Table 2 |
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|
Parameter estimates and likelihood scores for site models in PAML |
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|
model |
l |
Estimates of parameters |
2Δl |
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 ωs = 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, ωs = 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, ω2 = 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, ωs = 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 |
|
|
||||
|
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. |
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|
Tian et al. BMC Evolutionary Biology 2009 9:202 doi:10.1186/1471-2148-9-202 |
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