Table 2.

Evidence of positive selection among 82 amino acid residues of L. yavapaiensis MHC class IIB PBR sequences

MethodLRT for model allowing ω > 1 rate classes*Percentage of sites in ω > 1 rate classesMean ω per ω > 1 rate class
Rate class
 PARRIS9.16 (0.01)15%4.3
 Evolutionary fingerprint26.1 (0.006)27%4.4
Codon-specificCodon 3 dN–dSCodon 18dN–dSCodon 46 dN–dS
 SLAC18.1 (0.09)
 FEL1.1 (0.03)0.93 (0.03)0.74 (0.04)
 REL3.2 (0.99)3.3 (0.99)
  • dN–dS, normalized difference between nonsynonymous substitutions per nonsynonymous sites (dN) and synonymous substitutions per synonymous sites (dS); FEL, fixed-effects likelihood; LRT, likelihood ratio test; PARRIS, partitioning approach for robust inference of selection; PP, posterior probability; REL, random-effects likelihood; SLAC, single likelihood ancestral counting; ω, dN/dS ratio.

  • *Values in parentheses are P values.

  • Values in parentheses are P values/posterior probability.