**1. Introduction**

26 Gene Duplication

Stewart, N. S. & Rothwell, G. W. (1993). *Paleobotany and the Evolution of Plants.* pp. 438-467,

Sugaya, N. & Otsuka, J. (2002). The Lineage-Specific Base-Pair Contents in the Stem Regions

Van den Eynde, H.; De Baere, R.; De Roeck, E.; Van de Peer, Y.; Vandenberghe, A.;

Wheeler, D. L.; Church, D. M.; Edgar, R.; Federhen, S.; Helmberg, W.; Madden, T. L.;

Wise, D. M. (1988). The Diversity of Mitosis: the Value of Evolutionary Experiments.

Wright, S. (1949). Adaptation and Selection*.* In: *Genetics, Paleontology and Evolution.* G. L.

Yang, D.; Oyaizu, Y.; Oyaizu, H.; Olsen, G. J. & Woese, C. R. (1985). Mitochondrial Origin.

Plastids and Cyanobacteria. *J. Mol. Evol.*, Vol. 27, pp. 126-132

of Ribosomal RNAs and Their Influence on the Estimation of Evolutionary

Willekens, P. & De Wachter, R. (1988). The 5S Ribosomal RNA Sequences of a Red Algal Rhodoplast and Gymnosperm Chloroplast: Implication for the Evolution of

Pontius, J. U.; Schuler, G. D.; Schriml, L. M.; Sequeira, E.; Suzek, T. O.; Tatusova, T. A. & Wagner, L. (2004). National Center of Biotechnology Information. *Nucl. Acid* 

Jepson; G. G. Simpson & E. Mayer, (Eds.), pp. 365-389, Princeton Univ. Press,

Cambridge University Press, Cambridge

Distances. *J. Mol. Evol.*, Vol. 55, pp. 584-594

*Res.*, Vol. 32, Database Issue D35

Princeton, New Jersey

*Biochem. Cell Biol.,* Vol. 66, pp. 515-529.

*Proc. Natl. Acad. Sci. USA*, Vol. 82, pp. 4443-4447

Gene and genome duplication have been thought to play an import part during evolution since the 1930s (Bridges 1936; Stephens 1951; Ohno 1970) . Ohno (1970) proposed that the increased complexity and genome size of vertebrates has resulted from two rounds (2R) of whole genome duplication (WGD) in early vertebrate evolution, which provided raw materials for the evolutionary diversification of vertebrates. Recent genomic sequence data provide substantial evidence for the abundance of duplicated genes in many organisms. Extensive comparative genomics studies have demonstrated that teleost fish experienced another round of genome duplication, the so-called fish-specific genome duplication (FSGD) (Amores et al. 1998; Taylor et al. 2003; Meyer and Van de Peer 2005). Because the timing of this WGD and the radiation of teleost species approximately coincided, it has been suggested that the large number (about 27,000 species—more than half of all vertebrate species (Nelson, 2006)) of teleosts and their tremendous morphological diversity might be causally related to the FSGD event (Amores et al. 1998; Taylor et al. 2001; Taylor et al. 2003; Christoffels et al. 2004; Hoegg et al. 2004; Vandepoele et al. 2004). Semon and Wolfe (2007) showed thousands of genes that remained duplicated When Tetraodon and zebrafish diverged underwent reciprocal loss subsequently in these two species may have been associated with reproductive isolation between teleosts and eventually contributed to teleost diversification. A study in yeast demonstrated that speciation of polyploid yeasts may be associated with reciprocal gene loss at duplicated loci (Scannell et al. 2006). Thus, speciation accompanied by differential retention and loss of duplicated genes after genome duplication may be a powerful lineage-splitting force (Lynch and Conery 2000).

For two reasons, teleost fish represent an excellent model system to study the retention and loss of duplicated genes as well as their evolutionary trajectory following whole-genome

<sup>\*</sup> Corresponding author

(A)

(B)

Duplication

Speciation

FSGD

Gene\_*Xa*

Gene\_*X*

Gene\_*Xb*

duplicated genes actually resulted from the FSGD event.

Fig. 1. (A) Expected phylogenetic relationship of duplicated gene *Xa* and *Xb* in two related species A and B when speciation occurred after the duplication event; (B) Tree topology we used for duplicated gene identification in the database HOMLENS 4. 'N ≥ 2' means that duplicated gene pairs must exist at least in two species to increase the likelihood that the

Duplicated Gene Evolution Following Whole-Genome Duplication in Teleost Fish 29

two teleost genomes. Thus, our method would overlook duplicated genes that result from the FSGD and that are retained in only one teleost genome. While we cannot exclude this possibility, we note that our observations are consistent with a genome-wide study of Tetraodon, in which Jaillon et al. (2004) showed that up to 3 percent of duplicated genes may have been retained since the FSGD event. One plausible explanation of the difference in duplicated gene retention between teleost and yeast may come from the different ages of the genome duplication event. In addition, Kassahn et al. (2009) suggested that a minimum of 3 to 4 percent of protein-coding loci have been retained in two copies in each of the five model

Species A

Species B Species A Gene\_*Xa*

Gene\_*Xb*

*Homo sapiens*

N≥2

N≥2

Species B

duplication. First, many duplicated genes that resulted from the FSGD event were preserved in teleost genomes. Second, five teleost genomes have been sequenced and more teleost genomes are being sequenced. Here, we investigate retention, loss, and molecular evolution of duplicate genes after the FSGD in five available teleost geomes that include the genomes of zebrafish *Danio rerio*, stickleback *Gasterosteus aculeatus*, medaka *Oryzias latipes*, Takifugu *Takifugu rubripes*, and Tetraodon *Tetraodon nigroviridis*.
