A mutant 9°Nm DNA polymerase was adopted by Illumina Solexa, but the mutation sites are unknown due to commercial consideration [12].
Genetic drift thus would fix excessive slightly deleterious mutations in synonymous sites, due to Hill-Robertson interference among linked loci.
Additionally, we can expect genetic diversification among initially identical genomes due to the high mutation rate at microsatellite sites, due to internal recombination, duplication, or deletion involving dispersed genomic repeats (such as similar, but non-identical, viral elements), and due to the accumulation of novel viral sequences.
Author's response: Because we use the rate of only parallel synonymous evolution as a proxy for mutation rate, heterogeneity of the rate of evolution across synonymous sites, due to heterogeneous mutation and/or selection, should not be a problem.
This context-specific approach was also adopted by Radivojac et al. who developed a model using the output of phosphorylation-site predictor DisPhos to assess the probability of losing or gaining phosphorylation sites due to mutation.
Instead of searching for dissimilarities in a nucleotide sequence, the RFLP methodology identifies only the differences associated with the presence/absence of endonuclease recognition sites due to mutations, insertions or deletions.
The greater number of mutation sites identified in the present study was likely due to the larger number of strains sequenced, which increased the probability of detecting different mutation sites.
The more complex the coevolutionary network is for a particular site, the greater the selection coefficient may be against a mutation at that site due to the dramatic effect that this mutation would have on other coevolving protein regions.
Population genetic theories predict a time-dependent rate at constrained sites (but not at neutral sites) due to the removal of slightly deleterious mutations over time.
Interestingly, 75.9%, 84.9% and 100% of the mutation sites identified in 971-5, 972-4, and R955 occurred in polymorphic sites.
