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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.