Table 3. The list of genes under positive selection in Iodes genus.
| Species under selection | B | LRT | Test p-value | Uncorrected p-value | ω Distribution over Sites | Gene name |
|---|---|---|---|---|---|---|
| I. scandens | 0.0395 | 69.1914 | 0 | 0 |
ω1 = 0.219 (97%) ω2 = 10,000 (2.8%) |
acc D |
| I. liberica | 0.0161 | 13.5704 | 0.0046 | 0.0004 |
ω1 = 0.00 (100%) ω2 = 10,000 (0.21%) |
|
| I. seretii | 0.0177 | 20.9163 | 0.0001 | 0 |
ω1 = 0.00 (100%) ω2 = 10,000 (0.43%) |
atp B |
| I. scandens | 0.0395 | 43.2439 | 0 | 0 |
ω1 = 0.0396 (79%) ω2 = 10,000 (21%) |
atp F |
|
I. seretii I. perrieri I. liberica I. klaineana |
0.0033 | 41.7172 | 0 | 0 |
ω1 = 0.00 (98%) ω2 = 10,000 (2.3%) |
|
| I. liberica | 0.0161 | 41.5182 | 0 | 0 |
ω1 = 0.00 (99%) ω2 = 10,000 (0.78%) |
ccs A |
| I. perrieri | 0.0131 | 21.6819 | 0.0001 | 0 |
ω1 = 0.237 (99%) ω2 = 10,000 (0.81%) |
|
| I. liberica | 0.0161 | 31.5631 | 0 | 0 |
ω1 = 0.00 (91%) ω2 = 10,000 (9.2%) |
mat K |
|
I. cirrhosa I. scandens |
0.0034 | 232.27 | 0 | 0 |
ω1 = 1.00 (72%) ω2 = 10,000 (28%) |
|
| I. cirrhosa | 0.023 | 15.8778 | 0.0013 | 0.0001 |
ω1 = 1.00 (95%) ω2 = 10,000 (5.1%) |
|
| I. cirrhosa | 0.023 | 151.9285 | 0 | 0 |
ω1 = 0.0229 (92%) ω2 = 2,240 (8.0%) |
ndh A |
| I. scandens | 0.0395 | 138.8669 | 0 | 0 |
ω1 = 0.465 (90%) ω2 = 2,240 (10%) |
|
| I. seretii | 0.0177 | 125.9252 | 0 | 0 |
ω1 = 0.555 (92%) ω2 = 10,000 (8.2%) |
|
| I. perrieri | 0.0131 | 118.0196 | 0 | 0 |
ω1 = 0.0245 (95%) ω2 = 3,330 (5.0%) |
|
|
I. perrieri I. liberica I. klaineana |
0.0006 | 151.8593 | 0 | 0 |
ω1 = 0.00 (92%) ω2 = 3,330 (8.4%) |
|
| I. klaineana | 0.0074 | 18.3085 | 0.0003 | 0 |
ω1 = 0.271 (100%) ω2 = 10,000 (0.35%) |
|
| I. scandens | 0.0395 | 40.0987 | 0 | 0 |
ω1 = 0.434 (99%) ω2 = 10,000 (0.52%) |
ndh B |
| I. seretii | 0.0177 | 38.5771 | 0 | 0 |
ω1 = 0.00 (71%) ω2 = 1,850 (29%) |
ndh E |
| I. liberica | 0.0161 | 32.0969 | 0 | 0 |
ω1 = 0.176 (99%) ω2 = 10,000 (1.3%) |
ndh F |
| I. perrieri | 0.0131 | 63.2828 | 0 | 0 |
ω1 = 0.264 (97%) ω2 = 377 (2.6%) |
ndh F |
| I. scandens | 0.0395 | 90.4163 | 0 | 0 |
ω1 = 0.241 (96%) ω2 = 324 (4.1%) |
|
| I. seretii | 0.0177 | 13.5496 | 0.0039 | 0.0004 |
ω1 = 0.320 (99%) ω2 = 10,000 (0.82%) |
|
|
I. liberica I. klaineana |
0.0022 | 13.3158 | 0.0039 | 0.0004 |
ω1 = 0.375 (100%) ω2 = 10,000 (0.24%) |
|
| I. scandens | 0.0395 | 25.8917 | 0 | 0 |
ω1 = 0.749 (80%) ω2 = 100 (20%) |
ndh G |
|
I. cirrhosa I. scandens |
0.0034 | 29.2692 | 0 | 0 |
ω1 = 1.00 (99%) ω2 = 10,000 (1.2%) |
ndh K |
| I. perrieri | 0.0131 | 17.129 | 0.0008 | 0.0001 |
ω1 = 0.00 (93%) ω2 = 839 (6.7%) |
pet G |
| I. perrieri | 0.0131 | 362.9645 | 0 | 0 |
ω1 = 0.0306 (94%) ω2 = 10,000 (6.4%) |
