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As the analyses of omics such as genomes and transcriptomes have been progressed for the increasing number of species, it becomes possible to study an organism as a whole, with recognizing each and every underlying system as product of complexed expression of genes involved. In our laboratory, with emphasizing the viewpoints of molecular evolution and population genetics, a few biosystems have been studied to solve questions such as “How have the mutations of individual genes led to phenotypical changes and become subject to natural selection?” or “How have complex systems been formed through the accumulation of mutations?”. With the aims in mind, we have conducted specific researches on the followings: (1) the evolution of reproductive systems in Polygonaceae, such as the heteromorphic self-incompatibility system in buckwheat in which one genetic locus controls dimorphic flower type as well as self-incompatibility, (2) the evolution of immune systems such as adaptive and innate immune system of fishes, and (3) adaptive evolution of notothenioid fishes, which have attained numerous unique characters upon the cooling of the Southern Ocean after the geological isolation of Antarctica.