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From: "Ken Nordtvedt" <>
Subject: Re: [DNA] Another failure to get DYS463
Date: Sat, 8 Oct 2005 18:51:14 -0600
References: <20051008162620.50911.qmail@web31502.mail.mud.yahoo.com> <REME20051008132540@alum.mit.edu> <002301c5cc37$da5fb4a0$71509045@Ken1> <REME20051008202731@alum.mit.edu>


I don't believe the population explosion changes things at all. It explodes
the descendant population of the SNP if it had occured back further in time,
and of course it gives the recent populations more members on which the SNP
mutation could fall. Those factors just compensate for each other, i.e.
there are factors of generation population in both numerator and denominator
in forming the contribution of that generation to the present, so the final
product becomes generation independent.

I did think about the finite time extinction takes to finish, statistically
or practically speaking. It is only a consideration for the last 1/r
generations, and r is pretty big if we have had exploding population in the
last few centuries. And again, I think it is probably neutral to first
approximation between the survival of the growing descendant population of
an older SNP and the survival or creation of the SNP in a recent generation.

Remember, the present generation is both rich potential domicile for the
location of the SNP to originate, but also a fecund transmitter of the
descendant population of the SNP if it had occured in earlier times.

All I am trying to estimate is the RATIO of liklihoods for the creation
generation of the SNP, given that some one recently found it in the lab in
this generation's population.

Ken
----- Original Message -----
From: "John Chandler" <>
To: <>
Sent: Saturday, October 08, 2005 6:32 PM
Subject: Re: [DNA] Another failure to get DYS463


> Ken wrote:
>> Let's say I have very good reason to believe the SNP lies within
>> haplogroup
>> or clade X (this can be established by measuring the extended STR
>> haplotype). Haplogroup X has some population history P(g) in each
>> generation from g = 1 to today's g = G. So the SNP occured in one of
>> those
>> G generations. What's the probability of that generation being an early,
>> middle, or recent generation? It seems to me it is about the same for
>> any
>> generation?
>
> You're not taking into account the population explosion of the past
> few centuries. If we make the simplifying assumption that every male
> ever born has one new SNP of his very own, then there are about
> three BILLION utterly private SNPs right now (distributed among the
> 60 million bases of the Y chromosome, so that every base in fact has
> many independent private SNPs scattered around the world).
>
> The other factor favoring "privacy" of SNPs is extinction. The further
> you look back in time, the more likely it is that the SNP associated
> with any given male in generation g has died out and therefore is not
> the SNP you are asking about. You seem to have assumed that
> extinction of lines happens immediately, but that's clearly not so.
> It is progressive and, most importantly, has no effect whatsoever
> on the present generation.
>
> Bottom line: if you start with a test subject and keep looking at his
> DNA until you find a SNP, your argument holds true, but if you only
> look at the test subject *because* you noticed a SNP, you are weighting
> the statistics heavily in favor of the past few centuries.
>
> John Chandler
>
>
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