Table 5 |
||||
| Results of maximum-likelihood models for exon 2 of the DQB1 gene | ||||
| Model code | P | Log-likelihood | Parameter estimates | Positively selected sites |
| M0(one ratio) | 1 | −1067.274 | ω=0.496 | None |
| M1a(nearly neutral) | 1 | −1007.026 | p0= 0.869 (p1= 0.131) | Not allowed |
| M2a(positive selection) | 3 | −989.138 | p0=0.818, p1=0.176(p2= 0.006) ω2= 8.276 | 1V,6M,18L,20T,48S,49S,67L,72R,77L,79L,81T |
| M3(discrete) | 4 | −994.628 | p1= 0.059 (p2= 0.018) ω1= 0.076, ω2= 3.390 | Not allowed |
| M7(beta) | 2 | −1007.600 | p= 0.006, q= 0.036 | Not allowed |
| M8(beta and omega) | 4 | −989.309 | p0= 0.994 (p1= 0.006) p= 0.005, q= 0.020, ω= 8.643 | 1V,6M,18L,20T,22Y,29Y,30A,38E,48S,49S,62G,63T,67L,72R,77L,79L, 81T |
P is the number of parameters in the ω distribution, ω is the selection parameter, and pn is the proportion of sites falling into the ωn site class. For models M7 and M8, p and q are the shape parameters of the β function. Positively selected sites were identified in models M2a and M8 by the Bayes empirical Bayes procedure (Yang et al. 2005). Sites inferred under selection at the 99% level are listed in bold, and those inferred at the 95% level are shown in italics.
Luo et al. BMC Evolutionary Biology 2012 12:207 doi:10.1186/1471-2148-12-207
