Table 1.
The number of orthogroups identified between tetrapods and teleosts
| Gene/orthogroup category | Human centered | Medaka centered | Integrated* | |||
| Without criterion† | With criterion‡ | Without criterion | With criterion | Without criterion | With criterion | |
| Loci in query genome | 20,368 | — | 19,686 | — | — | — |
| No clear orthogroups | 4,809 | — | 4,134 | — | — | — |
| Putative orthogroups | 15,559 | 6,673 | 15,552 | 6,471 | — | — |
| Additional putative orthogroups from medaka-centered analysis§ | — | — | — | — | 1,617 | 684 |
| Integrated putative orthogroups | — | — | — | — | 17,176 (15,559 + 1,617) | 7,357 (6,673 + 684) |
| Multiply counted orthogroups | — | — | — | — | 1,823 (1,544 + 279) | 465 (409 + 56) |
| Identified orthogroups¶ | — | — | — | — | 15,353 (14,015 + 1,338) | 6,892 (6,264 + 628) |
| 1to2 category (paired by TGD) | — | — | — | — | 4,262 (3,723 + 539) | 1,237 (1,102 + 135) |
| 1to1 category (losing one gene lineage) | — | — | — | — | 11,091 (10,292 + 799) | 5,655 (5,162 + 493) |
| TGD-derived paired gene lineages/total loci (gene lineages) in common ancestor | — | — | — | — | 27.76% (4,262/15,353) | 17.95% (1,237/6,892) |
*
See Dataset S1 for the results from all protein-coding gene analyses. The numbers in parentheses indicate estimates derived from human- or medaka-centered analyses.
†
Orthogroups without the BS 70% criterion (Fig. S1C).
‡
Orthogroups with the BS 70% criterion.
§
The orthogroups without human ortholog.
¶
cDNA sequence alignments and rearranged ML trees are available at fish-evol.unit.oist.jp/db/TGD16/6892data.tar.gz.