Masatoshi Nei

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Masatoshi Nei
Masatoshi Nei - 2013.jpg
BornJanuary 2, 1931 (1931-01-02) (age 88)
Nationality USA
Alma materKyoto University
University of Miyazaki(1953)
Known forStatistical theories of molecular evolution and development of the theory of mutation-driven evolution
AwardsKyoto Prize (2013)
Thomas Hunt Morgan Medal (2006)
Barbara Bowman Award (2003)
International Prize for Biology (2002)
Member, National Academy of Sciences (1997)
Kihara Prize (1990)
Rockefeller Foundation Fellowship (1961)
Scientific career
Fieldsmolecular evolution
molecular phylogenetics
InstitutionsTemple University
Pennsylvania State University
University of Texas at Houston
Brown University
National Institute of Radiological Sciences
Kyoto University

Masatoshi Nei (根井正利, Nei Masatoshi) is a population geneticist currently affiliated with the Department of Biology at Temple University as a Carnell Professor. He was, until recently, Evan Pugh Professor of Biology at Pennsylvania State University and Director of the Institute of Molecular Evolutionary Genetics and had been there from 1990 to 2015.

He was born in 1931 in Miyazaki Prefecture, on Kyūshū Island, Japan. He was associate professor and professor of biology at Brown University from 1969 to 1972 and professor of population genetics at the Center for Demographic and Population Genetics, University of Texas at Houston, from 1972 to 1990. He is a theoretical population geneticist and evolutionary biologist. Acting alone or working with his students, he has continuously developed statistical theories of molecular evolution taking into account discoveries in molecular biology. He has also developed concepts in evolutionary theory and advanced the theory of mutation-driven evolution.

Work in population genetics[edit]

Theoretical studies[edit]

He is the first to show mathematically that in the presence of gene interaction natural selection always tends to enhance the linkage intensity between genetic loci or maintain the same linkage relationship.[1] He then observed that the average recombination value per genome is generally lower in higher organisms than in lower organisms and attributed this observation to his theory of linkage modification.[2] Recent molecular data indicate that many sets of interacting genes such as Hox genes, immunoglobulin genes, and histone genes have often existed as gene clusters for a long evolutionary time. This observation can also be explained by his theory of linkage modification. He also showed that, unlike R. A. Fisher's argument, deleterious mutations can accumulate rather quickly on the Y chromosome or duplicate genes in finite populations.[3][4] In 1969, considering the rates of amino acid substitution, gene duplication, and gene inactivation, he predicted that higher organisms contain a large number of duplicate genes and nonfunctional genes (now called pseudogenes).[5] This prediction was shown to be correct when many multigene families and pseudogenes were discovered in the 1980s and 1990s. His notable contribution in the early 1970s is the proposal of a new measure of genetic distance (Nei's distance) between populations and its use for studying evolutionary relationships of populations or closely related species.[6] He later developed another distance measure called DA, which is appropriate for finding the topology of a phylogenetic tree of populations.[7] He also developed statistics of measuring the extent of population differentiation for any types of mating system using GST measure.[8] In 1975, he and collaborators presented a mathematical formulation of population bottleneck effects and clarified the genetic meaning of bottleneck effects.[9] In 1979, he proposed a statistical measure called nucleotide diversity,[10] which is now widely used for measuring the extent of nucleotide polymorphism. He also developed several different models of speciation and concluded that the reproductive isolation between species occurs as a passive process of accumulation of interspecific incompatibility mutations [11][12]

Protein polymorphism and neutral theory[edit]

In the early 1960s and 1970s, there was a great controversy over the mechanism of protein evolution and the maintenance of protein polymorphism. Nei and his collaborators developed various statistical methods for testing the neutral theory of evolution by using polymorphism data. Their analysis of the allele frequency distribution, the relationship between average heterozygosity and protein divergence between species, etc., showed that a large portion of protein polymorphism can be explained by neutral theory.[13][14] The only exception was the major histocompatibility complex (MHC) loci, which show an extraordinarily high degree of polymorphism. For these reasons, he accepted the neutral theory of evolution.[14][15]

Human evolution[edit]

Using his genetic distance theory, he and A. K. Roychoudhury showed that the genetic variation between Europeans, Asians, and Africans is only about 11 percent of the total genetic variation of the human population. They then estimated that Europeans and Asians diverged about 55,000 years ago and these two populations diverged from Africans about 115,000 years ago.[16][17] This conclusion was supported by many later studies using larger numbers of genes and populations, and the estimates appear to be still roughly correct. This finding represents the first indication of the out-of-Africa theory of human origins.

