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. 2017 Mar 13;91(7):e01659-16. doi: 10.1128/JVI.01659-16

TABLE 1.

Synonymous and nonsynonymous substitutions by cladelet and surface exposure, with interaction coefficients from fixed- and random-effects generalized linear modelsa

Clade Buried
 Exposed
 Interactions
xN /cdn for xN xS /cdn for xS xN/xS xN /cdn for xN xS /cdn for xS xN/xS Fixed Random
c32 (m) 26 0.058 383 0.853 0.068 139 0.419 309 0.931 0.450 0.236 1.853
c23 23 0.051 277 0.617 0.083 90 0.271 207 0.623 0.435 −0.076 1.670
c29 31 0.069 268 0.597 0.116 77 0.232 212 0.639 0.363 −0.531 1.534
c31 12 0.027 164 0.365 0.073 46 0.139 152 0.458 0.303 −0.966 1.480
c21 12 0.027 157 0.350 0.076 55 0.166 149 0.449 0.369 0.082 1.551
c8 10 0.022 171 0.381 0.058 43 0.130 148 0.446 0.291 0.018 1.469
c6 27 0.060 281 0.626 0.096 114 0.343 235 0.708 0.485 0 1.746
c19 12 0.027 194 0.432 0.062 45 0.136 133 0.401 0.338 −0.119 1.471
c17 24 0.053 300 0.668 0.080 90 0.271 231 0.696 0.390 −0.119 1.662
c11 18 0.040 175 0.390 0.103 45 0.136 138 0.416 0.326 −0.524 1.425
c12 24 0.053 286 0.637 0.084 69 0.208 212 0.639 0.325 −0.384 1.545
c36 24 0.053 166 0.370 0.145 45 0.136 136 0.410 0.331 −0.812 1.379
c38 (m) 3 0.007 115 0.256 0.026 41 0.123 96 0.289 0.427 1.175 1.502
c51 16 0.036 196 0.437 0.082 42 0.127 143 0.431 0.294 −0.475 1.415
c55 8 0.018 117 0.261 0.068 20 0.060 105 0.316 0.190 −0.524 1.226
c54 11 0.024 173 0.385 0.064 34 0.102 130 0.392 0.262 −0.312 1.376
c41 12 0.027 170 0.379 0.071 33 0.099 147 0.443 0.224 −0.429 1.359
c48 18 0.040 167 0.372 0.108 46 0.139 132 0.398 0.348 −0.502 1.434
c43 (m) 37 0.082 428 0.953 0.086 233 0.702 387 1.166 0.602 0.400 2.036
Major 282 3,262 0.086 894 2,610 0.343 ϕ2 = 0.055
minor 66 926 0.071 413 792 0.521 ϕ2 = 0.111
Total 348 4,188 0.083 1,307 3,402 0.384
a

Clades are in tree order as displayed in Fig. 2. xN, number of nonsynonymous (amino acid) substitutions; xS, number of synonymous nucleotide substitutions;/cdn, substitutions divided by codons in buried (449) or exposed (332) sites; fixed, interaction coefficients from the fixed-effects model (GLM); random, interaction coefficients from the random-effects model (GLMER); ϕ2, square of Pearson's phi coefficient (χ2/n). Minor-group clades (boldface) show elevated proportions of nonsynonymous substitutions.