Archiver > GENEALOGY-DNA > 2010-03 > 1268622059

From: Bonnie Schrack <>
Subject: Re: [DNA] Clades, Definitions, Discoveries, FTDNA
Date: Sun, 14 Mar 2010 23:00:59 -0400

Steve wrote:
> That really is not going to happen. The mutation rate for SNPs is on the order of 1 time 10 to the negative 9th per generation. The whole point of a SNP is that it is a one time mutational event in human evolutionary history, occurring at one base pair out of about 3 billion base pairs total in the human genome, that will be passed down to all descendants of that individual. L21+ will only have occurred in the descendants of the first individual to have L21, the common ancestor. The man in J1 will not have this polymorphism.

Let me second what Mike wrote. It absolutely does happen, and
frequently. Furthermore, Thomas Krahn has been arguing for a new
understanding of SNP formation on the Y chromosome, together with a
number of other scientists -- that a large number of these SNPs aren't
the product of 'de novo' mutations, but are copied from the X or other
chromosomes. The Y is* not* non-recombining, after all. I realize this
is a big leap for people to make, after years of thinking the Y existed
in splendid isolation!

We're finding tremendous numbers of new SNPs in J, but quite a number of
them are known to have also occurred in one or two other haplogroups.
The latest example is M359, found in some 23andMe results. As long as
there is nothing 'wrong' with this SNP, i.e., it isn't part of an STR or
anything like that, it should become M359.3 in J2a, which will be a
subclade directly downstream of M410. I predict that it will turn out
to be upstream of P279, and then we'll really have to get creative about
how to rename the J2a clades! I'm thinking it might work best to call
M359 J2a3, and P279, J2a3a, to avoid having to rename everything else.

But all this is assuming that when Thomas tests more J2a* members,
someone other than the one guy turns out to be derived for M359! He's a
member of a great cluster in J2a* which has become much more
well-defined in the past year or so. They all share a deletion in
DYS447. We now have about ten lineages in the J project that are either
members or strong candidates. I'm very hopeful that this SNP will be
able to define this J2a* "Cluster A" as a formal subclade.

This is just one of many examples. The vast increase in our knowledge
of Y SNPs is revealing that there are many fewer *unique *SNPs than we
had thought. It's not going to be practical to throw them out of the
tree. If a SNP is found three times in the tree, who is to say that
it's valid in the haplogroup where it first appeared in the tree, but
not the second or third haplogroup where it's found? If you tried to
take out all the SNPs with multiple occurrences, you would be left with
a barren tree...


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