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Archiver > GENEALOGY-DNA > 2010-02 > 1266778615


From: Thomas Krahn <>
Subject: Re: [DNA] Y chromosome SNP occuring in More than onePaternal Lineages
Date: Sun, 21 Feb 2010 12:56:55 -0600
References: <mailman.6086.1266736315.2099.genealogy-dna@rootsweb.com> <003701cab314$5840ccc0$f7adcbc4@saphirconsult.local><E57761E5-F351-4464-AA23-E037C960DCC1@vizachero.com>
In-Reply-To: <E57761E5-F351-4464-AA23-E037C960DCC1@vizachero.com>


I am strongly favoring the theory that even most of the SNPs that we
observe are in deed products of recombination events.
The saga about a "non recombining Y" region (NRY) has been already
proven several times to be complete nonsense. Many mutations that we use
on the Y-tree can be traced back to highly similar sequences elsewhere
in the genome (often the X chromosome) that do in fact carry the derived
allele or even a complete pattern of multiple mutations that are
transferred as a block to the Y chromosome.

An impressive example of this kind is the L88 and neighboring SNPs.
http://ymap.ftdna.com/cgi-bin/gbrowse/hs_chrY/?start=16105232;stop=16105259;ref=ChrY;width=1024;version=100;grid=on;id=16a5bc02c5b6419841172f4b65599de2;label=CYT%3Aoverview-Ideogram-Palindromes-Genes-STRs-dbSNP-JW-KOREF-NA07022-NA18507-CV-YH-M-PS-other;h_feat=L88%40yellow

The complete set of mutations (L88, rs4048730, rs4048731, rs4048732,
L197, rs4048733, L198) can be found in the derived state at a highly
similar X chromosome region. In hg B the Y chromosome shows all the SNPs
except L197 in the derived state while a small group of J2 persons have
all SNPs including L197 in the derived status. So in case haplogroup B
is not downstream of J2 (which we are pretty sure because of hundreds of
other STRs and SNPs) this transfer must have happened at least twice at
independent occasions. The driving force behind such translocations is
usually recombination. This may not be necessarily a direct
recombination between the X and Y chromosome but it could be transported
by transposons ("jumping genes") or viruses.

In case of L192 (which Kamel was interested in) we have observed a
segment with an extremely high mutation frequency. This segment shows 16
SNPs on a single PCR product and at least 4 of them occur at different
haplogroups.
http://ymap.ftdna.com/cgi-bin/gbrowse/hs_chrY/?start=6813237;stop=6813572;ref=ChrY;width=1024;version=100;grid=on;id=16a5bc02c5b6419841172f4b65599de2;label=CYT%3Aoverview-Ideogram-Palindromes-Genes-STRs-dbSNP-JW-KOREF-NA07022-NA18507-CV-YH-M-PS-other;h_feat=L192%40yellow

Highly similar DNA sequences occur in the human reference genome at
various chromosomes, e.g:
Chr14:93128289-93128572
Chr12:23184339-23184607
ChrX:99774688-99774974
(and more)

Just by coincidence the Chr14 sequence carries a T at the L192
corresponding location. So this is likely where we got the derived
allele from.

I hope this helps,

Thomas

Vincent Vizachero wrote:
> Al gave a response already, and I agree that the "X crossover"
> scenario is highly unlikely.
>
> However I will also point out that even if the "X crossover" story
> were true the "usual" explanation and the imagined "X crossover"
> scenario are not actually different. As far as the Y phylogeny is
> concerned, you would still be looking at two different instances of
> the SNP. You would just have a different explanation. Biologically
> that might be interesting, but phylogenetically not so much.
>
> VV
>
>
> On Feb 21, 2010, at 11:38 AM, Kamel AL GAZZAH wrote:
>
>
>> The usual explanation of this, is that the same SNP happened two
>> times for
>> each Group in two sepoarate events.
>> But I wonder if the following senario is possible:
>> This SNP fisrts happened in X chromosome and then it has been
>> transmitted to
>> Y chromosome tby recombining two times, which means that two Y
>> Haplogroups
>> sharing the same SNP share a common Portion of X Chromosome.
>>
>
>
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