Table 1. List of amino acid replacements and results of positive selection tests on codons underlying these replacements.
| Gene | Position | α | β | Amino acid replacements | FUBAR (PP) | MEME (LRT) | FDR | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nat | Ngla | Nkni | Nobt | Noto | Npan | Nrus | Nsyl | Ntab | Ntom | Nund | |||||||
| atpB | 19 | 0.909 | 6.339 | K | N | N | K | K | N | N | N | N | N | N | 0.918 | 4.42 | 0.044 |
| 21 | 0.697 | 15.511 | P | P | P | P | P | P | P | P | P | P | P | 0.990 | 4.99 | 0.012 | |
| ndhD | 153 | 1.981 | 12.245 | C | C | C | C | C | C | C | C | C | C | C | 0.927 | 3.16 | 0.021 |
| 185 | 0.744 | 9.365 | V | L | V | V | V | V | V | L | L | V | V | 0.956 | 3.82 | 0.017 | |
| ndhF | 460 | 1.385 | 8.772 | V | V | V | V | V | V | V | A | A | V | V | 0.912 | 3.30 | 0.010 |
| rpoA | 201 | 1.149 | 8.426 | L | L | L | L | L | L | L | L | L | L | L | 0.940 | 3.84 | 0.023 |
Notes.
- α
- the mean synonymous substitution rate at a site
- β
- the mean non-synonymous substitution rate at a site
- PP
- posterior probability of positive selection at a site
- LRT
- Likelihood ratio test for episodic (positive) diversification
- FDR
- false discovery rate (FDR = 5%)
Species abbreviations
- Nat
- N. attenuata
- Ngla
- N. glauca
- Nkni
- N. knightiana
- Nobt
- N. obtusifolia
- Noto
- N. otophora
- Npan
- N. paniculata
- Nrus
- N. rustica
- Nsyl
- N. sylvestris
- Ntab
- N. tabacum
- Ntom
- N. tomentosiformis
- Nund
- N. undulata