TABLE 3.

ML analysis of the evolution of RYMV coat protein with models allowing ω to vary across amino acid sitesa

ModelbMLLikelihood ratio testP valuef
ωcω maxdFe
M00.12M0 vs M2<0.001
M10.25M1 vs M2<0.001
M20.120.300.27M0 vs M3<0.001
M30.121.930.01M1 vs M3<0.001
M70.12M2 vs M30.17
M80.121.980.01M7 vs M80.36
  • a Results were obtained with the CODEML program implemented in PAML.

  • b Models M0, M1, and M7 assume that no amino acid sites are under diversifying selection, whereas M2, M3, and M8 allow sites with a ω of >1.

  • c Mean value of ω over the whole ORF.

  • d Maximum ω category.

  • e Estimated frequency of sites belonging to the maximum ω category.

  • f Probability that twice the difference between the log likelihoods is smaller than a χ2 distribution.