Table 3.
Best-fitting model of sequence evolution for each locus
| Locus | Model | -lnL | AIC | α | I |
|---|---|---|---|---|---|
| LOC_Os01g01790 | TrN + Γ + I | 3,812.85 | 7,747.70 | 0.527 | 0.470 |
| LOC_Os01g09300 | K80 + Γ | 3,202.24 | 6,520.48 | 0.342 | - |
| LOC_Os01g11070 | HKY + Γ | 4,079.53 | 8,295.06 | 0.380 | - |
| LOC_Os01g13200 | HKY + Γ | 2,884.00 | 5,900.00 | 0.270 | - |
| LOC_Os01g19470 | HKY + Γ | 3,442.45 | 7,008.90 | 0.687 | - |
| LOC_Os01g21160 | TrN + Γ | 5,012.34 | 10,136.68 | 0.475 | - |
| LOC_Os01g24680 | TrN + Γ + I | 3,650.18 | 7,428.36 | 0.805 | 0.435 |
| LOC_Os01g37560 | HKY + Γ | 3,696.29 | 7,486.58 | 0.392 | - |
| LOC_Os01g39310 | K80 + Γ | 3,293.51 | 6,693.03 | 0.328 | - |
| LOC_Os01g48720 | HKY + Γ | 4,172.17 | 8,478.34 | 0.805 | - |
| LOC_Os01g53720 | HKY + Γ | 4,102.88 | 8,329.77 | 0.521 | - |
| LOC_Os01g55530 | K80 + Γ | 4,250.90 | 8,635.80 | 0.426 | - |
| LOC_Os01g56630 | HKY + Γ | 3,285.91 | 6,715.82 | 0.504 | - |
| LOC_Os01g60230 | HKY + Γ | 3,514.88 | 7,111.76 | 0.355 | - |
| LOC_Os01g61720 | TrN + Γ | 3,730.58 | 7,565.15 | 0.385 | - |
| LOC_Os01g62900 | TrN + Γ | 3,344.32 | 6,830.64 | 0.241 | - |
| LOC_Os01g67220 | TrN + Γ | 4,205.56 | 8,529.13 | 0.414 | - |
| LOC_Os01g68770 | TrN + Γ + I | 4,137.81 | 8,397.62 | 0.631 | 0.462 |
| LOC_Os01g70670 | K80 + Γ | 3,362.32 | 6,846.63 | 0.404 | - |
| LOC_Os01g72220 | K80 + Γ | 3,721.70 | 7,559.39 | 0.253 | - |
| LOC_Os01g73790 | TrNef + Γ + I | 2,953.10 | 6,028.21 | 0.689 | 0.617 |
| eIFiso4E | TrN + Γ + I | 1,592.24 | 3,300.49 | 1.004 | 0.666 |
| CRTISO | TVM + Γ + I | 1,515.13 | 3,162.26 | 0.807 | 0.621 |
| PinA | K80 + Γ | 1,345.73 | 2,779.45 | 0.243 | - |
| PinB | GTR + Γ | 1,460.81 | 2,993.62 | 0.264 | - |
| PSY2 | K80 + Γ + I | 1,210.07 | 2,530.14 | 0.648 | 0.596 |
| MATK | TVM + Γ | 4,255.67 | 8,659.34 | 0.373 | - |
| Supermatrix | GTR + I + Γ | 63,591.59 | 127,037.19 | 0.799 | 0.580 |
Γ: gamma distribution; I: proportion of invariable sites; lnL = log-likelihood; AIC: Akaike Information Criterion; α: shape parameter of the gamma distribution.