Table 3.
Variability and homoplasy in each type of data
| Clade | nucDNA variable characters | mtDNA variable characters | Ratio of variable characters nucDNA: mtDNA |
nucDNA consistency index/retention index |
mtDNA consistency index/retention index |
|---|---|---|---|---|---|
| Balistid fish | 341 | 337 | 1.01 | 0.5851/0.7298 | 0.4175/0.5380 |
| Scarine fish | 612 | 743 | 0.82 | 0.5579/0.7874 | 0.3805/0.6012 |
| Hemiphractid frogs | 441 | 1344 | 0.33 | 0.6427/0.8552 | 0.3065/0.4589 |
| Hylid frogs | 715 | 1442 | 0.50 | 0.2844/0.5646 | 0.1486/0.3135 |
| Plethodon salamanders | 1204 | 1400 | 0.86 | 0.6042/0.8132 | 0.3069/0.6329 |
| Phrynosomatid lizards | 1155 | 2258 | 0.51 | 0.5498/0.7490 | 0.3327/0.3284 |
| Alcid birds | 255 | 1559 | 0.16 | 0.6471/0.7918 | 0.4129/0.5823 |
| Caprimulgid birds | 790 | 522 | 1.51 | 0.4708/0.7560 | 0.2216/0.5078 |
| Cotingid birds | 440 | 493 | 0.89 | 0.5858/0.7162 | 0.2300/0.3154 |
| Dicaeid birds | 86 | 660 | 0.13 | 0.8043/0.9455 | 0.7067/0.3793 |
| Emydid turtles | 477 | 460 | 1.04 | 0.6581/0.8662 | 0.4591/0.7820 |
| Cervid mammals | 127 | 624 | 0.20 | 0.7414/0.9085 | 0.3097/0.4704 |
| Murid rodents (Philippines) | 640 | 628 | 1.02 | 0.4179/0.6474 | 0.1649/0.3342 |
| Murid rodents (Sahul) | 4226 | 1175 | 3.60 | 0.5094/0.7129 | 0.1666/0.2974 |
A summary of the number of variable characters that each data type (mtDNA, nucDNA) contributes to each combined analysis and the amount of homoplasy in each data set (lower values indicate more homoplasy; see Additional File 8 for additional details on each data set). The consistency index excludes uninformative characters. Outgroups were not included.