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In the famous book “The Origin of Species” by Darwin (1859), the gradual accumulation of selectively advantageous variants has been proposed qualitatively by obtaining a hint from the artificial selection of domestic animals and plants as well as from the observation of unique species in a geographically isolated region. The core of this proposal has become evident, after the re-discovery of Mendelian heredity, by the detection of hereditary variants, i. e., mutants, and extensive investigations have been carried out for the behavior of mutants especially in the Drosophila population (Dobzhansky, 1941; Mayer, 1942; Huxley, 1943; Simpson, 1944). In parallel, Darwinian evolution is mathematically formulated in population genetics to estimate the probability that a spontaneously generated mutant is fixed in, or eliminated from, the population according to the positive or negative value of a selective parameter (Fisher, 1930; Wright, 1949). Although the accumulation of such mutants as those found in the Drosophila was supposed to explain the whole process of evolution, the mutants detected at that time were mainly due to the point mutations in established genes, and most of them were defective. Thus, doubts remain about whether the gradual accumulation of such mutants gives rise to radically new organs such as wings and eyes. Another criticism against the survival of the fittest in Darwinian evolution is also raised by the ecological fact of diversity that different styles of organisms coexist in the same area (Nowak et al., 1994). The gene and genome sequencing, which started in the latter half of the last century, has brought new information about the evolution of organisms. First, the amino acid sequence similarities of paralogous proteins strongly suggest that the repertoire of protein functions has been expanded by gene duplication, succeeding nucleotide base substitutions, partial insertion and deletion, and further by domain shuffling in some cases (Ingram, 1963; Gilbert, 1978; Ferris & White, 1979). Such examples are now increasing, proposing many protein families and superfamilies. Second, the clustering analysis of proteomes reveals a characteristic feature that the proteins functioning in the core part are essentially common to both prokaryotes and eukaryotes, and that the decisive difference in gene repertoire between the organisms is observed in the peripheral parts displaying different living styles (Kojima & Otsuka, 2000 a, b, c; Kojima & Otsuka, 2002). These sequence data are now compiled into databases (e. g., Wheeler et al., 2004; Birney et al., 2006).

A Theoretical Scheme of the Large-Scale Evolution by Generating New Genes from Gene Duplication