Codon volatility does not reflect selective pressure on the HIV-1 genome.
Codon volatility is defined as the proportion of a codon's point-mutation neighbors that encode different amino acids. The cumulative volatility of a gene in relation to its associated genome was recently reported to be an indicator of selection pressure. We used this approach to measure selection on all available full-length HIV-1 subtype B genomes in the Los Alamos HIV Sequence Database, and compared these estimates against those obtained via established likelihood- and distance-based comparative methods. Volatility failed to correlate with the results of any of the comparative methods demonstrating that it is not a reliable indicator of selection pressure.
Pillai
Satish K
SK
University of California, San Diego, Stein Clinical Research Building, Room 325, 9500 Gilman Drive 0679, La Jolla 92093, USA.
Kosakovsky Pond
Sergei L
SL
Woelk
Christopher H
CH
Richman
Douglas D
DD
Smith
Davey M
DM
D005075:Biological Evolution; D003062:Codon / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D016013:Likelihood Functions; D011995:Recombination, Genetic; D012641:Selection, Genetic
D003062:Codon