Low levels of variation in ITS (Summary)

ROGER HYAM R.Hyam at RBGE.ORG.UK
Tue Mar 11 13:07:29 CST 1997


Dear All,

Back at the end of January I posted the following message:

******** Original Message *******
I would be interested in hearing from people who have tried to use
the ITS regions of nrDNA in phylogenetic analysis of morphologically
distinct organisms but who have not encountered sufficient variation
in the gene to get much resolution.

If anyone knows of places where this kind of experience has been
published I would also be interested, although I have a feeling it is
the kind of thing that doesn't get into print.

Answer off list if you like and I will put the results to the list if
I find anything interesting.
**********************************

I am now posting a summary of the replies I recieved. (Sorry if this
is a little delayed - I was waiting for some replies to further
leads.)

Low levels of variation were reported in a number of groups but often
on a second hand basis. (as in "I know a guy who didn't get any
variation", which is fine but I haven't got very far in contacting all
the 'guys' and so am loathed to list the groups here.)

It was felt that if low levels were encountered in a study then there
was little chance of the information being published, unless as a
foot note to other work. Because of this ITS appears to be more
useful in the liturature than it may actually be.

Two factors contribute to low levels of variation. Either a group has
evolved incredibly rapidly leaving no time for random mutations to
have occured or gene exchange is still occuring between members of
the study group causing mutations to be 'homogenised out'. It is
likely that both occur in some groups.

No progress was made in trying to spot groups for which ITS will be
useful and groups for which it will not. My hunch is to avoid things
that aren't fully sexually isolated for each other no matter what
their morphology. (but that is a general recommendation for
constructing phylogenies)

Two refernces were suggested by different contributers that may be
useful to those who are interested in this subject. These are:

Clark, Curtis.  1995.  Reconciling phenotypic and ITS sequence phylogenies
in the Encelia alliance (Asteraceae: Heliantheae) to study character
evolution.  Amer. J. Bot. 82(6), Supplement, p. 120.

Oxelman, B. 1996. RAPD patterns, nrDNA ITS sequences, and morphological
patterns in the Silene sedoides-group (Caryophyllaceae) - Plant Systematics
and Evolution  201:93-116.

The reason I posted the query is that I have detected little
variation in my work on Rhododendron subgenus Hymenanthes and, as I
am writing this up for a Ph.D., it would be nice to quote a few other
people who have similar 'problems'.

Many thanks to all who contributed.


Roger.




**********************
Roger Hyam
Royal Botanic Garden,
Inverleith Row,
Edinburgh, EH3 5LR
Scotland, U.K.
Tel. 031 552 7171
Fax. 031 552 0382
**********************




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