Distribution of Duplicated Genes in Fish Lineages
| Gene family | Actinopterygian lineage | Hovergen family no. | ||||||
| Cypriniformes | Percomorpha | Salmoniformes | Cyprinodontiformes | Siluriformes | Other Euteleostei | Anguilliformes | ||
| α globin[ii] | specific: 97 | specific: 70 | specific: 100 & 94 | no | no | FAM000215 | ||
| activin β b | specific: 82 | no | no | FAM000307 | ||||
| apo AI | no | no | specific: 100 | FAM001258 | ||||
| androgen receptor[iii] | shared: 83 | specific: 100 | shared: 83 | FAM001375 | ||||
| shared: 83 | ||||||||
| aromatase | shared: 89 | shared: 89 | shared: 89 | shared: 89 | FAM000502 | |||
| CAD[iv] | no | no | no | FAM000951 | ||||
| cholecystokinin[iii] | shared: 94 | shared: 94 | specific: 100 | FAM003983 | ||||
| shared: 94 | ||||||||
| complement C3 | specific: 100 | no | no | specific: 100 | FAM000664 | |||
| EF1-α | no | no | no | FAM000591 | ||||
| ependymin | specific: 100 | no | specific[v] | no | no | FAM000398 | ||
| factor B | specific: 100 & 100 | specific: 100 | no | FAM001595 | ||||
| gonadotropin α | specific: 71 | no | specific: 83 | no | no | no | FAM000012 | |
| gonadotropin β | no | no | no | no | no | no | FAM000013 | |
| GnRH[vi] | no | no | no | no | FMA002205 | |||
| GnRH II[vi] | no | no | no | no | no | FAM002205 | ||
| growth hormone | specific: 100 | no | specific: 100 | no | no | no | FAM000014 | |
| HNF forkhean domain | no | no | no | FAM001266 | ||||
| HSC70/HSP70 | specific: 100 | no | no | no | FAM000300 | |||
| ins-like growth factor II | no | no | no | FAM000006 | ||||
| lactate dehydrogenase A | no | no | no | no | FAM000364 | |||
| lactate dehydrogenase B | no | no | no | FAM000364 | ||||
| Na/H exchange | no | no | no | no | FAM000486 | |||
| OTX–Pit | specific: 100 | no | no | FAM001264 | ||||
| p53 | no | no | no | no | FAM001642 | |||
| prolactin | no | no | no | no | FAM000016 | |||
| Rag-1 | no | no | no | no | no | FAM000556 | ||
| somatolactin | no | specific: 100 | no | no | no | FAM000015 | ||
| TGF β2 | no | no | no | FAM000027 | ||||
| TSH β | no | no | no | FAM000013 | ||||
| trypsinogene | specific: 99 | specific: 100 | no | specific: 100[vii] | FAM001232 | |||
| tyrosinase | no | no | no | FAM000871 | ||||
| tyrosine hydroxylase | no | no | no | FAM000388 | ||||
| zona pelucida ZP2 | specific: 98 | shared: 77 | shared: 77 | shared: 77 | no | FAM001134 | ||
| Number of gene families | 29 | 28 | 26 | 14 | 9 | 8 | 14 | |
| Specific duplications[viii](%) | 34.5 | 10.7 | 34.6 | 7.1 | 0.0 | 12.5 | 0.0 | |
| Total duplications[ix](%) | 41.4 | 25.0 | 38.5 | 21.4 | 11.1 | 12.5 | 7.1 | |
[i] For each lineage in which a gene family has been characterized, the evidence for duplications is shown as follows: (Specific) evidence for a gene duplication specifically in this lineage, followed by bootstrap support; (shared) evidence for a gene duplication shared with at least one other lineage, followed by bootstrap support; (no) that there is no evidence for a gene duplication. When there are two independent gene duplications for the same gene family and the same lineage, both bootstrap supports are reported. Bootstrap support is the proportion of 2000 bootstrap replicates recovering the branch, using Neighbor-Joining with Poisson corrected distances, although other methods were also used (see text).
[ii] There may also be a duplication of a globin ancestral to all fish lineages sampled, but phylogenetic evidence is not conclusive.
[iii] For these gene families, there is both a duplication shared between lineages, and more recently a specific duplication in some of those lineages.
[iv] Carbamyl phosphate synthase.
[v] Neighbor-Joining is not conclusive whether the duplication is shared with esociformes, but Maximum Likelihood supports a salmoniforme-specific duplication.
[vi] Gonadotropin-releasing hormone.
[vii] Specific to Gadiformes.
[viii] Number of gene families with at least one duplication specific of the lineage, divided by the number of gene families sampled for the lineage.
[ix] Number of gene families with at least one duplication, specific or shared, divided by the number of gene families sampled for the lineage.