Supplementary Table 1. Results of Analysis of an Alignment of GH and CSH Coding Sequences

Supplementary Table 1. Results of analysis of an alignment of GH and CSH coding sequences using codeml.

1A. Analysis using model 1. This is the free-ratio model; dN/dS is not constrained so there is a different dN/dS on each branch. The model allows testing of whether dN/dS varies significantly among branches. DF: degrees of freedom.

lnLikelihooddN/dS

model 1 -2664.46variable

model 0 (NULL) -2701.85 0.334

2xΔlnLikelihood 74.78 (P <0.001; 38DF)

Conclusion: dN/dS varies among branches

1B. Analysis using model 2. For this model two dN/dS ratios were allowed, one for the branch leading to CSHs (the branch shown as a thick line in Fig. 7) and one for all other branches. This allows testing for adaptive evolution on the branch to CSHs. For the NULL, dN/dS is fixed at 1.00 on this branch.

lnLikelihooddN/dS

branch to CSHs all other branches

model 2 (2dN/dS values)-2691.01 13.980.287

model 2 (NULL)-2693.90 1.000.289

2xΔlnLikelihood 5.78 (P< 0.05; 1DF)

Conclusion: dN/dS on branch to CSHs significantly >1.0; adaptive evolution occurred on this branch

1C. Testing for adaptive evolution on branch to CSHs using branch-site model A. For the NULL, dN/dS is fixed at 1.00 on the branch leading to CSHs

lnLikelihood

model A-2668.51

model A (NULL)-2671.78

2xΔlnLikelihood 6.54 (P< 0.05; 1DF)

for model A:

dN/dS for site classes (K=4)

site class 0 1 2a 2b

proportion 0.43731 0.11591 0.35317 0.09361

background w 0.14238 1.00000 0.14238 1.00000

foreground w 0.14238 1.00000 30.2314 30.2314

for model A (NULL):

dN/dS (w) for site classes (K=4)

site class 0 1 2a 2b

proportion 0.00644 0.00172 0.78246 0.20938

background w 0.14353 1.00000 0.14353 1.00000

foreground w 0.14353 1.00000 1.00000 1.00000

Residues identified as probably subject to positive selection, with probability that dN/dS >1.0 :

26 S 0.513

28 F 0.990*

29 P 0.986*

31 I 0.931

39 N 0.867

43 R 0.985*

47 L 0.998**

52 F 0.608

66 E 0.911

73 Q 0.984*

74 N 0.758

75 P 0.865

79 L 0.599

83 E 0.988*

91 R 0.959*

111 Q 0.987*

118 Q 0.666

123 V 0.766

127 S 0.985*

131 G 0.986*

132 A 0.605

136 N 0.772

137 V 0.988*

139 D 0.555

160 P 0.909

166 F 0.687

180 D 0.987*

191 Y 0.778

206 I 0.933

Conclusion: adaptive evolution occurred on branch to CSHs; 29 residues identified as probably subject to positive selection.