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 1
Results of branch model and RELAX analyses of mitochondrial genes with internal branches.
Comparison
Gene
Branch model
RELAX
-2 ΔlnL (d.f. = 1)
P
ω1
ω2
-2 ΔlnL (d.f. = 1)
P
k
Plethodontidae vs. lunged salamanders
atp6
-11.0074
0.001
0.046
0.033
-22.0306
0.000
0.722
atp8
-0.7743
0.379
0.142
0.138
-0.2942
0.588
0.684
cox1
-45.3786
0.000
0.013
0.007
-30.5404
0.000
0.842
cox2
-42.3632
0.000
0.035
0.017
-50.8092
0.000
0.625
cox3
-3.9068
0.048
0.033
0.028
-6.8323
0.009
0.891
cytb
-1.4472
0.229
0.036
0.033
-4.4370
0.035
0.849
nad1
-4.6464
0.031
0.030
0.025
-6.3163
0.012
0.852
nad2
-36.1991
0.000
0.069
0.045
-28.5936
0.000
0.706
nad3
-1.6005
0.206
0.054
0.046
-7.5547
0.006
0.784
nad4
-16.1672
0.000
0.049
0.038
-11.2847
0.001
0.886
nad4L
-0.4267
0.514
0.043
0.039
-0.2034
0.652
0.953
nad5
-19.6304
0.000
0.056
0.044
-44.8124
0.000
0.759
nad6
-21.7759
0.000
0.072
0.040
-29.7902
0.000
0.614
Onychodactylus vs. lunged salamanders
atp6
-0.9611
0.327
0.024
0.033
-0.0133
0.908
1.036
atp8
-0.0915
0.762
0.105
0.138
-0.3936
0.530
7.676
cox1
-1.2064
0.272
0.005
0.007
-1.2101
0.271
1.111
cox2
-0.0705
0.791
0.016
0.017
-0.1654
0.684
1.019
cox3
-0.1605
0.689
0.031
0.028
-0.9278
0.335
0.876
cytb
-4.7672
0.029
0.020
0.033
-5.2470
0.022
1.477
nad1
-0.9503
0.330
0.019
0.025
-0.5157
0.473
1.103
nad2
-0.4529
0.501
0.053
0.045
-0.1290
0.719
0.968
nad3
-0.0766
0.782
0.051
0.046
-1.4217
0.233
1.115
nad4
-0.0001
0.994
0.038
0.038
-0.6303
0.427
1.129
nad4L
-0.7078
0.400
0.025
0.039
-0.8172
0.366
1.337
nad5
-0.1328
0.716
0.047
0.044
-0.0149
0.903
1.017
nad6
-0.5708
0.450
0.054
0.040
-1.4766
0.224
0.690
Values with italic showed . and indicate values in test and reference branches, respectively. Both values were calculated based on alternative models.
