Table 1. Estimated parameters under different codon substitution models for OXTR, AVPR1a, AVPR1b, and AVPR2.
Model | dN/dS | Estimated parameters | ℓ | p value | |
---|---|---|---|---|---|
AVPR1a | M7: β | 0.1504 | [p=0.22139, q=1.22306] | -10046.63 | M7 vs M8 p < 0.001 |
M8: β&ω | 0.1399 | p0=0.95125, (p2 =0.04875), ω2=1.04782 | -10036.96 | ||
AVPR1b | M7: β | 0.1723 | [p=0.33171, q=1.56124] | -10988.96 | M7 vs M8 p < 0.001 |
M8: β&ω | 0.1709 | p0=0.96686, (p2 =0.03314), ω2 =1.39536 | -10973.98 | ||
AVPR2 | M7: β | 0.1123 | [p=0.17525, q=1.33373] | -5496.23 | M7 vs M8 p = 0.04 |
M8: β&ω | 0.1053 | p0=0.96649, (p2 =0.03351), ω2 =1.00000 | -5493.606 | ||
OXTR | M1a: Nearly | 0.0896 | p0=0.93893, (p1=0.06107) | -4401.07 | |
Neutral | |||||
(ω0=0.03039), (ω1=1.00000) | M1a vs M2a p > 0.999 | ||||
M2a: Selection | 0.0896 | p0=0.93893, p1=0.06107, (p2=0.00000) | -4401.07 | ||
(ω0=0.03039), (ω1=1.00000), ω2=36.81273 |
p0 = proportion of sites where ω < 1, p1 = proportion of sites where ω = 1, and p2 = proportion of sites where ω > 1 (selection models only); ω0 < 1 (negative selection), ω1 ≅ 1 (neutral or relaxing selection), and ω2 > 1 (positive selection). ℓ= Log likelihood values. Likelihood ratio tests were performed between neutral models (M1a- nearly neutral, and M7 - beta) and models that identify positive selection (M2a - selection, and M8, β&ω - beta +selection). The comparisons M1 vs M2 and M7 vs M8 had 2 degrees of freedom. Within parentheses: fixed parameters; within brackets: βparameters p and q. dN/dS = non-synonymous/synonymous rate ratio.