Plant Virus Evolution
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I- Red queen hypothesis (Leigh Van Valen)
A- Organisms can't "stand still" in evolutionary time - must mutate to maintain pace.
II- Neutral evolution (Motoo Kimura)
B- Contrasts to "essentialist" (fixed) view of species
A- Mutations with no selective advantage can become fixed in populations
III- RNA polymerases have high mutation rate
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
A- 10-4 to 10-6 - no repair
IV- Concept of "quasispecies" (Manfred Eigen)
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"
A- Virus is actually a population (cloud) of sequences centering around a concensus
V- Mechanisms of sequence change
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"
A- Point mutations
VI- Origin of genes
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)
A- Origins much harder to fathom than adaptations
VII- Changing host range
C- Movement protein - host mRNA transport protein
D- RNA polymerase - host polymerases
A- In some specific cases point mutations will expand or contract host range
B- More often host ranges are "unable to expand"