psa A |
| I. seretii | 0.0177 | 332.4549 | 0 | 0 |
ω1 = 0.143 (95%) ω2 = 1,550 (4.9%) |
|
|
I. seretii I. perrieri I. liberica I. klaineana |
0.0033 | 158.1644 | 0 | 0 |
ω1 = 0.188 (90%) ω2 = 3,640 (10%) |
|
| I. perrieri | 0.0131 | 44.4643 | 0.0000 | 0.0000 |
ω1 = 0.0577 (72%) ω2= 2000 (28%) |
rpl 2 |
| I. liberica | 0.0161 | 10.1996 | 0.0253 | 0.0021 |
ω1= 1.00 (99%) ω2= 10,000 (1.5%) |
rpl 22 |
| I. scandens | 0.0395 | 15.2617 | 0.0021 | 0.0002 |
ω1= 0.195 (97%) ω2= 110 (3.3%) |
rpl 23 |
| I. scandens | 0.0395 | 19.7602 | 0.0002 | 0.0000 |
ω1= 0.173 (100%) ω2= 255 (0.32%) |
rpo B |
| I. perrieri | 0.0131 | 116.6650 | 0.0000 | 0.0000 |
ω1= 0.0980 (97%) ω2= 3,330 (2.5%) |
rpo C1 |
| I. scandens | 0.0395 | 44.2547 | 0.0000 | 0.0000 |
ω1= 1.00 (99%) ω2= 10,000 (0.94%) |
|
| I. seretii | 0.0177 | 72.9439 | 0.0000 | 0.0000 |
ω1= 0.304 (99%) ω2= 10,000 (0.86%) |
rpo C2 |
| I. scandens | 0.0395 | 98.4880 | 0.0000 | 0.0000 |
ω1= 0.336 (98%) ω2= 10,000 (2.3%) |
|
| I. liberica | 0.0161 | 28.3779 | 0.0000 | 0.0000 |
ω1= 0.540 (100%) ω2= 10,000 (0.47%) |
|
|
I. liberica I. klaineana |
0.0022 | 26.4708 | 0.0000 | 0.0000 |
ω1= 0.777 (100%) ω2= 5,480 (0.38%) |
|
| I. perrieri | 0.0131 | 14.7652 | 0.0017 | 0.0002 |
ω1= 0.402 (100%) ω2= 443 (0.18%) |
|
|
I. perrieri I. liberica I. klaineana |
0.0006 | 13.1292 | 0.0063 | 0.0005 |
ω1= 0.00 (99%) ω2= 10,000 (0.51%) |
rps 3 |
|
I. seretii I. perrieri I. liberica I. klaineana |
0.0033 | 9.9293 | 0.0290 | 0.0024 |
ω1= 0.00 (99%) ω2= 10,000 (1.1%) |
|
| I. perrieri | 0.0131 | 75.2232 | 0.0000 | 0.0000 |
ω1= 0.00 (79%) ω2= 320 (21%) |
rps 7 |
| I. scandens | 0.0395 | 12.6120 | 0.0081 | 0.0006 |
ω1= 0.00 (97%) ω2= 10,000 (3.4%) |
rps 18 |
| I. liberica | 0.0161 | 69.4590 | 0.0000 | 0.0000 |
ω1= 1.00 (83%) ω2= 3,330 (17%) |
rps 19 |
| I. cirrhosa | 0.0230 | 25.6408 | 0.0000 | 0.0000 |
ω1= 1.00 (99%) ω2= 10,000 (0.66%) |
ycf 1 |
| I. perrieri | 0.0131 | 22.7892 | 0.0000 | 0.0000 |
ω1= 0.00 (100%) ω2= 10,000 (0.30%) |
|
| I. scandens | 0.0395 | 194.6220 | 0.0000 | 0.0000 |
ω1= 0.286 (98%) ω2= 10,000 (2.0%) |
ycf 2 |
| I. liberica | 0.0161 | 134.1704 | 0.0000 | 0.0000 |
ω1= 0.0920 (99%) ω2= 6,070 (1.1%) |
|
|
I. liberica I. klaineana |
0.0022 | 51.3748 | 0.0000 | 0.0000 |
ω1= 0.399 (100%) ω2= 3,330 (0.36%) |
|
| I. liberica | 0.0161 | 40.5254 | 0.0000 | 0.0000 |
ω1= 0.367 (95%) ω2= 10,000 (4.9%) |
ycf 3 |
Notes.
- B
- Optimized branch length
- LRT
- Likelihood ratio test statistic for selection
- Test p-value
- p-value corrected for multiple testing
- Uncorrected p-value
- Raw p-value without correction for multiple testing
- ω
- The ratio of nonsynonymous to synonymous substitution