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From: Bonnie Schrack <>
Subject: Re: [DNA] Y chromosome SNP occurring in More than one PaternalLineages
Date: Sun, 21 Feb 2010 19:21:46 -0500


Thomas wrote:
> 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.
Thank you, Thomas! I'm so glad to see you posting this, which I hope
will help people learn about this new understanding of Y SNPs. As some
may know, L88.2 is the SNP that was found in my father's sample (its
first known occurrence in J), and then Thomas, exploring the region,
found a whole string of other SNPs.

Thomas wrote:
> 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.
Here I have to remind Thomas that according to the information he sent
me in September of last year, it was haplogroup E1b1a (E-M2) which had
the X-Y recombination event with almost all of the same SNPs; and the J
SNP that was not present in E-M2 was L198, the SNP that was unique to my
father's lineage. He wrote at that time:
> There is certainly no doubt that your dad has received the
> polymorphisms through an independent X-Y recombination event than hg E-M2.
>
> . . . we need to add two new L markers to the list:
> L197 = ChrY:16105247 T to C in order to give it a unique name.
> L198 = ChrY:16105255 A to C as a new UEP downstream of J-L26/L27
>
> L198 should get the defining SNP of your father's branch.

Now, I'm afraid I have to disagree with Vince, who I respect, and
usually agree with on most things. He wrote:
> 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.
If a SNP were *not* a product of recombination, and were found to have
mutated in more than one haplogroup, these multiple mutations could be
caused by an unstable location on the Y chromosome which was prone to
shift back and forth unpredictably between two alleles. This would
make such a location entirely unsuitable for use on the phylogenetic
tree. A lineage could be derived for it, and if the SNP changed back,
descendants could be ancestral. I believe you can think of examples of
this.

However in the case of a SNP occurring more than once which was caused
by recombination events from the X, there would not be any reason to
expect it to be unstable, or shift back to the ancestral state. Would
it be possible for a recombined block from the X (or another chromosome)
to revert back to the normal Y sequence? I don't know whether there
would be a way for that to happen. I hope Thomas or others who have
in-depth knowledge of molecular biology will reply.

One of the more recent articles to discuss the new view that there is
frequent X-Y recombination is this:

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDD-4WNH0NH-6&_user=10&_coverDate=07%2F10%2F2009&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1215931823&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=fd546a8ee96b865de3898678e1d67f34
Am. J. of Human Genetics
Volume 85, Issue 1, 10 July 2009, Pages 130-134
doi:10.1016/j.ajhg.2009.06.009
*
Gene Conversion between the X Chromosome and the Male-Specific Region of
the Y Chromosome at a Translocation Hotspot*

Zoƫ H. Rosser, Patricia Balaresque and Mark A. Jobling
Published online: July 2, 2009.

Outside the pseudoautosomal regions, the mammalian sex chromosomes are
thought to have been genetically isolated for up to 350 million years.
However, in humans pathogenic XY translocations occur in XY-homologous
(gametologous) regions, causing sex-reversal and infertility. Gene
conversion might accompany recombination intermediates that resolve
without translocation and persist in the population. We resequenced X
and Y copies of a translocation hotspot adjacent to the PRKX and PRKY
genes and found evidence of historical exchange between the
male-specific region of the human Y and the X in patchy flanking
gene-conversion tracts on both chromosomes.* The rate of X-to-Y
conversion (per base per generation) is four to five orders of magnitude
more rapid than the rate of Y-chromosomal base-substitution mutation*,
and given assumptions about the recombination history of the X locus,
tract lengths have an overall average length of not, vert, similar100
bp. Sequence exchange outside the pseudoautosomal regions could play a
role in protecting the Y-linked copies of gametologous genes from
degeneration.

I hope we can bend our minds around this new paradigm and explore its
implications.

I also have some great news which I haven't shared until now. Since
September we had not found any other member of J who had these SNPs,
although I've supposed that a couple of other Swiss families whose
haplotypes are extremely similar to ours would also be positive for them.

Recently, however, one other sample has finally been found positive for
both L88.2 and L198, and this is very interesting. He's from the
Al-Ahsa region of Saudi Arabia, along the Gulf, where a concentration of
J2 is found. We are actively investigating what the ancient origins of
his family may have been. This is a 49/67 match, which as far as I can
tell, indicates a common ancestor very likely lived sometime in the last
2000 years, probably between 1600 and 1800 years ago. This is why
Thomas can now say "a small group of J2 persons have all SNPs. . ."
And I now have some reason to believe that my paternal lineage was not
brought to Europe by the migrations of Neolithic farmers.

Bonnie






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