Table 1 Parameters used to simulate realistic datasets on the plethodontid salamander phylogeny
Gene | Base frequencies (pi(A), pi(C), pi(G), pi(T)) | R Matrix (A⇔C, A⇔G, A⇔T, C⇔G, C⇔T, G⇔T) | Gamma shape | P invar | Length (bp) | Max branch length |
|---|---|---|---|---|---|---|
atp6 | 0.397 0.230 0.061 0.312 | 0.396 6.362 0.323 0.276 4.258 1.0 | 0.4908 | 0.2436 | 683 | 0.75 |
cob | 0.407 0.236 0.063 0.294 | 1.0 10.749 1.0 1.0 27.120 1.0 | 0.3611 | 0.2980 | 1141 | 0.71 |
cox3 | 0.403 0.228 0.072 0.297 | 0.620 10.185 0.632 0.694 20.706 1.0 | 0.4079 | 0.3985 | 784 | 0.70 |
3rd positions | 0.478 0.194 0.054 0.274 | 0.118 6.885 0.109 0.000 6.205 1.0 | 0.7208 | 0.0063 | 3661 | 1.13 |