Table 2.
Results from branch models that assume branch-specific changes in the selection coefficient (ω) in Neobatrachia, based on nucleotide single-gene alignments and mt and nuclear nucleotide data sets
|
models |
null model |
"Neob-stem" |
"All Neob" |
"All Nobleob" |
"All Ranoides" |
||||
|---|---|---|---|---|---|---|---|---|---|
| gene | Backgr | Backgr | Branch | Backgr | Branch | Backgr | Branch | Backgr | Branch |
|
atp6 |
0.03086 |
0.03076 |
0.03585 |
0.03045 |
0.03126 |
0.03086 |
1.1225 |
0.03082 |
0.04203 |
|
atp8 |
0.1481 |
0.14592 |
1.50841 |
0.13361 |
0.16694 |
0.14838 |
0.13614 |
0.14683 |
0.35429 |
|
cob |
0.03357 |
0.03313 |
0.06875 |
0.03302 |
0.0342 |
0.03347 |
0.04419 |
0.03353 |
0.0431 |
|
cox1 |
0.01129 |
0.011 |
0.03737 |
0.00783 |
0.0144 |
0.01122 |
0.02381 |
0.01115 |
0.03898 |
|
cox2 |
0.02236 |
0.02224 |
0.02642 |
0.02186 |
0.02271 |
0.02234 |
0.0236 |
0.02227 |
0.03366 |
|
cox3 |
0.02741 |
0.02704 |
0.08793 |
0.02482 |
0.03046 |
0.02727 |
0.03895 |
0.02733 |
0.05843 |
|
nad1 |
0.03005 |
0.02977 |
0.05077 |
0.02823 |
0.03211 |
0.03001 |
0.03416 |
0.02996 |
0.04253 |
|
nad2 |
0.02817 |
0.02813 |
0.03252 |
0.02803 |
0.02835 |
0.02818 |
0.02814 |
0.02814 |
0.03007 |
|
nad3 |
0.06499 |
0.06457 |
0.14425 |
0.06435 |
0.06582 |
0.06467 |
0.10545 |
0.06499 |
0.93185 |
|
nad4 |
0.03632 |
0.03622 |
0.0392 |
0.0358 |
0.03675 |
0.03626 |
0.04061 |
0.0363 |
0.03703 |
|
nad4L |
0.04471 |
0.04458 |
0.04792 |
0.04662 |
0.04311 |
0.04474 |
0.04294 |
0.04468 |
0.04637 |
|
nad5 |
0.03516 |
0.03503 |
0.03793 |
0.03459 |
0.03571 |
0.0351 |
0.03749 |
0.03511 |
0.03836 |
|
nad6 |
0.02901 |
0.02895 |
0.03107 |
0.02753 |
0.03081 |
0.02897 |
0.03286 |
0.02895 |
0.03359 |
| all mt genes |
0.04693 |
0.04632 |
0.08313 |
0.04483 |
0.04914 |
0.04673 |
0.06435 |
0.04667 |
0.07065 |
|
bdnf |
0.04595 |
0.04723 |
0.01186 |
0.04393 |
0.04979 |
0.04577 |
0.05385 |
0.04545 |
0.11214 |
|
cxcr4 |
0.06461 |
0.06454 |
0.06745 |
0.06028 |
0.07344 |
0.06588 |
0.03076 |
0.06441 |
0.0748 |
|
h3a |
0.00476 |
0.00483 |
0.0001 |
0.00599 |
0.00283 |
0.005 |
0.0001 |
0.00488 |
0.0001 |
|
pomc |
0.08214 |
0.0808 |
0.23558 |
0.09098 |
0.07043 |
0.08298 |
0.05716 |
0.08548 |
0.02649 |
|
rag1 |
0.05736 |
0.05778 |
0.03692 |
0.05249 |
0.06532 |
0.05772 |
0.0438 |
0.05802 |
0.01704 |
|
rag2 |
0.16003 |
0.15849 |
0.24864 |
0.16786 |
0.1515 |
0.16003 |
0.0001 |
0.1612 |
0.04584 |
|
rho |
0.0903 |
0.092 |
0.02424 |
0.07483 |
0.11389 |
0.09175 |
0.02681 |
0.09226 |
0.04981 |
|
slc8a1 |
0.03996 |
0.04067 |
0.0001 |
0.03588 |
0.04702 |
0.0402 |
0.03164 |
0.04055 |
0.01522 |
|
slc8a3 |
0.02649 |
0.02684 |
0.0144 |
0.02623 |
0.02707 |
0.02664 |
0.01996 |
0.0268 |
0.01046 |
| all nuc genes | 0.06908 | 0.06922 | 0.06195 | 0.06426 | 0.07719 | 0.06976 | 0.04153 | 0.06984 | 0.03298 |
The table shows ω values estimated for the whole frog tree (null model) and values estimated for specific (Branch) and remaining background (Backgr.) branches under the four alternative models tested. Bold italics highlight results that are significantly different to the null model (LRT p < 0.05). See Additional file 3 for full details.