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Archiver > GENEALOGY-DNA > 2011-05 > 1305900088


From: Ann Turner <>
Subject: Re: [DNA] Y-chromosome Adam 142 thousand years old;revised phylogeny
Date: Fri, 20 May 2011 07:01:28 -0700
References: <BANLkTimAbuJWejh1SDUiehF0mbv3wuhBhg@mail.gmail.com><COL115-W608E55002DB245BDE5BAE9A0710@phx.gbl>
In-Reply-To: <COL115-W608E55002DB245BDE5BAE9A0710@phx.gbl>


Yes, the mutation rate is critical. I'm leaving for a three-week trip soon,
so I may not be able to follow up on this as much as I'd like. I haven't
even read the article yet, so take this with a grain of salt.

But for starting points, the traditional mutation rate for autosomal SNPs
was 2 * 10 ^ -8. Full genome sequencing for a father/mother/child trio cut
that almost in half, to 1.1 * 10 ^ -8.

http://www.sciencemag.org/content/328/5978/636.abstract

The Y study based on deep rooting pedigrees came up with a rate of 3 * 10 ^
-8.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748900/

So I need to understand why 1 * 10 ^ -9 was the rate used in the Cruciani
paper.

Ann Turner

On Fri, May 20, 2011 at 6:35 AM, Steven Bird <> wrote:

>
> Thank you, Dienekes, for the post and the link.
>
>
>
> Several things in this paper deserve mention beyond the obvious point of
> the major revision of the Y tree that this represents.
>
>
>
> The dating of the root of the Y tree at 142 KYA seems to bring it much more
> in line with that for mtDNA. However, as Cruciani notes, the date estimate
> hinges entirely on the mutation rate for the UEPs that occur in the MSY
> region. He uses a rate that I quoted some time ago (in another context) for
> UEPs (SNPs), namely 1.0 X 10 to the -9 (p. 2 of paper), which is identical
> to the estimated SNP rate for all other human chromosomes. At the time, and
> I can't recall if it was Ken or John who brought it up, it was mentioned
> that the Y SNP mutation rate was higher. If so, that would shorten up the
> dating again somewhat. Please forgive me for asking again, but what was the
> reference for the somewhat faster SNP rate for the Y?
>
>
>
> I like C.'s approach of "first principles" analysis, that is, going back
> and reanalyzing the region of interest without regard to previously
> hypothesized trees. It is often good to start with a clean slate and no
> preconceptions and see what emerges.
>
>
>
> The point concerning the geographic origins of the new root of the
> phylogeny emerging potentially in central-Northwest Africa is very
> interesting and ties in nicely with another article that I saw just a few
> days ago from Nature:
>
>
>
> http://s1.zetaboards.com/anthroscape/topic/4193212/1/
>
>
>
> Time to rethink human origins again?
>
>
>
> Steve
>
>
>
>
>
>
>
>
>
>
>
> > My post:
> >
> http://dienekes.blogspot.com/2011/05/father-of-us-all-142-thousand-years-ago.html
> >
> > Paper:
> > http://www.cell.com/AJHG/fulltext/S0002-9297(11)00164-9
> >
> > The American Journal of Human Genetics, 19 May 2011
> > doi:10.1016/j.ajhg.2011.05.002
> >
> >
>
>
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