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HIV's genome of RNA includes code for reverse transcriptase (RT), an enzyme that acts early in infection to synthesize a DNA genome off of an RNA template. The HIV genome also codes for protease (PR), an enzyme that acts later in infection by cutting long viral polyproteins into smaller, functional proteins. Both RT and PR represent potential targets for antiretroviral drugs. Drugs called nucleoside analogs (NA) act against RT, whereas drugs called protease inhibitors (PI) act against PR.
-Which of these makes determining the evolutionary relatedness of different species based on the amino acid sequence of homologous proteins generally less accurate than determinations of relatedness based on the nucleotide sequences of homologous genes?

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Silent mutations are nucleotide changes that do not result in changes to the resulting amino acid sequence. Therefore, they do not affect the function of the protein and are not useful for determining evolutionary relatedness based on protein sequence. However, they can be informative in determining relatedness based on nucleotide sequences. Gene duplications, translocation events, crossing-over, and independent assortment can all affect the resulting protein sequence and can be informative for determining relatedness based on protein sequence.

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