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 2
Results of branch model and RELAX analyses of mitochondrial genes without internal branches.
Comparison
Gene
Branch model
RELAX
-2 ΔlnL ()
-2 ΔlnL ()
Plethodontidae DD vs. lunged salamanders
atp6
-7.4708
0.006
0.048
0.033
-14.0500
0.000
0.773
atp8
-0.0262
0.871
0.147
0.139
-0.0706
0.790
1.222
cox1
-45.1340
0.000
0.015
0.007
-34.4024
0.000
0.826
cox2
-45.5633
0.000
0.044
0.018
-51.4044
0.000
0.555
cox3
-6.7130
0.010
0.039
0.028
-8.6419
0.003
0.842
cytb
-2.2026
0.138
0.035
0.030
-4.8904
0.027
0.827
nad1
-8.5458
0.003
0.032
0.023
-10.9626
0.001
0.762
nad2
-33.2628
0.000
0.072
0.041
-32.1149
0.000
0.652
nad3
-0.2201
0.639
0.053
0.049
-9.6473
0.002
0.689
nad4
-18.0457
0.000
0.055
0.038
-17.7786
0.000
0.826
nad4L
-0.0002
0.989
0.040
0.040
0.0000
1.000
1.000
nad5
-16.8708
0.000
0.055
0.040
-38.3770
0.000
0.803
nad6
-11.6646
0.001
0.073
0.042
-13.0165
0.000
0.705
Plethodontidae MM vs. lunged salamanders
atp6
-4.4268
0.035
0.049
0.033
-1.6165
0.204
0.859
atp8
-0.4924
0.483
0.101
0.139
-1.4104
0.235
1.759
cox1
-0.0082
0.928
0.007
0.007
-0.5711
0.450
1.047
cox2
-2.5963
0.107
0.024
0.018
-2.2037
0.138
0.914
cox3
-1.9094
0.167
0.022
0.028
-1.4144
0.234
1.132
cytb
-4.5094
0.034
0.040
0.030
-1.4137
0.234
0.800
nad1
-1.2678
0.260
0.027
0.023
-0.3337
0.564
0.967
nad2
-5.3517
0.021
0.056
0.041
-5.3525
0.021
0.851
nad3
-2.4007
0.121
0.071
0.049
-1.9701
0.160
0.763
nad4
-0.0627
0.802
0.039
0.038
-0.6735
0.412
1.057
nad4L
-0.0001
0.994
0.040
0.040
-0.1075
0.743
1.065
nad5
-4.5264
0.033
0.050
0.040
-13.2843
0.000
0.834
nad6
-6.8491
0.009
0.077
0.042
-9.0366
0.003
0.679
Plethodontidae DD vs. Plethodontidae MM
atp6
-0.0041
0.949
0.048
0.049
-0.4736
0.491
0.832
atp8
-0.5788
0.447
0.147
0.101
-1.4551
0.228
0.617
cox1
-17.9793
0.000
0.015
0.007
-18.0031
0.000
0.573
cox2
-8.2538
0.004
0.044
0.024
-7.8247
0.005
0.647
cox3
-8.4264
0.004
0.039
0.022
-10.0902
0.001
0.614
cytb
-0.8062
0.369
0.035
0.040
-0.7953
0.373
0.892
nad1
-0.8558
0.355
0.032
0.027
-1.6064
0.205
0.824
nad2
-3.1405
0.076
0.072
0.056
-3.0969
0.078
0.835
nad3
-1.2157
0.270
0.053
0.071
-0.3625
0.547
0.905
nad4
-6.4172
0.011
0.055
0.039
-12.1234
0.000
0.809
nad4L
-0.0003
0.987
0.040
0.040
-0.4868
0.485
0.846
nad5
-0.6011
0.438
0.055
0.050
-49.3683
0.000
0.944
nad6
-0.0398
0.842
0.073
0.077
-0.6219
0.430
1.084
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 taxa, respectively.
