2013 Kyoto Prize Laureates

Basic Sciences

Biological Sciences(Evolution, Behavior, Ecology, Environment)

Masatoshi Nei

/  Evolutionary Biologist

1931 - 2023

Professor, Pennsylvania State University

Commemorative Lectures

Theory and Reality of Evolutionary Biology


11 /11 Mon

Place:Kyoto International Conference Center


From Molecular Population Genetics to Comparative Genomics


11 /12 Tue

13:00 - 16:50

Place:Kyoto International Conference Center

Achievement Digest

Research on the Evolution of Biological Populations Using Quantitative Analyses of Genetic Variation and Evolutionary Time

Dr. Masatoshi Nei made it possible to discuss evolutionary divergence, genetic diversity, and the mode of selection on genes in a quantitative manner by devising diverse statistical methods such as Nei’s genetic distance, and applying them to molecular data. Using these methods, Dr. Nei’s research has yielded important contributions to molecular evolutionary biology, as well as many other academic disciplines including ecology and conservation biology.


Dr. Masatoshi Nei contributed greatly to the transformation of evolutionary biology into an exact science by developing diverse statistical methods to analyze variations in proteins and DNA nucleotide sequences. Evolution occurs through the repeated appearance of novel mutations that propagate within a population and ultimately replace earlier genes. Dr. Nei’s methods of analysis facilitated a quantitative study of genetic variation and evolutionary time—yielding an understanding of evolutionary phenomena based on molecular data for a wide range of species, from unicellular organisms to human beings, in three major ways.

First, Dr. Nei developed “Nei’s genetic distance,” which quantifies differences between populations in terms of allele and allozyme frequencies. Genetic distance has made it possible to estimate migration rates between populations, and to know the time of splitting of populations or species. Using this principle, Dr. Nei solved a major evolutionary question by estimating the divergence time of three major genetically differentiated human groups—Caucasoid, Negroid and Mongoloid—using genetic distance based on protein polymorphism. He also developed a series of new methods, including GST (the coefficient of gene differentiation) and nucleotide diversity. With these techniques, Dr. Nei’s work became instrumental for refining the measurement of evolutionary differentiation and genetic diversity within and between populations.

Second, Dr. Nei and his collaborators developed tools to establish phylogenetic relationships between genes. Especially notable is the “neighbor-joining method” for a molecular phylogenetic tree. This very efficient algorithm has been adopted extensively to produce phylogenetic trees that include many species. In a related major achievement, Dr. Nei clarified the relationship between species phylogeny and gene phylogeny. Today, his methods remain standard tools for deducing phylogenetic relationships of closely related species, such as humans, chimpanzees and gorillas.

Third, Dr. Nei improved a method of estimating the rates of nucleotide substitution, for substitutions that change an amino acid and for those that do not, separately. Thus, the method became easier to use and gained widespread popularity. Dr. Nei showed that comparisons between two substitution rates could reveal the evolutionary mechanism of genes. One notable application of this technique was his demonstration of “positive selection” in the MHC gene cluster, which serves to maintain high genetic diversity.

Many analytical methods developed by Dr. Nei have contributed not only to evolutionary biology but also to a broad range of other academic disciplines, including ecology and conservation biology.

Dr. Nei has also written influential textbooks, helped establish an international society of molecular evolution, and founded its highly-cited scientific journal, thus making major contributions to the education of students and the general public.

For these reasons, the Inamori Foundation is pleased to present the 2013 Kyoto Prize in Basic Sciences to Dr. Masatoshi Nei.


Born in Miyazaki, Japan
B.S., Miyazaki University
Ph.D., Kyoto University
Assistant Professor, Faculty of Agriculture, Kyoto University
Geneticist, National Institute of Radiological Sciences
Head, Population Genetics Laboratory, National Institute of Radiological Sciences
Associate Professor, Brown University
Professor, Brown University
Professor, University of Texas at Houston
Director, Institute of Molecular Evolutionary Genetics, Pennsylvania State University
Professor, Pennsylvania State University
Selected Awards and Honors
Kihara Prize, Genetics Society of Japan
International Prize for Biology, Japan Society for the Promotion of Science
Thomas Hunt Morgan Medal, Genetics Society of America
American Academy of Arts and Sciences, National Academy of Sciences
Selected Publications
Genetic Distance Between Populations, American Naturalist 106: 283-292, 1972.
Genic Variation Within and Between the Three Major Races of Man, Caucasoids, Negroids, and Mongoloids (with Roychoudhury, A. K.), American Journal of Human Genetics 26: 421-443, 1974.
The Neighbor-Joining Method: a New Method for Reconstructing Phylogenetic Trees (Saitou, N and Nei, M), Molecular Biology and Evolution 4: 406-425, 1987.
Pattern of Nucleotide Substitution at Major Histocompatibility Complex Class I Loci Reveals Overdominant Selection (Hughes, A. L. and Nei, M.), Nature 335: 167-170, 1988.
Evolution by the Birth-and-Death Process in Multigene Families of the Vertebrate Immune System (with Gu, X. and Sitnikova, T.), Proc. Natl. Acad. Sci. USA 94: 7799-7806, 1997.
The New Mutation Theory of Phenotypic Evolution, Proc. Natl. Acad. Sci. USA 104: 12235-12242, 2007.
Mutation-Driven Evolution, Oxford University Press, 2013.

Profile is at the time of the award.

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