From: rybicki@uctvax.uct.ac.za
Newsgroups: bionet.molbio.evolution
Subject: virus evolution / phylogenies
Date: 13 Aug 92 17:32:10 +0200
Organization: University of Cape Town

this may be a re-post: I never found out whether I got it on the Net
originally!

Dear evolutionists:

I am interested in the molecular evolution of both RNA and DNA plant viruses,
to the extent that I have been semi-obsessed for the last few years with
comparing sequences and doing phylogenetic reconstructions.  So much so that my
bench work has suffered; however, now everything does what it is supposed to,
CLUSTALV and PAUP and PHYLIP (and Hennig86) are working fine, and the trees 
are looking good.  I can bootstrap, and draw meaningful-looking trees.  I am
now getting onto the shaky ground of making sense of what the perceived
phylogenies mean - and I'm talking about do they mean the viruses diverged
around the time of the angiosperm radiation, or are they tied up with the
Gondwanaland breakup, and so on.  As far as I am aware there is precious little
available in the literature on virus molecular clocks, whether RNA or DNA, and
especially not for plant viruses.  I must say that although I am quite prepared
to believe that RNA viruses POTENTIALLY evolve much faster than DNA, that as a 
result they have pretty much got to where they're going in their niche, and do
not vary much IN THAT NICHE, because to do so is to lose fitness rapidly -
therefore, RNA virus ancestry can probably be traced a lot further back than
most people would believe.  I know Adrian Gibbs seems to believe this too - I
would be most interested in other (informed) opinion!  I am particularly
interested in potyviruses, and have a database of 45+ coat protein sequences of
poty- and poty-like viruses that tells me that poty-like viruses diverged
rather far back - and as all the poty-like are viruses of monocots, and
potyviruses sensu stricto are mainly viruses of dicots, I would like to believe
that the deep divides one can see in phylogenetic reconstructions from coat
protein data reflect host plant evolution - perhaps even traceable back to the
monocot-dicot divergence?  Any news on that by the way?  Any advance on 200
Myr, and what did ancestral plants look like before tyhe split (M or D?).

As for plant DNA viruses, I am working with geminiviruses: these are +/-2700
nuc ssDNA circular-genome beasties with 2 genome components
(whitefly-transmitted viruses of dicots, mainly New World); 1 genome component
and infect dicots, whitefly transmitted (Old World); 1 component and infect
dicots, leafhopper-transmitted (mainly New World); or 1 component and infect
Gramineae, leafhopper transmitted.  The pattern of divergence of the
Gramineae-infecting viruses is fascinating, as viruses found in and around
Africa group in a cluster distinct from viruses from elswhere, as do viruses
from Australia.  These viruses also have the deepest divergences between
sequences; all the 2-component viruses are quite closely related and indeed
share the same vector - all recently diverged from one source?  And how recent
is recent if they have tightly-conserved little DNA genomes which cannot be
allowed to vary much?  Why no Gramineae viruses from the Americas?  Why are the
dicot-infecting whitefly-transmitted one-component viruses most closely (though
distantly) related to African cassava mosaic?  Whence came the other component? 
Are the leafhopper-transmitted one-component viruses ancient (and how ancient?)
recombinants between dicot-whitefly and monocot-leafhopper viruses?

And who cares?

I DO!  Anyone with any ideas, please write.

Ed Rybicki
Dept Microbiology
University of Cape Town
PB Rondebosch, 7700
South Africa

(internet) ed@micro.uct.ac.za
-- 
 _________________________________________________________________________
|                                 |                                       |
|  Ed Rybicki                     |    Now you've got the hang of it      |
|  Dept Microbiology              | There's nothing you can't do with it  |
|  University of Cape Town        |         If you're very into it        |
|  PB Rondebosch 7700             |         You can't go wrong....        |
|  South Africa                   |                                       |
|  fax 27 21 650 4023             |              - Mad John               |
|  ed@micro.uct.ac.za             | (Ogden's Nut-Gone Flake, Small Faces) |
|_________________________________|_______________________________________|