Table 4.
Codeml analysis results of a mitocoding gene located on a NUMT that is shared among seven ape species
| Model | ln likelihood | ω values | Comparison |
|---|---|---|---|
| One ratio | lnL1 = 6,946.87 | ω = 0.06 | |
| Two ratio (fixed) | lnL2a = 6,905.41 | ω1 = 0.05, ω2 = 1 | |
| Two ratio | lnL2b = −6,902.98 | ω1 = 0.05, ω2 = 2.9 | 2Δ (lnL2a, lnL2b) |
| P = 0.027 (χ2, d.f. = 1) |
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Rate heterogeneity between the NUMT clade and the mitochondrial sequences was inferred by comparing a two-ratio model with a one-ratio model (single dN/dS = ω value for the entire tree). Positive selection was inferred from a two-ratio model and a fixed two-ratio model for which the dN/dS of the NUMT subtree was fixed to ω2 = 1. The tree and sequences used in the analysis are shown in Figure 6.
