Plant Virus Evolution


Eigen, M. Viral quasispecies. Scientific American 269(1), 32-39 (1993).
Escriu F,, Fraile A,, Garcia-Arenal F. The evolution of virulence in a plant virus Evolution 57, 755-765 (2003)
French, R., Stenger, D.C. Evolution of Wheat Streak Mosaic Virus: Dynamics of Population Growth Within Plants May Explain Limited Variation. Ann. Rev. Phytopath. 41 , 199-214 (2003)
Garcia-Arenal F., Fraile A., Malpica J.M. Variability and genetic structure of plant virus populations Ann. Rev. Phytopath. 39, 157-186 (2001)
Kimura, M. Neutral theory of molecular evolution Scientific American, 248 (5) 98- (1979).
Roossinck M.J. Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses. J. Virol. 76, 3382-87 (2002)


I- Red queen hypothesis (Leigh Van Valen)
A- Organisms can't "stand still" in evolutionary time - must mutate to maintain pace.
B- Contrasts to "essentialist" (fixed) view of species
II- Neutral evolution (Motoo Kimura)
A- Mutations with no selective advantage can become fixed in populations
B- Contrary to classical genetic thinking
C- Time required to "fix" a gene varies inversely with population size.
D- "Population bottlenecks" will favor fixation.
E- Now clear that "neutral mutations" are the most common sort
F- "Silent mutations", generally 3rd position (in the codon) provide the best evidence
G- Neutral mutations produce the most reliable "molecular clock"
H- Now clear that mutations cover the full range of neutral to highly selected

III- RNA polymerases have high mutation rate
A- 10-4 to 10-6 - no repair
B- Much more than one mutation per genome will be lethal (error catastrophe)
C- Mutation rate limits genome sizes
D- Much less than one mutation will prevent virus from "keeping up"

IV- Concept of "quasispecies" (Manfred Eigen)
A- Virus is actually a population (cloud) of sequences centering around a concensus
B- Accurate polymerase will give a resticted (narrow) population
C- Less accurate polymerase will give a relaxed (broad) population
D- One can imagine situations (i.e. different animal organs) where optimal sequences vary
E- Sequences one mutation removed from "viable" can be expected to recover
F- Seqeunces two or more mutations from "viable" are unlikely to recover
G- Actual situation in plant viruses seems closer to "B"
V- Mechanisms of sequence change
A- Point mutations
B- Indels (insertions - deletions) - these occur only in nonessential (unselected) regions.
C- Reassortment (multicomponent viruses) this is surprisingly rare
D- Recombination (usually by copy-choice mechanism)

VI- Origin of genes
A- Origins much harder to fathom than adaptations
B- Capsid
C- Movement protein - host mRNA transport protein
D- RNA polymerase - host polymerases

VII- Changing host range
A- In some specific cases point mutations will expand or contract host range
B- More often host ranges are "unable to expand"