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As shown in this new figure supplement, the mutations are deleterious in all three backgrounds, supporting the idea that these mutations are constrained by epistasis inherent to NP itself.
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Despite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation.
There is theoretical arbitrariness in saying that, up to here the range of mutation is constrained by the system, and beyond here it is not constrained at all, when no reason is given for why such a dividing line should be placed at one point rather than another.
Large populations are constrained to near deterministic fixation of rare large-benefit mutations.
But these are constrained, too.
It was recently proposed that the mitochondrial mutation rate might consequently be constrained to low values in long-lived animals in order to avoid premature somatic senescence [ 10].
Although mutations at some loci will be constrained by function due to their requirement for growth or viability under the selection conditions, normal morphology, or ability to cross for genetic analysis, for example, the majority of mutations are expected to be unrelated to the selection.
Epistatic interactions can also constrain evolution, with some mutations tolerated only after critical compensatory mutations.
The linear trajectory of viruses in antigenic space - in which at each point in time there is only one dominant circulating strain - can be explained minimally as a result of immune pressure driving antigenic diversity that is constrained by both mutation rates and the effect of each individual mutation on the antigenic profile of the virus.
Identifying very recent changes in population growth is difficult largely because the rate at which such demographic changes are recorded is constrained by low rates of mutation.
Thus, despite being constrained by its housekeeping function, NPC1 appears to retains a sizeable sequence space accessible to adaptive mutation.
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