Table 1. Evolutionary analysis of Solanaceae PIF genes.
| PIF1a | PIF1b | PIF3 | PIF4 | PIF7a | PIF7b | PIF8a | ||
|---|---|---|---|---|---|---|---|---|
| Number of sequences | 3 | 3 | 3 | 3 | 3 | 3 | 3 | |
| Number of codons | 552 | 499 | 702 | 495 | 435 | 397 | 461 | |
| Mean dNa ± SD | 0.02±0.01 | 0.05±0.03 | 0.02±0.01 | 0.01±0.01 | 0.01±0.01 | 0.06±0.04 | 0.02±0.01 | |
| Mean dSb ± SD | 0.08±0.04 | 0.08±0.04 | 0.07±0.03 | 0.04±0.01 | 0.05±0.03 | 0.16±0.11 | 0.07±0.02 | |
| Mean Ncc ± SD | 55.03±0.80 | 54.38±0.45 | 50.21±0.73 | 51.41±0.31 | 53.08±0.53 | 54.03±0.52 | 59.20±0.42 | |
| M0d | ω0g | 0.29 | 0.73 | 0.45 | 0.28 | 0.36 | 0.42 | 0.26 |
| p0h | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | |
| lnli | -2752.11 | -2668.30 | -3471.89 | -2250.83 | -2047.17 | -2327.67 | -2241.83 | |
| M1ae | ω0 | 0.29 | 0.00 | 0.00 | 0.00 | 0.36 | 0.00 | 0.19 |
| p0 | 1.00 | 0.36 | 0.57 | 0.73 | 1.00 | 0.58 | 0.91 | |
| ω1j | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | |
| p1k | 0.00 | 0.64 | 0.43 | 0.27 | 0.00 | 0.42 | 0.09 | |
| lnl | -2752.11 | -2666.07 | -3469.56 | -2249.99 | -2047.17 | -2318.59 | -2241.72 | |
| M2af | ω0 | 0.29 | 0.00 | 0.00 | 0.00 | 0.36 | 0.14 | 0.19 |
| p0 | 1.00 | 0.59 | 0.69 | 0.79 | 1.00 | 0.69 | 0.91 | |
| ω1 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | |
| p1 | 0.00 | 0.00 | 0.00 | 0.17 | 0.00 | 0.29 | 0.06 | |
| ω2l | 1.00 | 1.94 | 1.51 | 2.62 | 1.00 | 19.48 | 1.00 | |
| p2m | 0.00 | 0.41 | 0.31 | 0.05 | 0.00 | 0.02 | 0.03 | |
| lnl | -2752.11 | -2664.59 | -3469.21 | -2249.89 | -2047.17 | -2313.73 | -2241.72 | |
| 2Δl (M1a-M0)n | 0 | 4.44 | 4.66 | 1.7 | 0 | 18.15 ** | 0.24 | |
| 2Δl (M2a-M1a)o | 0 | 2.98 | 0.7 | 0.19 | 0 | 9.72* | 0 | |
a dN a dN: non-synonymous distances and the corresponding standard deviation (SD)
b dS: synonymous distances and the corresponding standard deviation (SD)
c Nc: effective number of codons and the corresponding standard deviation (SD)
d M0: the null hypothesis, one-ratio model
e M1a: nearly neutral model
f M2a: positive selection model
g ω0: ω estimates for the codons under purifying selection
h p0: estimated proportion of codons under purifying selection
i lnl: log likelihood of model
j ω1: ω estimates for the codons under neutral evolution
k p1: estimated proportion of codons under neutral evolution
l ω2: ω estimates for codons under positive selection
m p2: estimated proportion of codons under positive selection
n 2Δl (M1a–M0): the likelihood ratio statistics (2Δl) is approximated by the χ2 distribution (degree of freedom = 1), null hypothesis (M0) rejected is highlighted in bold
o 2Δl (M2a-M1a): the likelihood ratio statistics (2Δl) is approximated by the χ2 distribution (degree of freedom = 2), M1a rejected is highlighted in bold. Single and double asterisk indicate P<0.01 and P<0.001, respectively.