Table 3.
Formal tests for recombination
| Parameter | Homoplasy test (ref. 35) | LPT (ref. 32) |
|---|---|---|
| True homoplasies | 5 | — |
| Expected homoplasies | 0.42 | — |
| Polymorphic sites | 17 | 17 |
| Se | 330 | — |
| Probability, P | <0.001 | ∼0.001–0.004 |
Se, effective number of sites, estimated by using the liverwort cob sequence as an outgroup (35). LPT, Likelihood permutation test (32). These tests were conducted with all 1,041 sites—i.e., including both silent and replacement polymorphisms. In addition, the homoplasy test yields significant results when applied to only third-codon positions (P = 0.001), and synonymous sites (P < 0.01). —, Not applicable.