Hi Joe
Joe Felsenstein wrote in message <63acpl$ad5 at net.bio.net>...
>In article <637ntb$s0t at net.bio.net>, toni <toniv at iname.com> wrote:
>>Nobody talks about quasispecies?
>>The flip answer is "no, they don't". The more interesting answer is
>"should they?" It is important to talk about genetic variation in
>species. When someone working on humans or Drosophila does this, they
>say they are talking about genetic variation in natural populations.
>When a virologist talks about it, they say they are talking about
>quasispecies, which sounds infinitely more mysterious and novel.
>>So the question is, is anything gained by considering it as a
>discussion of "quasispecies" rather than "genetic variation"?
It turns out that when Eigen first introduced the term "quasispecies" he was
actually likening species to chemical species. He has a very precise
mathematical characterization of the quasispecies as the equilibrium
frequencies of a pool of closely related (read "similar") variants that
jointly act as an entity. These entities differ from host to host, so that
they behave as chemical species might. However, since each entity cannot be
characterized by a certain molecular form but rather the equilibrium
frequencies of different forms (equivalent, I think, to the largest
eigenvalue of the transition matrix), he used the term "quasispecies".
I must admit that slip-sliding between chemical and biological species
concepts is confusing. When I was first introduced to the term
"quasispecies" as it is used in HIV, I thought that it was "quasi-" because
viruses cannot truly be classified as species, but behave genetically as
though they are (at least in the case of HIV).
As to whether anything is gained by using the term "quasispecies", I guess
it depends on whether you are doing the kind of modelling that Eigen and his
co-workers are doing. Even if you are not, it may be suitable to adopt the
term simply to distinguish the swarm of viral variants that has no Latin
binomial from other biological entities that do.
-- Allen Rodrigo
