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Table 2 Parameter estimates and likelihood scores for site models in PAML

From: Evolution and functional divergence of NLRPgenes in mammalian reproductive systems

model

l

Estimates of parameters

l

Positively selected sites (BEB)

Nlrp4_mouse

M1a

-7999.63

ρ0 = 0.33

 

Not allowed

M2a

-7986.58

ρ0 = 0.28,(ρ1 = 0.67), ρs = 0.05

ω s = 3.93

26.09*

(M2a vs M1a)

2 sites > 95%

133C, 677V

M7

-7999.85

p = 0.04, q = 0.02

 

Not allowed

M8a

-7999.55

ρ0 = 0.34,(ρ1= 0.66),

p = 0.81, q = 6.69

27.56*

(M8 vs M7)

Not allowed

M8

-7986.07

ρ0 = 0.94,ρs = 0.06,

p = 0.20, q = 0.09,

ω s = 3.64

26.98*

(M8 vs M8a)

4 sites > 95%

133C, 153S, 657N, 677V

Nlrp9_mouse

M1a

-7140.29

ρ0 = 0.36043

 

Not allowed

M2a

-7107.99

ρ0 = 0.28, ρ1 = 0.66, ρs = 0.06,

ω 2 = 10.17

64.60*

(M2a vs M1a)

10 sites > 95%, 2 sites > 99%

106H, 123 E, 356F, 360L, 378R, 513E, 536V, 571V, 661L, 948A

M7

-7140.98

p = 0.02, q = 0.01

 

Not allowed

M8a

-7140.29

ρ0 = 0.36,(ρ1 = 0.64),

p = 0.01, q = 98.97

65.99*

(M8 vs M7)

Not allowed

M8

-7107.99

ρ0 = 0.94, ρs = 0.06,

p = 0.01, q = 0.01,

ω s = 10.20

64.60*

(M8 vs M8a)

11 sites > 95%, 6 sites > 99%

106H, 123 E, 278L, 356F, 360L, 378R, 513E, 536V, 571V, 661L, 948A

  1. NOTE. - Log-likelihood values (l) are given for each model. The value ωS is the average dN/dS ratio for sites under positive selection in the models M2a and M8, p and q are the shape parameters for the beta distribution of ω in M7 and M8. ρ0, ρ1, and ρS are the proportions of codons subject to purifying, neutral, and positive selection, respectively. * p value is significant at 0.001. Predicted positively selected sites with posterior probabilities > 95% are listed, and the sites with p > 99% are in boldface. Site numbers and amino acids refer to the reference sequences Nlrp4a (NP_766484) and Nlrp9a (NP_001041684) for the two datasets, respectively.