retroviruses; mammals

[Eric Zurcher]

At 14:06 29/09/99 PDT, Ken Kinman wrote:
>     Although many viruses are probably "escaped genes", I think the
>statement by Margulis and Schwartz is perhaps a little simplistic.
>     I would guess that viruses have been popping in and out of genomes
>since the origin of life (pardon my using non-scientific jargon like
>"popping in and out").  It would not surprise me at all if it turned out
>that all DNA viruses (for example) had a common viral ancestry independent
>of the genes they might borrow from their hosts.  Wouldn't these borrowed
>host genes would be the first to go when a virus adapts to a new kind of
>host (e.g., pull out the old "reptile" domain and plug in a new "mammal"
>domain).
>     Whether you want to call them alive or not really doesn't matter much
>to me.   But until I am told otherwise by a virologist with convincing
>arguments, I will hold onto my belief in a very ancient origin of viruses,
>and that their histories may eventually be traced.  Any virologists
>listening in?
>                  -------Ken Kinman

Well, folks, I'm neither a virologist or a taxonomist, but a "computer guy"
who has had the good fortune of working with both, so perhaps I can add to
this discussion.

Viral taxonomy is a bit different from that of other organisms (assuming we
regard viruses as organisms at all). Virologists have there own (rather
different) code of classification and nomenclature (available at
<http://www.ncbi.nlm.gov/ICTV/rules.htm>). The concept of a "species" is
certainly fuzzy; the code gives this definition: "A virus species is
defined as a polythetic class of viruses that constitutes a replicating
lineage and occupies a particular ecological niche". (Ken will probably be
happy to note the  mixture of "cladistic" [replicating lineage] and
"eclectic" [ecological niche] elements of this definition.)

Our knowledge of viral evolution has changed a lot recently with the advent
of relatively cheap and easy genome sequencing. I get the impression from
what I've read that there is apparently a substantial amount of lateral
gene transfer going on (this seems to be true for bacteria as well). For
viruses, this transfer might be virus-virus or virus-host. In any case,
some researchers suggest that there can be no clear phylogeny for viruses
(or bacteria) as organisms - instead we have to look at the phylogenies of
genes (or perhaps segments or clusters of genes). Alternatively, I suppose,
one could accept the notion of organismal phylogenies, but these would
nearly always be highly reticulate.

Regarding the notion of viruses being escaped genes, I believe there is
some debate as to whether Barbara McClintock's transposons are best
regarded as plant genes, or very specialized plant viruses.

Here's a bit of additional grist for the mill. The following is an abstract
of a paper by Luis Villarreal of UC Irvine, presented at the recent
International Congress of Virology in Sydney:

=======================================================================

"Representations of the Tree of Life do not generally include possible
contributions to host evolution by viruses. However, recent results of
whole genome analysis suggest that lateral gene transfer is much more
prevalent than previously recognized. The DNA replication proteins of
bacteria and eukaryotes are fundamental to cell function and have clear
functional homologs between these orders [sic]. However, these replication
gene sets have dissimilar sequence and hence appear to have an unrelated
evolutionary lineage which presents a dilemma for connecting the base of
the Tree of Life. Yet the replication proteins of eukaryotes clearly
resemble the replication proteins of various DNA viruses, including viruses
of bacteria (phage T4). In this presentation, I examine the DNA polymerase
of viruses of simple eukaryotes (algae) and present a phylogenetic analysis
which supports the provocative thesis that persisting viruses may have
provided the origin of replication proteins of all eukaryotes and thus a
DNA virus may link the bacterial and eukaryotic orders [sic]. Thus is
appears that viral evolution should be considered as a crucial element of
host evolution."

=======================================================================



Eric Zurcher
CSIRO Division of Entomology
Canberra, Australia
E-mail: ericz at ento.csiro.au