Molecular phylogenetics[edit]

Around 1980, Nei and his students initiated a study of inference of phylogenetic trees based on distance data. In 1985 they developed a statistical method for testing the accuracy of a phylogenetic tree by examining the statistical significance of interior branch lengths. They then developed the neighbor-joining and minimum-evolution methods of tree inference.[18][19] At present, the neighbor-joining method is most widely used in molecular phylogenetics,[20] though some theoreticians advocate the likelihood and the Bayesian methods.[21] They also developed statistical methods for estimating evolutionary times from molecular phylogenies. In collaboration with Sudhir Kumar and Koichiro Tamura, he developed a widely used computer program package for phylogenetic analysis called MEGA.[22]

MHC loci and positive Darwinian selection[edit]

Nei's group invented a simple statistical method for detecting positive Darwinian selection by comparing the numbers of synonymous nucleotide substitutions and nonsynonymous nucleotide substitutions. .[23] Applying this method, they showed that the exceptionally high degree of sequence polymorphism at MHC loci is caused by overdominant selection.[24] Although various statistical methods for this test have been developed later, their original methods are still widely used.[25]

New evolutionary concepts[edit]

Nei and his students studied the evolutionary patterns of a large number of multigene families and showed that they generally evolve following the model of a birth-and-death process.[26] In some gene families this process is very fast, caused by random events of gene duplication and gene deletion and generates genomic drift of gene copy number. Nei has long maintained the view that the driving force of evolution is mutation including any types of DNA changes (nucleotide changes, chromosomal changes, and genome duplication) and natural selection is merely a force eliminating less fit genotypes (theory of mutation-driven evolution).[14][25] He conducted statistical analyses of evolution of genes controlling phenotypic characters such as immunity and olfactory reception and obtained evidence supporting this theory.[25]

New journal, new society[edit]

He founded the journal Molecular Biology and Evolution in 1983 and the Society for Molecular Biology and Evolution in 1993, together with Walter M. Fitch.[27]

Professional Activities and Memberships[edit]

  • 2011: Honorary Advisory Member, 2011 Annual Meetings, Society for the Study of Molecular Biology and Evolution, Kyoto University
  • 2004-2011: Advisory Board, Gene
  • 2003-2015: Editorial Board, Proceedings of National Academy of Sciences
  • 2002-2004: Consulting Editor, Journal of Molecular Evolution
  • 2001: Honorary Member, Japan Society of Animal Genetics and Breeding
  • 2000: Honorary Member, Japan Society for Histocompatibility and Immunogenetics
  • 1999: President, American Genetic Association
  • 1997: Member, National Academy of Sciences, USA
  • 1996: Honorary Member, Japan Society of Human Genetics
  • 1995-2007: Associate Editor, Journal of Heredity
  • 1994: President, Society for Molecular Biology and Evolution
  • 1993: Elected Fellow, American Association for the Advancement of Science
  • 1992-1995: Council Member, Society for Molecular Biology and Evolution
  • 1990: Elected Fellow, American Academy of Arts and Sciences
  • 1989: Honorary Member, Genetics Society of Japan
  • 1985-1997: Advisory Board, Gene Geography, Rome, Italy
  • 1983-1993: Editor, Molecular Biology and Evolution
  • 1979-2001: Editorial Board, Journal of Molecular Evolution
  • 1977-1985: Associate Editor, Genetics
  • 1973-1984: Associate Editor, Theoretical Population Biology
  • 1973-1976: Editorial Board, Evolutionary Theory

