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Subject: Re: [DNA] Variance Assessment of R:U106 DYS425Null Cluster
Date: Tue, 9 Feb 2010 12:53:54 +0000 (UTC)
In-Reply-To: <809631690.1414571265719065460.JavaMail.root@sz0002a.westchester.pa.mail.comcast.net>


>From: "Alister John Marsh" < >
>I am not a mathematician, so you may be able to correct me, but would not
the history of this group have a bearing on the expected number of
mutations?  What I mean is, suppose B, D, E, F, G, H were brothers (who have
identical haplotypes), and the other two A and C of unknown relationship to
the 5 brothers?  Would that in effect mean that comparing haplotypes A, B,
C, would be a more meaningful way to assess age since common ancestor using
your formula for this group?



Dear John,



You cannot group haplotypes without a certain and justified reason. "Suppose" and "what if" do not work here. When you toss a coin you cannot say - "what if a coin always lands on a tail, and heads are just aberrations? So we strike them out".



The criteria in haplotype handling which I have described earlier include haplotypes grouping, dissection of them onto branches, however, based on certain repetitive features in haplotypes, not single (random) mutations as in haplotypes A, B and C which you have mentioned. A haplotype tree dissects datasets into branches, however, sometime it can be done just visually (it is not preferred, but sometimes possible, in rather obvious cases).     



Having said this, I will move to your specific example.


>I have an example for you to consider.  Can you make anything of the 11
haplotypes of 37 markers below? (Haplotypes are shown below - AK)

>I don't know when the common ancestor was for this group, but I know dates
it must have been before, and can speculate dates it was probably before. (...)



>I don't know the ancestral haplotype. What do you think the ancestral
haplotype was? How far back do you estimate to the common ancestor using
your system, and what confidence interval range would you give for that
estimate?  I have been puzzling over this group for years, and it would be
interesting to see how your estimates compare to my current thinking on the
group.  

Of course I "can make anything" on that series. Thank you for it. The series is a bit more complicated compared to those I have shown earlier. It represents two subsets, or branches, or "mini-lineages" meaning that the principal lineage in the same, however, there was an offshot recently, just a few generations before present, and it created a fork. Hence, the dataset shows two "local lineages", each one with its common ancestor, which deviates from each other by four mutations in the 37 marker haplotypes.



It can be pictured as an iceberg with two tips, one small and one taller, however, deep underwater, it has its "common ancestor" of the both tips. That is why there is no a clearly visible base (ancestral) haplotype in your series. It is a superposition of the two series.



The age of one "tip of the iceberg" is about 400 years. It is of a larger subset, haplotypes "A" through "I" in your designation.  The age of the smaller subset, and only two haplotypes from it are shown in your series, is "formally" 50+/-50 years, and I tend to place it at 100 years before present. It is probably some older, when more haplotypes are included. Judging (quantitatively) from 4 mutations between them, their common ancestor lived about 825 years ago, in the 12th century, give or take a century.



Well, your call?      

Anatole Klyosov



*************************************



John:

For this group, I have many more haplotypes, but only the above complete to
37 markers.  The criteria I used for selecting this group, was that they
were all I had which were complete to 37 markers, so I have not tried to
make some tricky selection to mislead you.  Some of the above have been
tested to 130+ markers, and a number to 67 or 76 or more markers.

I have some speculative ideas about when the common ancestor might have been,
based in part on genealogical data which might imply opportunities for a
common ancestor to have lived.


I have an advantage over you in that I do have more marker
information, and some paper trail and context information.  But I would be
interesting to see how you evaluate this group based on the limited
information I have given you above.


A 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 16 17 17
 11 11 19 23 15 14 18 17 35 38 12
B 13 24 14 10 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 16 16 17
 11 11 19 23 15 14 18 17 35 39 12
C 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 16 16 17
 11 11 19 23 15 14 18 17 35 39 12
D 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 29 14 16 16 17
 11 11 19 23 15 14 14 17 35 39 12
E 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 17 17 17
 11 11 19 23 15 14 19 17 35 39 12
F 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 16 17 17
 11 11 19 23 15 14 19 17 35 39 12
G 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 16 17 17
 11 11 19 23 15 14 18 17 34 39 12
H 13 24 14 11 12 14 12 12 11 13 13 29 17 9 10 11 11 25 15 19 28 14 16 17 17
 11 11 19 23 15 14 18 17 35 39 12
I 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 28 14 16 17 17
 11 11 19 23 15 14 18 17 36 39 12
J 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 25 15 19 29 14 15 17 17
 11 11 19 23 15 14 18 17 35 37 12
K 13 24 14 11 12 14 12 12 11 13 13 29 16 9 10 11 11 26 15 19 29 14 15 17 17
 11 11 19 23 15 14 18 17 35 37 12




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