Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae
Table 3
Results of branch model and RELAX analyses of nuclear genes.
Comparison
Gene
Branch model
RELAX
-2 ΔlnL ()
-2 ΔlnL ()
(All branches)
Plethodontidae vs. lunged salamanders
bdnf
0.0317
0.859
0.020
0.021
0.0742
0.785
1.033
pomc
1.5407
0.215
0.087
0.084
0.0440
0.834
1.035
rag1
9.8984
0.002
0.073
0.046
9.2968
0.002
0.670
rag2
1.5442
0.214
0.173
0.142
7.0458
0.008
0.708
(Terminal branches)
Plethodontidae vs. lunged salamanders
bdnf
0.2244
0.636
0.017
0.024
0.4279
0.513
1.111
pomc
0.8963
0.344
0.078
0.103
1.2456
0.264
1.424
rag1
2.7077
0.100
0.079
0.058
2.7967
0.094
0.790
rag2
1.8219
0.177
0.217
0.164
2.4296
0.119
0.796
Plethodontidae DD vs. lunged salamanders
bdnf
0.5339
0.465
0.012
0.022
0.7742
0.379
1.183
pomc
0.0061
0.938
0.105
0.103
0.3638
0.546
1.313
rag1
1.6841
0.194
0.077
0.058
1.6312
0.202
0.443
rag2
0.3989
0.528
0.193
0.164
0.6024
0.438
0.811
Plethodontidae MM vs. lunged salamanders
bdnf
-0.0371
—
0.026
0.022
0.0037
0.951
1.013
pomc
5.7446
0.017
0.041
0.103
1.8583
0.173
1.607
rag1
1.8707
0.171
0.082
0.058
2.6868
0.101
0.807
rag2
2.3532
0.125
0.249
0.164
3.1834
0.074
0.672
Plethodontidae DD vs. Plethodontidae MM
bdnf
0.4522
0.501
0.012
0.026
0.3311
0.565
1.229
pomc
3.4992
0.061
0.105
0.041
0.4250
0.514
0.816
rag1
0.0406
0.840
0.077
0.082
0.5278
0.468
1.106
rag2
0.6134
0.434
0.193
0.249
0.6722
0.412
1.483
Values with italic showed . and indicate values in test and reference branches, respectively. Both values were calculated based on alternative models. DD and MM represent direct-developing and metamorphosing branches, respectively. All and terminal branches with parentheses denote the comparison of all (internal and terminal) branches and only terminal branches, respectively. Dash showed that values could not be calculated due to the lower lnL of the alternative model than the null model.
