Table 3. Cophylogenetic reconciliations proposed by CoRe-Pa.
| Quality | Total cost | Cospeciation | Sorting | Duplication | Host-switch | |
|---|---|---|---|---|---|---|
| Fully resolved | 0.0054 | 0.61 | 12 (0.017) | 51 (0.0040) | 15 (0.013) | 0 (0.97) |
| 0.04 | 9.53 | 11 (0.25) | 33 (0.074) | 12 (0.20) | 4 (0.47) | |
| Basal polytomy | 0.012 | 7.98 | 13 (0.16) | 40 (0.051) | 11 (0.19) | 3 (0.60) |
| 0.018 | 0.032 | 10 (0.000998) | 65 (0.00017) | 17 (0.00067) | 0 (0.998) |
Quality value, total value, and number of cospeciation, sorting, duplication and host-switch events invoked (with estimated cost in brackets) for the two best CoRe-Pa reconciliations of Tropheini (based on the AFLP markers as published by Koblmüller et al.8) and Cichlidogyrus (based on the concatenated nuclear-mitochondrial dataset) trees. Topology-based cophylogenetic analyses used either a fully resolved parasite ML tree or a parasite ML tree with nodes supported by a bootstrap value under 70 collapsed. Solutions depicted in bold are visualized in Fig. 3.