**7. References**

22 Gene Duplication

animals show the living style defined as the diploid organism in the present chapter. Such divergence of body plans occasionally occurred afterwards in each of the above phyla. The examples well investigated in paleontology are the divergence of *Placodermi*, cartilaginous fish and bony fish, the divergence of amphibians, reptiles and mammals, and the divergence of dinosaurs and birds, which occurred in the *Chordata* within the recent 4x108 years (Carroll, 1988). The seed plants also show the similar tendency in the successive divergence of *Coniferophyta*, *Anthophyta* and their relatives (Fairon-Demaret & Scheckler, 1987; Rothwell et al., 1989; Rowe, 1992; Stewart & Rothwell, 1993; Kawai & Otsuka, 2004), although many of these seed plants can also self-reproduce by the parthenogenesis and their explosive feature seems mild. Although the explosive divergence of body plans can be also explained by the biological activity expressed in terms of the interaction between differentiated cells (Otsuka, 2008), the present study derives this divergence from the aspect of the generation of new

The fossil record of these examples indicates that the original style of organisms prospered over a wide region when new styles of organisms diverged, being consistent with the present theory. The prosperity of the original style of organisms means that their biological activity is high, and this is necessary to permit the existence of variants carrying duplicated genes in the population and further to enhance the chance of assembling many kinds of new genes into a genome by hybridization. This is in contrast with Darwinian evolution generating new species adapted to the special environment of a geographically isolated

Finally, some discussions will be given to the problem why the cell differentiation has been shifted from the monoploid state to the diploid state. This problem arises from the present result that the diploid organism is not necessarily superior to the monoploid organism with the ability of exchanging homologous chromosomes in assembling many kinds of new genes for cell differentiation. The main reason of this shifting may be the protection of differentiated cells from the point mutations due to the miss in repairing damaged nucleotide bases. First of all, many more genes are needed to develop the higher hierarchy of cell differentiation. In fact, the genome size of higher eukaryotes is expanded to the order of *108 ~ 109 bp*, e. g., *1.2x108 bp* encoding *24,000* genes in *Arabidopsis thaliana*, *1.4x108 bp* encoding *13,000* genes in *Drosophila melanogaster* and *3.1x109 bp* encoding *30,000*  genes in *Homo sapiens* (Wheeler et al., 2004). Second, it takes a longer time, one or more years, to develop the higher hierarchy of cell differentiation to form an adult form in the higher eukaryotes, although the growth rate and the lifetime seem to be further regulated differently depending on species. On the other hand, the mutation rate due to the miss in repair is *10-9* per site per year in eukaryotes as well as in prokaryotes (Kimura, 1980; Otsuka et al., 1997). As the evidence for the above discussion, the males of some species of ants and bees are born by the haploid parthenogenesis, showing that the monoploid state is sufficient for the high hierarchy of cell differentiation during their short lifetime. Although the accuracy in repairing damaged DNAs can be raised by the additional energy for proofreading (Hopfield, 1974), the evolution of organisms has not been directed to use such additional energy. On the contrary, the nucleotide base substitution rate becomes about tenfold faster in animal mitochondrial genome than in the host cell genome, as is used to resolve the phylogeny of recently diverged animals (Hasegawa et al., 1985; Pesole et al., 1999; Otsuka et al., 2001). This faster mutation rate strongly suggests that the energy to proofread the small genome of mitochondria is diminished and instead the saved energy is used to raise the biological activity of the host cell. For the

genes from gene duplication in diploid organisms.

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**2** 

**Teleost Fish** 

*1,2Switzerland 3PR China* 

*University of Zurich, Zurich* 

**Duplicated Gene Evolution Following** 

Baocheng Guo1,2,3, Andreas Wagner1,2 and Shunping He3\* *1 Institute of Evolutionary Biology and Environmental Studies,* 

*2 The Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne 3Fish Phylogenetics and Biogeography Group, Key Laboratory of Aquatic Biodiversity and* 

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

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

**1. Introduction** 

 \*

Corresponding author

lineage-splitting force (Lynch and Conery 2000).

*Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan* 

**Whole-Genome Duplication in** 

