| How duplicate genes evolve after duplication has been an important issue in the field of molecular evolution. Because the fate of duplicate genes is largely determined at the early stage of evolution after duplication, my thesis is focused on the evolutionary patterns of young duplicate genes. In addition, I consider long-term retention of duplicate genes. First, using suitable data from the whole human genome and stringent statistical methods, I found that in ∼60% of the cases the two young duplicate genes evolve at unequal rates at the amino acid level. Second, I developed a method that uses the spatial distribution of amino acid substitutions to detect relaxation of functional constraints. This and the above analysis suggest that in the majority of cases one copy evolves faster than the other and accumulates amino-acid substitutions evenly across the sequence, whereas the other copy evolves more slowly and accumulates amino-acid substitutions unevenly across the sequence. Such different evolutionary patterns may be largely due to different intensities of functional constraints on the two copies and may lead to a high chance of loss of a duplicate copy. Third, I found that the age distributions of duplicate genes differ among human, Drosophila, Arabidopsis, and nematode, and, contrary to a recent claim, only the distribution in human is L-shaped. Further, I developed a method to study the rate of loss of duplicate genes in human and found that the rate of loss decreases with evolutionary time. This finding suggests that those duplicate genes that have survived the early stage may have gained some selective advantage so that their chance of retention increases with time. In summary, my study provided a general picture of the evolution of young duplicate genes and resolved some long-standing controversies. |
