Table S2. Results of positive selection using site-specific models
Gene family
Lineage
d N / d S under
2Dl M2a vs.
2Dl M8 vs.
2Dl M8 vs.
M01
M12
M72
M8a2
M2a estimates
p0 = 0.4931, w0 = 0.1595
serine
Bd
0.4585
185.34**
193.05**
peptidase
bacteria
0.0118
0
0
2.39
Bd
0.6953
28.92**
28.86**
28.85**
oomycetes
0.3929
0
0
0
0.6429
132.04**
131.28**
127.86**
M2a3
p2 = 0.0690, w2 = 3.4028
14**
-
-
-
30, 19*,
p0 = 0.8499, w0 = 0.1103
DXX-DAB
p1 = 0.0000, w1 = 1.0000
-
p0 = 0.6276, w0 = 0.0000
p1 = 0.2532, w1 = 1.0000
DFB
oomycetes
0.2704
0
39.96**
38.90**
0.8835
100.35**
100.02**
100.02**
Bd
DX8
-
-
90, 21*,
p1 = 0.1676, w = 3.8022
b ( p = 0.0050, q = 0.0164)
139, 59*,
-
101, 18*,
8**
p0 = 0.5227, w0 = 0.0941
oomycetes
0.5229
86.52**
99.79**
p1 = 0.4020, w1 = 1.0000
82.72**
DXX-DXV
Bd
0.6522
p1 = 0.3876, w1 = 1.0000
23.10**
p2 = 0.1864, w2 = 2.9195
1
p1 = 0.1660, w = 4.5517
b ( p = 0.0126, q = 0.0163)
p1 = 0.0945, w = 5.3047
b ( p = 0.2479, q = 0.2952)
114, 2*
p1 = 0.2230, w = 2.6785
b ( p = 0.0235, q = 0.0304)
p0 = 0.4260, w0 = 0.0000
24.00**
p1 = 0.0236, w = 169.9797
b ( p = 0.4493, q = 0.7257)
41, 12*, 5**
p2 = 0.0754, w2 = 6.0483
23.36**
-
14**
-
-
p2 = 0.1541, w2 = 4.7513
37, 21*,
59, 13*, 6**
11**
p1 = 0.3725, w1 = 1.0000
M83
b ( p = 0.0535, q = 0.3036)
p2 = 0.1192, w2 = 4.6036
p0 = 0.4734, w0 = 0.0000
p1 = 0.1408, w = 6.3279
PSS under
43, 8*
p2 = 0.1501, w2 = 6.1007
Bd
M8 estimates
p1 = 0.0862, w = 2.6007
b ( p = 0.6592, q = 0.9363)
p1 = 0.4739, w1 = 1.0000
148.36**
PSS under
24**
23, 2*, 1**
146, 40*,
16**
59, 13*,6**
164, 22*,
3**
p0 = 0.5518, w0 = 0.1289
oomycetes
0.5923
169.59**
207.20**
p1 = 0.3664, w1 = 1.0000
159.34**
p2 = 0.0818, w2 = 11.3186
p1 = 0.0944, w = 9.8335
b ( p = 0.7937, q = 1.0542)
31, 17*,
61, 18*, 8*
p1 = 0.1371, w = 4.7019
b ( p = 0.0220, q = 0.0279)
91, 29*,
28, 11*, 4**
p1 = 0.0546, w = 9.6020
b ( p = 0.0202, q = 0.0168)
28, 11*, 4**
p1 = 0.0817, w = 17.0427
42, 18*,
27, 16*,
12**
p0 = 0.4690, w0 = 0.0000
Bd
0.7843
99.09**
98.83**
p1 = 0.4050, w1 = 1.0000
98.65**
p2 = 0.1260, w2 = 4.9696
DXX-DHA
p0 = 0.4309, w0 = 0.0247
oomycetes
0.6320
69.96**
71.46**
p1 = 0.5164, w1 = 1.0000
69.43**
p2 = 0.0526, w2 = 9.9395
p0 = 0.5433, w0 = 0.0000
DFA-DDC
Bd
0.6880
58.05**
58.48**
58.03**
p1 = 0.3756, w1 = 1.0000
36, 17*, 8**
oomycetes
0.2560
0
0.16
0
-
-
Bd
0.4980
28.56**
28.82**
28.51**
25, 8*, 3**
oomycetes
0.4726
82.51**
93.84**
87.67**
29, 13*, 9**
14**
13**
10**
-
-
28, 9*, 5**
DN17
40, 18*,
11**
1. The ratio average across all sites and lineages under PAML model M0.
2. Double asterisks represent for chi-square () test, while single asterisk represents .
3. Positively selected sites, the number of amino acid residues with the posterior probability (PP) of positive selection greater than 0.05. Double asterisks represent the number of sites with PP
>0.99, while single asterisk represents PP >0.95.
