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Archiver > GENEALOGY-DNA > 2007-05 > 1178061583


From: James Heald <>
Subject: Re: [DNA] The new J2 Cohen-Levi Modal Haplotype
Date: Wed, 02 May 2007 00:19:43 +0100
References: <3b2a446a0704240151h228095by315a555a63a5a81b@mail.gmail.com> <462DDF28.2070307@ucl.ac.uk> <3b2a446a0704240443r41f1b887wc21a185a8227c866@mail.gmail.com> <462E225F.2030701@ucl.ac.uk><3b2a446a0705011334g27d33728h20538d36e5b843ab@mail.gmail.com>
In-Reply-To: <3b2a446a0705011334g27d33728h20538d36e5b843ab@mail.gmail.com>


Sasson,

Good to see you being flexible to revise your assumptions in response to
(I hope useful) commentary.

However, I'd still flag some issues:

(i) With regard to SCs, all 4/6 matches and no 6/6 matches at all is
still not very supportative.

(ii) With regard to ACs, there seems to be a reasonable correspondence
between between Behar's AC haplotypes and the ACs that can be found in
public databases. But those ACs' extended haplotypes do /not/ look
particularly closely related. They do /not/ appear to share a very
recent common ancestor.

(iii) Dating. It is now known that variance method estimates of TMRCAs
like those in Thomas et al (1998) tend to wildly underestimate the
true TMRCAs, and ignore the very heavy tails on these distributions
towards longer times. This may have arisen in part due to an
over-assumption of what a "statistically unbiased estimator" actually
promises. (Hint: it doesn't mean the estimate is likely to be right -
or even an average of what is likely to be right).

All best,

James.


Sasson Margaliot wrote:

> James
>
> Thank you for pointing out several difficulties of the original formulation
> of the CLMH Hypothesis, in particular emphasizing the fact that "3 off out
> of 6 isn't particularly impressive".
>
> After careful examination of data, it turns out that in the Behar et al.
> 2003 data there are eleven consistent Cohen and Levi haplotypes, which exist
> in J2a1 and which are not more than two steps from the central haplotype.
>
> The adjusted J2-Cohen-Levi modal is just 1 step off the traditional CMH.
>
> #1 (*14*,*15*,23,10,11,12) 2 1SC,2AC,3SL
> #2 (*14*,16,23,10,11,12) 1 CMH
> #3 (*14*,16,*22*,10,11,12) 2 1AC,1AL
> #4 (*14*,16,23,10,*12*,12) 2 1SC (59.1% in
> J2a)
> #5 (*14*,*17*,23,10,11,12) 2 1SC,1AC,1AL (37.9%
> in J2a)
> #6 (15,*14*,23,10,11,12) 2 2SL
> #7 (15,*15*,*22*,10,11,12) 2 1AC
> #8 (15,*15*,23,10,11,12) 1 3AC
> #9 (15,*15*,*24*,10,11,12) 2 8AC
> #10 (15,16,23,10,11,12) 0 10AC,1AL new CLMH
> #11 (15,16,*24*,* 9*,11,12) 2 4SC
>
> In this Network , the variance is not entirely inconsistent with a MRCA some
> 150 (or so) generations ago, which is null hypothesis.
>
> The modal haplotype (#10) has the greatest numer of individuals - eleven -
> in this Network.
>
> There are also 7 other haplotypes in J2a1, and only 7 haplotypes in J1.
>
>
> Sasson Margaliot
>
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