Table 5.
Likelihood Values and Parameter Estimates for SULT1A Genes
| Model | f.p.* | Log L | Parameter Estimates† | ||
| One-ratio | 39 | - 5,047.81 | KA/KS = 0.15 | ||
| Free-ratios | 69 | - 5,005.18 | KA/KS ratios for each branch shown in Figure 2 | ||
| Site-specific | |||||
| Neutral | 36 | - 5,021.14 | p0 = 0.48 | (p1 = 0.52) | |
| KA/KS 0 = 0 | KA/KS 1 = 1 | ||||
| Selection | 38 | - 4,884.89 | p0 = 0.41 | p1 = 0.13 | (p2 = 0.46) |
| KA/KS 0 = 0 | KA/KS 1 = 1 | KA/KS2 = 0.19 | |||
| Discrete (k = 2) | 37 | - 4,931.05 | p0 = 0.68 | p1 = 0.32 | |
| KA/KS 0 = 0.06 | KA/KS 1 = 0.77 | ||||
| Discrete (k = 3) | 40 | - 4,880.78 | p0 = 0.59 | p1 = 0.33 | (p2 = 0.08) |
| KA/KS 0 = 0.02 | KA/KS 1 = 0.31 | KA/KS2 = 1.24 | |||
| Beta | 37 | - 4,884.27 | p = 0.27 | q = 1.07 | |
| Beta+selection | 39 | - 4,879.97 | p = 0.30 | q = 1.33 | |
| p0 = 0.98 | p1 = 0.02 | KA/KS = > 2.0 | |||
| Branch-site specific | |||||
| Model A | 38 | - 5,013.29 | p0 = 0.48 | p1 = 0.49 | (p2 = 0.03) |
| KA/KS 0 = 0 | KA/KS 1 = 1 | KA/KS2 = > 2.0 | |||
| Model B | 40 | - 4,886.52 | p0 = 0.68 | p1 = 0.30 | (p2 = 0.02) |
| KA/KS 0 = 0.04 | KA/KS1 = 0.56 | KA/KS2 = > 2.0 | |||
*f.p. is the number of free parameters in each model. †Evidence for positive selection is shown in boldface. Proportions of sites in each KA/KS class, p0, p1, and p2, were not free parameters when in parentheses. Neutral site-specific model assumes two site classes having fixed KA/KS ratios of 0 and 1, with the proportion of sites in each class estimated as free parameters. Selection site-specific model assumes a third proportion of sites with KA/KS estimated from the data. Discrete model assumes 2 or 3 site classes (k) with the proportion of sites, and KA/KS ratios for each proportion, estimated as free parameters. Beta model assumes a beta distribution of sites, where the distribution is shaped by the parameters p and q. Beta+selection model assumes an additional class of sites having a KA/KS ratio estimated from the data. Model A, an extension of the neutral model, assumes a third site class on the 1A3/1A4 branch with KA/KS estimated from the data. Model B, an extension of the discrete model with two site classes (k = 2), also assumes a third site class on the 1A3/1A4 branch with KA/KS estimated from the data.