Table 4

Results of maximum-likelihood models for exon 2 of the DQA1 gene
Model code P Log-likelihood Parameter estimates Positively selected sites
M0(one ratio) 1 −774.550 ω=0.643 None
M1a(nearly neutral) 1 −760.293 p0= 0.723 (p1= 0.277) Not allowed
M2a(positive selection) 3 −752.443 p0= 0.911, p1= 0.033(p2= 0.056) ω2= 5.148 13T,16F,35G,42R,45E,46L,48K,50G,54P,56G,59R,61L,63T,64S,70I,71M,74R
M3(discrete) 4 −752.206 p0= 0.736, p1= 0.244 (p2= 0.018) ω1= 1.298, ω2= 8.174 Not allowed
M7(beta) 2 −761.268 p= 0.008, q= 0.028 Not allowed
M8(beta and omega) 4 −752.248 p0= 0.974 (p1= 0.025) p= 0.008, q= 0.023, ω= 7.292 10L,13T,16F,29Q,35G,42R,43W,45E,46L,48K,50G,51G,54P,56G,59R,61L,63T,64S,70I,71M,74R,79A

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.

Luo et al. BMC Evolutionary Biology 2012 12:207   doi:10.1186/1471-2148-12-207

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