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From: Bonnie Schrack <>
Subject: Re: [DNA] Challenge to YDNA J Gurus
Date: Thu, 01 Mar 2007 18:35:11 -0500


Hi Ken,

Thanks for the worthwhile challenge. I look forward to offering
something like this very soon for all who are interested, it's just that
I'm pretty tired at the moment. I just finalized my purchase of a new
(used) car yesterday, and today went to Motor Vehicles to get the new
tags, etc. Tomorrow is that panel discussion event. But I will look
for every opportunity to work on this.

I can certainly provide the modal haplotypes for a number of clades,
although the number of samples we have is not what I would really like
yet.

I can run a genetic distance matrix at Dean McGee's utilities site and
it will produce TMRCA estimates -- should I use the McDonald mutation
rates and the 50% probability?

I see that you don't want all 67 markers, but only the slowest mutating
ones. The trouble is that these rates differ by haplogroup. Do you
really think Chandler's rates are the ones I should go by? Why do you
specify only 30 markers out of 67? That means there are 37 that you
consider too fast. I wouldn't think it would be necessary to throw out
that many. Why don't you offer some suggestions about a cut-off for
fast vs. slow mutation rates.

I just took at look at John's article and I see that it only covers the
first 37 markers. Most of the last 30 of the 67 are slow-mutating. But
where do you suggest I should find estimates of their rates? I should
be able to see for myself which are mutating most frequently in our
project data, but I don't know if that would be objective enough.

Sorry if these mutation rates have been discussed a lot on the list
already, it's not possible for me to follow every discussion. After
all, when I need to go back and gather information on a given topic, it
will be there in the archive, and you are still there.

Best,

Bonnie


> It seems that the J specialists may have enough 67 marker haplotypes
> now to have determined 67 marker modal haplotypes for a number of
> robustly distinct clades in y-haplogroup J, including in J1 and in J2
> (I call such haplotypes "founders' haplotypes").
>
> If so, I believe it would be of interest to see a genetic distance
> matrix between those several founders' haplotypes.
>
> It is important, I believe, to with discipline pick the 30 or so
> slowest mutating markers from the 67 (using Chandler's rates, for
> example), paying no regard to which of these slow markers are
> particularly useful or not in identifying the separate clades. Paying
> such attention will bias the marker selection and increase the
> apparent time between founders. Picking the slow markers minimizes
> occurrences of unseen back mutations having taken place in the
> generational strings between the founders.
>
> This matrix of GDs will give an overview sense for the time periods
> which occured between the existences of the founders relative to
> haplogroup breakup times.
>
> Rough rule of thumb is to divide the GD by twice the sum of mutation
> rates for the 30 or so slow markers you chose to use. This is a
> characteristic time in generations between a split up of the parent
> clade to the times of the founders for the subclades.
>
> Most of us sense that J is a particularly old haplogroup by the
> standards of the other haplogroups commonly dealt with in Europe. It
> would be interesting to see the time scales that emerge from the GD
> matrix. Maybe someone has done this already, and I have just missed it?


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