Table 1.
Parameter estimates for different model selection tests
| Gene name | Model | d.f. | 2ΔL | LRT P-value | Positive selection sites (BEB) |
|---|---|---|---|---|---|
| Site Model | |||||
| atpA | M2a vs. M1a | 2 | 21.874 | 0 | L308** |
| M8 vs. M7 | 2 | 113.077 | 0 | Dismiss | |
| M8 vs. M8a | 1 | 1.5231 | 0.2172 | Not allowed | |
| atpB | M2a vs. M1a | 2 | 11.6161 | 0.0029 | H123*, S252**, S474* |
| M8 vs. M7 | 2 | 111.2862 | 0 | Dismiss | |
| M8 vs. M8a | 1 | 0.5467 | 0.4597 | Not allowed | |
| atpE | M2a vs. M1a | 2 | 0 | 1 | Dismiss |
| M8 vs. M7 | 2 | 14.7578 | 0.0006 | W20*, L62** | |
| M8 vs. M8a | 1 | 7.7754 | 0.0053 | Not allowed | |
| atpH | M2a vs. M1a | 2 | 6.786 | 0.0336 | L80* |
| M8 vs. M7 | 2 | 26.0509 | 0 | L57*, P74*, L80** | |
| M8 vs. M8a | 1 | 5.5447 | 0.0185 | Not allowed | |
| cemA | M2a vs. M1a | 2 | 19.1067 | 0.0001 | G152*, R154*, V158* |
| M8 vs. M7 | 2 | 25.0987 | 0 | G152*, R154**, R155*, V158*, V159* | |
| M8 vs. M8a | 1 | 14.358 | 0.0002 | Not allowed | |
| matK | M2a vs. M1a | 2 | 0 | 1 | Dismiss |
| M8 vs. M7 | 2 | 37.4691 | 0 | E118*, A346* | |
| M8 vs. M8a | 1 | 11.667 | 0.0006 | Not allowed | |
| ndhB | M2a vs. M1a | 2 | 32.8718 | 0 | P9*, Q68*, T78**, L180*, R209* |
| M8 vs. M7 | 2 | 58.0883 | 0 | I6*, P9**, T56*, M60*, Q68**, T78**, L180**, L206*, R209** | |
| M8 vs. M8a | 1 | 17.7176 | 0 | Not allowed | |
| ndhF | M2a vs. M1a | 2 | 0 | 1 | Dismiss |
| M8 vs. M7 | 2 | 51.2991 | 0 | T473*, G516*, L624**, L629* | |
| M8 vs. M8a | 1 | 11.8531 | 0.0006 | Not allowed | |
| ndhG | M2a vs. M1a | 2 | 11.7994 | 0.0077 | K139* |
| M8 vs. M7 | 2 | 32.2417 | 0 | K139* | |
| M8 vs. M8a | 1 | 6.2642 | 0.0091 | Not allowed | |
| ndhK | M2a vs. M1a | 2 | 15.1025 | 0.0005 | K221** |
| M8 vs. M7 | 2 | 54.8315 | 0 | Dismiss | |
| M8 vs. M8a | 1 | 5.3409 | 0.0919 | Not allowed | |
| petB | M2a vs. M1a | 2 | 63.9595 | 0 | S2** |
| M8 vs. M7 | 2 | 81.0342 | 0 | S2**, R118* | |
| M8 vs. M8a | 1 | 6.6194 | 0.0101 | Not allowed | |
| psbF | M2a vs. M1a | 2 | 7.2313 | 0.0269 | S27* |
| M8 vs. M7 | 2 | 14.4889 | 0.0007 | S27**, S28* | |
| M8 vs. M8a | 1 | 8.3591 | 0.0038 | Not allowed | |
| psbL | M2a vs. M1a | 2 | 18.1735 | 0.0001 | W20**, L24**, S31* |
| M8 vs. M7 | 2 | 23.78 | 0 | L13*, W20**, L24**, S31** | |
| M8 vs. M8a | 1 | 18.1734 | 0 | Not allowed | |
| psbZ | M2a vs. M1a | 2 | 6.885 | 0.032 | S35* |
| M8 vs. M7 | 2 | 23.5259 | 0 | S35** | |
| M8 vs. M8a | 1 | 8.7711 | 0.0031 | Not allowed | |
| rpl16 | M2a vs. M1a | 2 | 60.897 | 0 | I2** |
| M8 vs. M7 | 2 | 102.3139 | 0 | I2** | |
| M8 vs. M8a | 1 | 43.9429 | 0 | Not allowed | |
| rpoA | M2a vs. M1a | 2 | 66.9924 | 0 | Q106*, R128*, S173**, D233**, C236*, P241*, Q245*, P249*, F272* |
| M8 vs. M7 | 2 | 92.6536 | 0 | Q106*, R128*, S147*, S173**, D233**, C236*, P241**, Q245*, P249*, F272* | |
| M8 vs. M8a | 1 | 61.6783 | 0 | Not allowed | |
| rpoB | M2a vs. M1a | 2 | 0 | 1 | Dismiss |
| M8 vs. M7 | 2 | 93.4487 | 0 | R575*, V597*, E598*, R604**, S606**, P628* | |
| M8 vs. M8a | 1 | 13.6511 | 0.0002 | Not allowed | |
| rpoC2 | M2a vs. M1a | 2 | 28.6437 | 0 | F1020*, P1074** |
| M8 vs. M7 | 2 | 67.1979 | 0 | F1020*, P1074** | |
| M8 vs. M8a | 1 | 29.8592 | 0 | Not allowed | |
| rps7 | M2a vs. M1a | 2 | 14.8195 | 0.0006 | S94**, S115* |
| M8 vs. M7 | 2 | 25.8359 | 0 | S94**, S115* | |
| M8 vs. M8a | 1 | 15.2237 | 0.0001 | Not allowed | |
| ycf3 | M2a vs. M1a | 2 | 12.2851 | 0.0021 | P55** |
| M8 vs. M7 | 2 | 29.1111 | 0 | L75*, Q125*, P55** | |
| M8 vs. M8a | 1 | 10.7695 | 0.001 | Not allowed | |
| Branch-site Model | |||||
| Epiphytic clade | |||||
| ndhI | Model A vs. Model A null | 1 | 5.1717 | 0.023 | S50** |
| psaB | Model A vs. Model A null | 1 | 8.405 | 0.0037 | T511* |
| rps19 | Model A vs. Model A null | 1 | 5.5583 | 0.0184 | R17** |
| Aquatic clade | |||||
| ndhG | Model A vs. Model A null | 1 | 10.0159 | 0.0016 | W121* |
| rpl33 | Model A vs. Model A null | 1 | 4.2567 | 0.0391 | T16* |
d.f.: difference in the number of parameters in the ω distribution; LnL: log-likelihood value; LRT: likelihood ratio test; BEB: Bayes empirical Bayes analysis; * P > 95%; ** P > 99%.