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From: Dienekes Pontikos <>
Subject: Re: [DNA] Y-chromosome Adam 142 thousand years old;revised phylogeny
Date: Fri, 20 May 2011 16:47:57 +0300
References: <BANLkTimAbuJWejh1SDUiehF0mbv3wuhBhg@mail.gmail.com><COL115-W608E55002DB245BDE5BAE9A0710@phx.gbl>
In-Reply-To: <COL115-W608E55002DB245BDE5BAE9A0710@phx.gbl>


They use this rate:

To estimate the age of ancestral nodes in the tree, we used the rho
statistic,20,21 considering a germline MSY mutation rate of 1.0 × 10-9
single-nucleotide substitutions (SNS) per base per year.

According to this recent reference:

http://www.cell.com/current-biology/abstract/S0960-9822(09)01454-7

That I also blogged about here, suggesting that it could be used to
derive the age of Y-chromosome Adam

http://dienekes.blogspot.com/2009/08/human-y-chromosome-mutation-rate.html

I'm glad someone did!
On Fri, May 20, 2011 at 4:35 PM, Steven Bird <> wrote:
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> Thank you, Dienekes, for the post and the link.
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> Several things in this paper deserve mention beyond the obvious point of the major revision of the Y tree that this represents.
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> 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?
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> 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.
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> 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:
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> http://s1.zetaboards.com/anthroscape/topic/4193212/1/
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> Time to rethink human origins again?
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> Steve
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> > My post:
>> http://dienekes.blogspot.com/2011/05/father-of-us-all-142-thousand-years-ago.html
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>> 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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--
Dienekes' Anthropology Blog: http://dienekes.blogspot.com
Dodecad Ancestry Project: http://dodecad.blogspot.com


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