Table 1.
Number of known and retrieved orthologous RAD tags in each species pair. “Orthologous tags”: total number of orthologous RAD tags present in pairwise alignments (D. melanogaster vs. each of the 11 other species). “Retrieved orthologous tags”: proportion of orthologous tags clustered by SiLiX. “In clusters including paralogs”: proportion of the retrieved orthologous tags clustered in groups containing more than one locus. Loci are defined here based on genome sequences (see main text). Node depth from Tamura et al. (2004)
| Species pair D. melanogaster | Node depth (My) | Orthologous tags | Retrieved orthologous tags (%) | In clusters including paralogs (%) |
|---|---|---|---|---|
| D.sechellia | 5.4 | 2978 | 99 | 5 |
| D.simulans | 5.4 | 2892 | 99 | 4 |
| D.erecta | 12.6 | 2390 | 97 | 3 |
| D.yakuba | 12.8 | 2314 | 97 | 8 |
| D.ananassae | 44.2 | 916 | 68 | 9 |
| D.persimilis | 54.9 | 648 | 65 | 9 |
| D.pseudoobscura | 54.9 | 648 | 66 | 9 |
| D.wilistoni | 62.2 | 242 | 49 | 6 |
| D.grimshawi | 62.9 | 290 | 60 | 8 |
| D.virilis | 62.9 | 286 | 59 | 5 |
| D.mojavensis | 62.9 | 298 | 59 | 8 |