I used DnaSP software to perform a nucleotide diversity analysis on a viral alignment file. After observing the data I saw that some positions have high values (0.79) and some positions have lower values (0.42). So what is the probable explanation for this?
Differing selection pressure on different genes, and on different regions of each gene. In the lentiviruses, for example, the pol gene is much more highly conserved than the env gene, because polymerase needs to be conserved to replicate the virus genome and it is not expressed on the surface of the virus where it could be exposed to host immune selection pressure. Within the pol gene, there are codon encoding the catalytic active site which are invariant across millions of years of evolution.
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