Table S3a The pairwise coefficients of type I (θI) functional divergence between subgroups of bHLH-PAS proteins in animals
Vertebrate
Arthropod
BMAL2/BMAL1 BMAL2/NPAS2 BMAL2/CLK BMAL1/NPAS2 BMAL1/CLK NPAS2/CLK CYC/CLK
MFE Theta 0.72
0.47
0.53
0.93
0.93
0.06
0.64
MFE se
0.16
0.14
0.15
0.17
0.17
0.12
0.12
MFE r X
0.17
0.34
0.30
0.04
0.04
0.55
0.29
MFE r max 0.63
0.64
0.63
0.59
0.58
0.59
0.80
MFE z score -5.63
-4.00
-4.35
-6.23
-6.17
-0.49
-8.09
LRT Theta 10.66
17.49
9.85
15.97
21.26
0.80
50.48
Table S3b The pairwise coefficients of type II (θII) functional divergence between subgroups of bHLH-PAS proteins in animals
Vertebrate
Arthropod
BMAL2/BMAL1 BMAL2/NPAS2 BMAL2/CLK BMAL1/NPAS2 BMAL1/CLK NPAS2/CLK CYC/CLK
θII
0.08
0.30
0.26
0.45
0.49
0.00
0.25
θ SE
0.11
0.12
0.12
0.08
0.07
0.10
0.15
Ar
0.85
0.90
1.05
0.66
0.60
4.90
0.86
PIr
0.31
0.31
0.31
0.31
0.31
0.31
0.31
p
0.23
0.59
0.58
0.57
0.55
0.15
0.59
d
0.18
0.54
0.58
0.25
0.13
0.16
0.61
F00,N
0.41
0.25
0.29
0.31
0.33
0.52
0.20
F00,R
0.00
0.04
0.06
0.13
0.14
0.00
0.01
F00,C
0.03
0.05
0.06
0.12
0.14
0.01
0.03
Table S3c The pairwise coefficients of type I (θI) functional divergence between
subgroups of PER proteins in vertebrates
PER3/PER2 PER3/PER1 PER2/PER1
MFE θ
0.43
MFE se
0.10
MFE r X
0.39
MFE r max 0.67
MFE z score -5.42
LRT θ
34.50
0.21
0.10
0.47
0.59
-2.31
6.70
0.12
0.08
0.56
0.64
-1.61
4.16
Table S3d The pairwise coefficients of type II (θII) functional divergence between
subgroups of PER proteins in vertebrates
PER3/PER2 PER3/PER1 PER2/PER1
θII
θ SE
Ar
PIr
p
0.20
0.13
0.81
0.31
0.40
d
0.29
F00,N 0.17
F00,R 0.01
F00,C 0.02
-0.03
0.14
-1.42
0.31
0.36
-0.06
0.12
-0.19
0.31
0.30
0.45
0.24
0.00
0.02
0.36
0.30
0.01
0.01
Table S3e The pairwise coefficients of type I (θI) functional divergence between
subgroups of PHY proteins in angiosperms
PHYA/ PHYA/ PHYA/ PHYB/ PHYB/ PHYC/
PHYB PHYC PHYE PHYC PHYE PHYE
MFE θ
0.41
MFE se
0.05
MFE r X
0.40
MFE r max 0.67
MFE z score -10.68
LRT θ
0.31
0.05
0.40
0.58
-6.73
0.38
0.07
0.30
0.48
-5.94
0.32
0.05
0.39
0.57
-6.67
0.05
0.06
0.44
0.47
-0.89
0.19
0.08
0.33
0.41
-2.48
112.24 54.94 69.20 57.57 15.46 13.03
Table S3f The pairwise coefficients of type II (θII) functional divergence between
subgroups of PHY proteins in angiosperms
θII
θ SE
Ar
PHYA/
PHYB
0.06
0.06
1.69
PHYA/ PHYA/ PHYB/ PHYB/ PHYC/
PHYC PHYE PHYC PHYE PHYE
-0.07 0.01 0.05 -0.03 -0.08
0.06 0.06 0.06 0.05 0.06
-0.47 8.20 1.68 -1.50 -0.51
PIr
p
d
F00,N
F00,R
F00,C
0.31
0.41
0.46
0.26
0.01
0.01
0.31
0.41
0.52
0.27
0.01
0.01
0.31
0.43
0.55
0.26
0.02
0.01
0.31
0.41
0.47
0.26
0.01
0.02
0.31
0.27
0.32
0.32
0.01
0.01
0.31
0.44
0.57
0.27
0.02
0.02
Legends of Tables S5 a-f and S6 a-f
Type I divergence
MFE θ: coefficients of type-I functional divergence
MFE se: standard error of Theta-I
MFE r X: coefficient of correlation between clusters
MFE r max: maximum value of r X
MFE z score: determines if an r value follows the normal distribution (|Z| > 1.96)
LRT θ: likelihood ratio test
Sites: Position of amino acids in the alignment. For Tables S5 a, c and e, positions
2-153 of locate in DNA photolyase related domain, position 182-451 locate in FAD
binding domain
Type II divergence
θII: coefficients of type-II functional divergence
θ SE: standard error of Theta-II
Ar: radical changes under type-II functional divergence
PIr: radical changes under nonfunctional divergence
p: the proportion of (overall) differences between nodes
d: distance between nodes
F00,N: observed proportion of no difference in all substitutions between nodes
F00,R: observed proportion of radical changes in all substitutions between nodes
F00,C: observed proportion of conserved changes in all substitutions between nodes
Sites: Position of amino acids in the alignment. For Tables S5 b, d and f, positions 2153 locate in DNA photolyase related domain, position 182-451 locate in FAD
binding domain