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Archiver > GENEALOGY-DNA > 2007-07 > 1184190719


From: (John Chandler)
Subject: Re: [DNA] Help please with marker 458
Date: Wed, 11 Jul 2007 17:51:59 -0400 (EDT)
References: <008701c7b415$794b0120$2401a8c0@your447023ae6b><REME20070703220030@alum.mit.edu><a81622ac0707041809y68277e45iaa87951637aacb9a@mail.gmail.com><REME20070705181857@alum.mit.edu><a81622ac0707051724y16754956obfb853b6686e74ed@mail.gmail.com><REME20070707152459@alum.mit.edu><a81622ac0707071304x11373a0en3b0b4e52a7b2e3c@mail.gmail.com><REME20070707183721@alum.mit.edu><a81622ac0707071637o34a3421dr36660529da9f75a4@mail.gmail.com><REME20070709202718@alum.mit.edu><a81622ac0707092003u290a5dd4s96c4a87a62fe3230@mail.gmail.com>
In-Reply-To: <a81622ac0707092003u290a5dd4s96c4a87a62fe3230@mail.gmail.com>(jmknapp@gmail.com)


Joe wrote:
> Just as an aside, is there anything in this model that specifically
> breaks your method? I thought it was not supposed to be sensitive to
> population structure, or whether the population is constant or
> exponentially growing.

In principle, it should be ok, but I do make the assumption that
all haplotypes descend from a common ancestor, whereas your
starting population is a host of identical clones.

> I see no oscillations such as you brought up.

Nonethless, your FFT showed what looked like significant power in
the frequencies of interest. You apparently need to do some
smoothing to see the oscillations.

> I'll think about what I need to do to the program to do what you
> suggest re an expanding population. One issue is that I'm limited by
> memory concerns to about 2,500,000 people total in the simulation, so
> an exponentially increasing population will hit that limit pretty
> quick.

Yes, that could be problem unless you pick the expansion rate very
precisely.

> BTW, re decescendants of the original population, as far as haplotypes
> go anyway, the founding haplotype at least is still the MRCA at the
> end of the run.

I'm not sure what you mean by MRCA here. In the 10-tribe case, there
is obviously not any common ancestor at all, and my suspicion is that,
even in the one-tribe case, there are many members of the original
population who still have living male-line descendants after 10,000
years, but I was hoping you could give a definitive answer for the
relative numbers in these two cases. Are you talking about the
modal haplotype (or, more likely, the haplotype consisting of the
modal alleles on all loci)?

John Chandler

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