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Archiver > GENEALOGY-DNA > 2010-02 > 1266482946


From: Sasson Margaliot <>
Subject: Re: [DNA] "counting mutations" versus "GD from the modal"
Date: Thu, 18 Feb 2010 10:49:06 +0200
References: <3b2a446a1002170905h6bec6379h5e6b6bfbaaf5d684@mail.gmail.com><201002180706.o1I764nl011236@mail.rootsweb.com>
In-Reply-To: <201002180706.o1I764nl011236@mail.rootsweb.com>


> Here is quite a bit of J1 Cohen data
> on the haplogroup J project at
> http://www.familytreedna.com/public/Y-DNA_J/default.aspx?section=yresults
> in the subgroup J1e Cohanim, P58+, L147+, L222-, YCAII=22-22.
> Is that the data that you used for your analysis?

Tim,

1) I didn't do the analysis. I just heard about it being done.

2) The Project you mention has a lot of data on both J1 and J2,
and it is already analysed into various important sub-clusters.

3) It is not the same thing as a J1 part of database of samples
collected from Cohens.

4) In my opinion the J2 part of J database that is
also interesting.



Sasson



On Thu, Feb 18, 2010 at 9:05 AM, Tim Janzen <> wrote:

> Dear Sasson,
> I think you bring up some good points below. One of the issues with
> intraclade TMRCA estimates using the variance method is that a dominant
> closely related group of haplotypes can "swamp" the data from one or more
> distantly related haplotypes. If you have a group of say 100 haplotypes
> and
> 95 of them are from descendents of a common ancestor who lived 1400 years
> ago and the other 5 are from a branch that shares a common ancestor who
> lived 4000 years ago then the data from the 95 haplotypes will skew the
> intraclade TMRCA estimate to be much lower than the true TMRCA if all 100
> haplotypes are included in the same dataset. The right thing to do in this
> situation would be to choose 5 or fewer random haplotypes from the group
> that descends from a common ancestor who lived 1400 years ago and pair
> those
> haplotypes with the other 5 are from a branch that shares a common ancestor
> who lived 4000 years ago for an intraclade TMRCA estimate.
> One way to spot clusters of closely related haplotypes is to check
> their genetic distances. This can help give information about clusters of
> haplotypes that might be skewing the TMRCA estimate lower. Analysis of the
> underlying tree structure such as Anatole is doing is also another way to
> get at this same information.
> This whole issue will become less and less of a problem as we get
> more complete Y chromosome sequences that help us better determine the Y
> SNP
> structure in haplogroup J1 and other haplogroups. Then we can group these
> haplotypes in smaller and smaller clusters.
> I would be interested in taking a look at the J1 Cohen data if it is
> available. There is quite a bit of J1 Cohen data on the haplogroup J
> project at
> http://www.familytreedna.com/public/Y-DNA_J/default.aspx?section=yresultsin
> the subgroup J1e Cohanim, P58+, L147+, L222-, YCAII=22-22. Is that the
> data
> that you used for your analysis?
> Sincerely,
> Tim Janzen
>
>
> -----Original Message-----
> From:
> [mailto:] On Behalf Of Sasson Margaliot
> Sent: Wednesday, February 17, 2010 9:06 AM
> To:
> Subject: Re: [DNA] "counting mutations" versus "GD from the modal"
>
> Let me give a specific example: the collection of J1 Cohens. It was fed to
> Generations2, returning 2300 years. Then it was examined according to
> Anatole's method, and it was discovered that the set has a prominent
> sub-set corresponding to a branch which is 1400 years old. The MRCA of
> the rest is more like 4000. All numbers are approximate, but the situation
> is precisely clear.
>
> You see, all the extra-precision of Generation2 algorithm didn't help at
> all.
>
> This is the famous Cohen problem, which is in the center of attention for
> more than ten years, the last 15 years, of hobbyists and academics alike -
> but it was ONLY possible to receive the right results by subjecting the
> data
> to Anatole's method.
>
> Sasson
>
>
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