Re: Origin and Diffusion of mtDNA Haplogroup X

On Wed, 5 Nov 2003 15:37:24 +0100, [EMAIL PROTECTED] (mb) wrote:

>Gisele Horvat <[EMAIL PROTECTED]> wrote:
>
>> I wonder what coalescence time would have been determined if the
>> calculation had been based upon more than two sequences.  
>
>Btw. I was just evaluating a program I recently revised and let it trace
>haplogroups from a mtDNA collection. 
>
>At this occation I retrieved 'gi|29690980|Navajo_Na3X' which is
>identical to what is labeled Nav125 in Figure 1 of the paper. Since they
>didn't note the GenBank identifier I'd have to dig through the
>literature in order to look up if the sequences are actually the same.
>Something I'm to lazy to do since this stuff doesn't interest me that
>much.
>
>Case you eventually should have the GenBank ID for Nav125 you may post
>it here. If the ID's are not identical then there might at least exist
>three X2a seqs, although I don't think they missed one.

Michael,

Na3X (Mishmar's) is the Navajo sequence shown:

("...5 complete sequences (Lev2, MM, E18, Nav125, and Oj2) were taken
from the literature (Levin et al.1999; Maca-Meyer et al.2001; Mishmar
et al. 2003; Bandelt et al., in press)."

I have no idea why it was called Nav125 in Reidla's article.  

The authors went to the trouble of obtaining 5 additional complete Old
World haplogroup X sequences and they surveyed 13,589 Old World mtDNAs
but did not attempt to add, to the genetic record, one iota of Native
American haplogroup X information:

"The data obtained from the analyses of complete
mtDNA sequences belonging to haplogroup X were then
used to survey 13,589 mtDNAs (21,682 when mtDNA
data from the literature are included) from 66 populations
of Eurasia and North Africa (table 1).

This would be my main complaint.  The article is not really about
haplogroup X as the title suggests but, rather, about Old World
haplogroup X.  How can any group of researchers have a good knowledge
of the diversity of these sequences in the Americas when they are only
looking at two complete ones?  I don't want to complain too loudly,
though, because I'm greatful for all the RFLP information they
obtained.

Did you notice that the Navajo sequence had the variant at 14560 like
the X1 Druze example shown in Figure 1?  Reidla et al. failed to
mention it and yet, it seems unlikely to me that the same mutation
occurred in both Old World and New World haplogroup X sequences
independently and what about the recurrent 13708A variant in
sub-groups X2d and X2b?  This variant was considered to be definitive
of Eurasian haplogroup J.  Lev2 has two coding region mutations
(13708A + 12612G) in common with haplogroup J...  The authors did
mention that the 153G HVR II variant is found in *Native American*
haplogroup A sequences but did not really suggest a connection.  In
the New World, A should be closest to X based upon coding region
variants.

A couple of Old World haplogroups (I & N1b) which should be closer to
X than most European/Near Eastern haplogroups have the 1719A variant.
Therefore, how can the absence of it in certain sequences be
indicative of the "root" haplogroup X sub-group?  There are many
unanswered questions...  Certainly, as Doug Weller suggested, this is
not the last word on the subject.

Gisele