wednesday, July 13, 2005 9:38 AM
> Subject: Re: [DNA] 25/1/14 and early Scots groups (WAS: R1b 37 STR cluster
> analysis e...
>
>
> > wrote:
> >
> > >
> > >
> > > Messy, isn't it? The "factor of 3" reduction of father/son mutation
rate
> is
> > > a rather recent phenomenon. Rootsi & others have "borrowed" it from a
> 2004
> > > paper by Peter Underhill & Lev Zhivotovsky (Stanford & Russian
Academy
> of
> > > Sciences, resp).
> >
> > >
> > > It's not clear to me that there's any deliberate choice of fudge
factor.
> > > Ken, you say "unconscious". I think, perhaps. And perhaps it's naive
to
> think
> > > that generally, a population's overall mutation rate would be close to
> the
> > > "input" average father/son rate:
> >
> >
> > No. No.
> >
> > There is every reason to believe that the rates are the same. The only
> > reasons why they should not be the same require invoking the Industrial
> > Revolution as an excuse: either it's a bunch of chemicals changing the
> > actual mutation rate, or the exact people whose "lives were saved" by
> > modern hygiene and medicine are those with high mutation rates.
> >
> > Unless there was an actual mutation rate change, the "apparent"
> > difference must be caused by population bottleneck effects. And there
> > is no reason to suspect that these are in same in all subpopulations
> > of mankind (or womankind, for mtDNA).
> >
> > To be scientifically honest, papers should use the real mutation rates
> > and propose models that give the answers they want to get.
> >
> > Doug McDonald
> >
> >
> >
> > ==============================
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> >
>
>
>
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>


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