2
Table S3. Results of positive selection using branch-site models
Gene family
Model
ln L
Anull
-24280.5596
A
-24278.1363*
Anull
-6101.3305
A
-6101.3305
Anull
-15292.8392
A
-15292.8394
Anull
-11680.5755
A
-11675.7478**
Anull
-11622.7872
serine peptidase
DXX-DAB
DFB
DX8
DXX-DXV
Parameter estimates
p0 = 0.5906, p1 = 0.3718, p2 a = 0.0231, p2 b = 0.0145
Background: w0 = 0.2782, w1 = 1.0000, w2 a = 0.2782, w2 b = 1.0000
Foreground: w0 = 0.2782, w1 = 1.0000, w2 a = 1.0000, w2 b = 1.0000
p0 = 0.5171, p1 = 0.3186, p2 a = 0.1017, p2 b = 0.0626
Background: w = 0.2770, w = 1.0000, w2 a = 0.2770, w = 1.0000
Foreground: w0 = 0.2770, w1 = 1.0000, w2 a = 197.6290, w1 = 197.6290
p0 = 0.4227, p1 = 0.3908, p2 a = 0.0970, p2 b = 0.0896
Background: w0 = 0.1003, w1 = 1.0000, w2 a = 0.1003, w2 b = 1.0000
Foreground: w0 = 0.1003, w1 = 1.0000, w2 a = 1.0000, w2 b = 1.0000
p0 = 0.4227, p1 = 0.3908, p2 a = 0.0970, p2 b = 0.0896
Background: w0 = 0.1003, w1 = 1.0000, w2 a = 0.1003, w2 b = 1.0000
Foreground: w0 = 0.1003, w1 = 1.0000, w2 a = 1.0000, w1 = 1.0000
p0 = 0.3557, p1 = 0.3887, p2 a = 0.1221, p2 b = 0.1335
Background: w0 = 0.1047, w1 = 1.0000, w2 a = 0.1047, w2 b = 1.0000
Foreground: w0 = 0.1047, w1 = 1.0000, w2 a = 1.0000, w2 b = 1.0000
p0 = 0.2862, p1 = 0.3128, p2 a = 0.1916, p2 b = 0.2094
Background: w0 = 0.1047, w1 = 1.0000, w2 a = 0.1047, w2 b = 1.0000
Foreground: w0 = 0.1003, w1 = 1.0000, w2 a = 2.6825, w2 b = 2.6825
p0 = 0.3544, p1 = 0.3702, p2 a = 0.1347, p2 b = 0.1407
Background: w0 = 0.1073, w1 = 1.0000, w2 a = 0.1073, w2 b = 1.0000
Foreground: w0 = 0.1073, w1 = 1.0000, w2 a = 1.0000, w2 b = 1.0000
p0 = 0.2882, p1 = 0.3195, p2 a = 0.1760, p2 b = 0.1663
Background: w0 = 0.1228, w1 = 1.0000, w2 a = 0.1228, w2 b = 1.0000
Foreground: w0 = 0.1228, w1 = 1.0000, w2 a = 28.8214, w2 b = 28.8214
p0 = 0.5439, p1 = 0.2926, p2 a = 0.1063, p2 b = 0.0572
0
1
3
2b
PSS
13
-
-
104
Background:
Foreground:
A
-11620.6559*
Background:
31
Foreground:
Anull
-8100.5876
Background:
Foreground:
DXX-DHA
A
-8100.5876
Background:
-
Foreground:
Anull
-4466.5119
Background:
Foreground:
DFA-DDC
A
-4464.0021*
Background:
11
Foreground:
Anull
-4466.5119
Background:
Foreground:
DN17
A
-4464.0021*
Background:
35
Foreground:
4
Fig. S2. Amino acid residues that are critical to functional divergence between serine
peptidase clades A and B. Gaps of the alignment have been deleted using PAL2NAL.
The critical amino acid residues for functional divergence with posterior probability
higher than 0.95 are illustrated by the arrows.
5