Table 1.
Summary of PAML Analyses of Comparisons of dN/dS Ratios in Coding mtDNA and the Rate of Evolution of Functional Noncoding mtDNA in Sexual versus Asexual Potamopyrgus antipodarum.
| Model | No. Free Parameters | lnL | χ2 (df) | dN/dS or Ratea |
| Coding | ||||
| One ratio | 1 | −19680.08 | NA | 0.101 |
| Two ratio (sex vs. asex) | 2 | −19674.046 | vs. one ratio: 12.068 (1)*** | Sex: 0.084 Asex: 0.161 |
| Two ratio (T, I)b | 2 | −19675.866 | vs. one ratio: 8.428 (1)** | T: 0.143 I: 0.0851 |
| Four ratio (SexT, AsexT, SexI, AsexI) | 4 | −19671.78 | vs. one ratio: 16.6 (3)*** | SexT: 0.103 AsexT: 0.204 SexI:0.079 |
| vs. two ratio (sex/asex): 4.532 (2) | AsexI: 0.123 | |||
| vs. two ratio (T vs. I): 8.172 (2)** | ||||
| One ratio (pruned)c | 1 | −16807.664 | NA | 0.098 |
| Two ratio (pruned, sex vs. asex) | 2 | −16805.709 | vs. one ratio: 3.91 (1)* | Sex: 0.086 Young asex: 0.162 |
| Functional noncoding | ||||
| One rate | 1 | −6114.496 | NA | NA |
| Two rate (sex vs. asex) | 2 | −6112.204 | vs. one rate: 4.584 (1)* | Sex: 1.00 Asex: 1.598 |
| Two rate (T vs. I) | 2 | −6113.924 | vs. one rate: 2.144 (1) | T: 1.283 I: 1.00 |
| Four rate (SexT, AsexT, SexI, AsexI) | 4 | −6109.782 | vs. one rate: 9.428 (3)** | SexT: 1.526 AsexT: 5.973 SexI: 1.00 |
| vs. two rate (sex/asex): 4.844 (2) | AsexI: 1.962 | |||
| vs. two rate (T vs. I): 8.284 (2)** | ||||
| One rate (pruned) | 1 | −5554.967 | NA | NA |
| Two rate (pruned, sex vs. asex) | 2 | −5554.812 | vs. one rate: 0.155 (1) | Sex: 1.00 Asex: 1.367 |
NOTE.—df, degrees of freedom; NA, not applicable.
a
First branch type entered in the control file automatically set to 1 by baseml; all other rates are estimated relative to this value.
b
“T” indicates terminal branches and “I” indicates internal branches.
c
“Pruned” represents analyses from pruned trees containing only sexuals and young asexual lineages.
*Indicates significance at P < 0.05, **Indicates significance at P < 0.025, and ***Indicates significance at P < 0.001.