**5. Conclusion**

32 Gene Duplication

*Danio rerio*

*Takifugu rubripes*

*Tetraodon nigroviridis*

*Gasterosteus aculeatus*

*Oryzias latipes*

*Astatotilapia burtoni*

*Oreochromis niloticus*

Hypothetical *Hox* cluster complement of teleost ancestor

the FSGD event.

**Teleost ancestor**

**4. Molecular evolution of duplicated genes** 

Fig. 3. *Hox* gene clusters, the best-studied examples of differential duplicate gene retention and loss in teleosts. Hypothetical *Hox* clusters of the teleost ancestor (modified from Guo et al. 2010), and *Hox* clusters of teleost model fish species, together with specific gene loss events shown on a phylogenetic tree of select fish species (adapted form Hoegg et al. 2007). was lost independently in the Otocephala and Euteleostei after the FSGD event. The ongoing process of *Hox* gene loss and retention in teleosts illustrates again that degeneration of functionally important duplicated genes can last for hundreds of millions of years after

We next wished to study patterns of sequence evolution in the 1,500 duplicate gene families we had identified. To this end, we downloaded both nucleic acid and amino acid sequences for genes in these families. For each species, we retained only one gene copy in each duplicated clade (Figure 1B) for further analysis, and discarded all other copies in those gene families where additional duplications have occurred after the FSGD event. We then aligned the amino acid sequences within each gene family with MUSCLE (Edgar In summary, we used a phylogenetic method to identify 1,500 duplicated gene families in five teleost species that are likely to have resulted from the FSGD event. Only a small fraction of genes in extant teleost genomes have been retained in the FSGD event. Differential retention and loss of duplicated gene is pervasive in the five species we studied, as is illustrated by genes in the teleost *Hox* gene clusters. Sequence analysis suggests that some duplicated genes pairs may evolve asymmetrically. Our work provides a framework for future studies of the evolutionary trajectory of duplicated genes in the teleost genome.

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