"Rob Halgren" wrote in message
...
tennis maynard wrote:
Though I feel it would be more appropriate to comment in two weeks when
I receive my copy here at the end of the postal world, Ohio, if we must
jump the gun, I take my cue from your note to OGD quoting the article I
won't see for fourteen more days:

On page 135, second paragraph they write "The individual and combined
analyses demonstrate the distinctiveness of the molecular sequence data
of
Phrag. kovachii. All four plants of Phrag. kovachii were identical for
each
sequence analysed."

I think the key phrase is: "for each sequence analyzed". Indicating to
me that only certain parts of its DNA were analyzed. I'm not entirely
sure, but think items ALL of whose DNA has been sequenced are pretty
rare.

Why yes, I am a bioinformatician... This is what I do for a living. I
haven't seen the article on P. kovachii yet (and knowing how things
work, might not for a week). However, it is not at all unusual that
they might sequence four markers with identical sequence. Why?

They probably have selected genes that they know are well conserved.
While it is true that these genes will vary in sequence across long
evolutionary distances, they don't vary that much in the short term. In
fact, if they were really variable, we could never use those sequences
to determine the relationship between kovachii and other phragmipediums.

In a very abstract and simplified nutshell, it is the difference
between the marker sequences that gives an indication of how far apart
(in time) two species are. If you have only a few changes between the
species, you hypothesize that they are closely related. More changes
indicate that they may be more distantly related. However, you can't
have too many changes.

Why does P. kovachii look so different (even amongst themselves) if
they are identical at these four markers? Simple, these markers are
derived from genes that are required for survival (Cytochrome C,
ribosomal proteins, etc). The four examined don't reflect even a tiny
percentage of all the genes in the organism. Genes that have absolutely
required functions can't change that much (or they lose function).
Genes for flower size, color, and other things can (and do) vary quite a
bit, even in the same population. Quite a bit means (in humans, which
have been most studied for obvious reasons) 1 in every 100 bases or so.

Does that help?

Rob

You'll really like the article, Rob.

On page 134 Fig. 4 shows a portion of the ITS matrix (whatever that is).
Its 768 bases long. There are also gaps. (I understand the shotgun method
of sequencing DNA by necessity produces gaps.) But I'm not sure these are
the same sort of gaps.

The authors say that kovachii is separated from besseae by 29 bases, and
from schlimii by 48 (of the bases shown, they undoubtedly have more but
space allowed printing of only these 768).

Ok, I guess I'll have to defer discussion until everyone gets their copy of
'Orchids'.

K Barrett