2013Basic SciencesBiological Sciences (Evolution, Behavior, Ecology, Environment)
Masatoshi Nei photo

Masatoshi Nei

  • U.S.A. / January 2, 1931
  • Evolutionary Biologist
  • Professor, Pennsylvania State University

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.


Brief Biography

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.


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

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.


Abstract of the Lecture

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

I was a normal boy when I was young and had no particular interest in becoming a scientist. This situation suddenly changed in 1946 when I lost my left eyesight by explosion of an ignition equipment of a war-time bomb. This accident forced me to stay in a clinic for about one month, and during this period I thought about my future life seriously for the first time. My interest for studying population genetics and evolution occurred in the first college year mainly because I discovered that I could use my talent of mathematics in this field. At that time evolutionary biology was largely speculative and based on the study of morphological characters, which are strongly affected by environmental factors. In my judgment this was not a serious scientific discipline. However, population genetics was more solid and dealt with the theoretical basis of evolution, animal and plant breeding, and medical genetics at the gene level. I therefore decided to study mathematical population genetics and tried to make it useful for understanding long-term evolution of organisms. Fortunately, around 1960 the molecular approach of evolutionary study was introduced, and we could develop new evolutionary theories by taking into account molecular data. One of my first studies at this time was concerned with the effect of gene duplication on phenotypic evolution. This study predicted that vertebrate organisms contain a large number of duplicate genes and pseudogenes (nonfunctional genes). Thirty years later, study of genomic sequences proved that this was indeed the case. I also developed the theory of genetic distance for measuring the extent of genetic divergence between populations. I then applied this theory to human populations and concluded that the first splitting of human populations occurred between Africans and non-Africans about 100,000 years ago and that non-African populations later migrated to occupy the rest of the world. Recent genomic data again support the major aspects of this conclusion. This genetic distance theory is now widely used in evolutionary biology and conservation biology of various organisms. I also developed a neighbor-joining method of phylogenetic analysis, which has been cited more than 33,000 times by now. Furthermore, I developed a method for measuring the extent of natural selection at the DNA sequence level, which is now used as a standard method of studying evolution. I also analyzed the evolutionary pattern of many immunological and non-immunological genes controlling phenotypic characters. On the basis of these studies, I developed a new evolutionary theory called “Mutation-Driven Evolution” (Oxford University Press, 2013).

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From Molecular Population Genetics to Comparative Genomics

Tuesday, November 12, 2013
Kyoto International Conference Center
Coordinator and Moderator
Yoh Iwasa (Chairman, Kyoto Prize Committee; Professor, Kyushu University)
Organized by Inamori Foundation
Supported by Kyoto Prefectural Government, Kyoto City Government, NHK
With the cooperation of Japanese Society for Bioinformatics, Japanese Society for Histocompatibility and Immunogenetics, The Anthropological Society of Nippon, The Botanical Society of Japan, The Ecological Society of Japan, The Genetics Society of Japan, The Japan Society of Human Genetics, The Society of Evolutionary Studies, The Society of Population Ecology, The Society for the Study of Species Biology


Opening Address Yoh Iwasa
Introduction of Laureate Takashi Gojobori (Member, Kyoto Prize Committee; Project Professor, National Institute of Genetics)
Laureate’s Lecture Masatoshi Nei (the Laureate in Basic Sciences)
“Darwinism and a New Theory of Mutation-driven Evolution”
Lecture Naruya Saitou (Professor, National Institute of Genetics)
“Human Evolution and Origin of Japonesian”
Lecture Yoko Satta (Member, Kyoto Prize Selection Committee; Professor, The Graduate University for Advanced Studies)
“The Polymorphism and Evolutionary Rate of MHC Genes and the Maintenance Mechanism”
Lecture Koichiro Tamura (Professor, Tokyo Metropolitan University)
“Bioinformatics in Molecular Evolutionary Genetics Analysis”
Lecture Mitsuyasu Hasebe (Member, Kyoto Prize Committee; Professor, National Institute for Basic Biology, National Institutes of Natural Sciences)
“Evolution of Genome, Body Plan, and Carnivory in Land Plants”