| Fish Species Used | Old Results | New Results with Phylomarker |
| 1. Exons in four model species of fish | ||
| Danio rerion(version: Z.0) | 6746 | 8256 |
| Takifugu rubripes (version: Fugu 2.0): | 3483 | 4391 |
| Gasterosteus aculeatus(version: BROAD S1): | 3283 | 3262 |
| Oryzias latipes (version: MEDAKA 1): | 2873 | 2479 |
| Tetraodon nigroviridis | N/A | 2314 |
| 2. Putative single copy exons in four model species of fish | ||
| Danio rerion: | 2797 | 1894 |
| Takifugu rubripes: | 1822 | 835 |
| Gasterosteus aculeatus: | 2132 | 1150 |
| Oryzias latipes: | 1809 | 948 |
| Tetraodon nigroviridis | N/A | 858 |
| 3. Putative orthologs between model fish species | ||
| Danio rerion vs Takifugu rubripes: | 138 | 27 |
| Danio rerion vs Gasterosteus aculeatus: | 131* | 60 |
| Danio rerion vs Oryzias latipes: | 113* | 49 |
| Danio rerion vs Tetraodon nigroviridis | N/A | 42 |
| Takifugu rubripes vs Gasterosteus aculeatus: | 281 | 62 |
| Takifugu rubripes vs Oryzias latipes: | 208 | 34 |
| Takifugu rubripes vs Tetraodon nigroviridis: | N/A | 160 |
| Tetraodon nigroviridis vs Oryzias latipes: | N/A | 36 |
| Tetraodon nigroviridis vs Gasterosteus aculeatus: | N/A | 66 |
| Gasterosteus aculeatus vs Oryzias latipes: | 225 | 129 |
| * 20% coverage applied instead of 50% | ||
| 4. Putative orthologs among 3 model fish species | ||
| (Takifugu rubripes vs Oryzias latipes) AND (Takifugu rubripes vs Gasterosteus aculeatus): | 155 | 25(80/20) |
| (Takifugu rubripes vs Oryzias latipes) AND (Takifugu rubripes vs Danio rerion): | 61 | 8(80/20) |
| (Takifugu rubripes vs Oryzias latipes) AND (Takifugu rubripes vs Tetraodon nigroviridis) | N/A | 17(80/20) |
| (Takifugu rubripes vs Gasterosteus aculeatus) AND (Takifugu rubripes vs Danio rerion): | 63 | 9(80/20) |
| (Takifugu rubripes vs Tetraodon nigroviridis) AND (Takifugu rubripes vs Gasterosteus aculeatus) | N/A | 37(80/20) |
| (Takifugu rubripes vs Tetraodon nigroviridis) AND (Takifugu rubripes vs Danio rerion) | N/A | 8(80/20) |
| 5. Putative orthologs among 4 model fish species | ||
| (Takifugu rubripes vs Oryzias latipes) AND (Takifugu rubripes vs Gasterosteus aculeatus) AND (Takifugu rubripes vs Danio rerion):: | 41 | N/A |