Awards and honors[edit]

  • 2013: Kyoto Prize in Basic Sciences
  • 2013: C.C. Li Lecture, University of Pittsburgh
  • 2013: New Species of Gammaproteobacteria, Neiella marina, named in honor of Masatoshi Nei[28]
  • 2011: C.C. Tan Distinguished Lecture, Fudan University
  • 2011: Pennsylvania State University SMBE Symposium Honoring the 80th Birthday of Masatoshi Nei
  • 2006: Masatoshi Nei Legacy Symposium Held at the 2006 Molecular Biology and Evolution Society Meeting
  • 2006: Thomas Hunt Morgan Model, Genetics Society of America
  • 2003: Barbara Bowman Award, Texas Genetics Society
  • 2002: Honorary Doctorate, Miyazaki University
  • 2002: 2002 International Prize for Biology, Japan Society for the Promotion of Science
  • 2001: Wilhelmine E. Key Invitational Lecture, Annual Meeting of the American Genetics Association
  • 2000: Certificate of Award, "Highly Cited Researchers"
  • 2000: Masatoshi Nei Annual Lecture established for the Society for Molecular Biology and Evolution
  • 1999: P.R. Krishnaiah Memorial Lecture, Pennsylvania State University
  • 1990: Kihara Prize, Genetics Society of Japan
  • 1977: Japan Society of Human Genetics Award
  • 1960: Rockefeller Foundation Fellowship


  • 2015–Present: Laura Carnell Professor of Biology, Temple University, Main Campus
  • 1994-2015: Evan Pugh Professor of Biology, Pennsylvania State University, University Park
  • 1990-2015: Director, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park
  • 2001 & 2011: Visiting Professor of Biology, Tokyo Institute of Technology, Tokyo
  • 1990-1994: Distinguished Professor of Biology, Pennsylvania State University, University Park
  • 1972-1990: Professor of Population Genetics, University of Texas at Houston, Houston
  • 1978-1980: Acting Director, Center for Demographic and Population Genetics, University of Texas at Houston, Houston
  • 1971-1972: Professor of Biology, Brown University, Providence
  • 1969-1971: Associate Professor of Biology, Brown University, Providence
  • 1965-1969: Head, Population Genetics Laboratory, National Institute of Radiological Sciences, Japan
  • 1962-1965: Geneticist, National Institute for Radiological Sciences, Japan
  • 1958-1962: Assistant Professor, Kyoto University, Kyoto

See also[edit]


  1. ^ Nei, Masatoshi (1967). "Modification of linkage intensity by natural selection". Genetics. 57 (3): 625–641. PMC 1211753. PMID 5583732.
  2. ^ Nei, Masatoshi (1968). "Evolutionary change of linkage intensity". Nature. 218 (5147): 1160–1161. doi:10.1038/2181160a0. PMID 5656638.
  3. ^ Nei, M. (1970) Accumulation of nonfunctional genes on sheltered chromosomes. Am. Nat. 104:311-322
  4. ^ Nei, M. and A. K. Roychoudhury (1973) Probability of fixation of nonfunctional genes at duplicate loci. Am. Nat. 107:362-372
  5. ^ Nei, M. (1969) Gene duplication and nucleotide substitution in evolution. Nature 221:40-42
  6. ^ Nei, M. (1972) Genetic distance between populations. Am. Nat. 106:283-292
  7. ^ Nei, M., F. Tajima, & Y. Tateno (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J. Mol. Evol. 19:153-170.
  8. ^ Nei, M. (1973) Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA 70:3321-3323.
  9. ^ Nei, M., T. Maruyama and R. Chakraborty (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1-10
  10. ^ Nei, Masatoshi; Li, Wen-Hsiung (October 1979). "Mathematical model for studying genetic variation in terms of restriction endonucleases". Proc. Natl. Acad. Sci. USA 76 (10):5269-5273. PMC 413122. PMID 291943,
  11. ^ Nei, M. T. Maruyama, and C. I. Wu (1983) Models of evolution of reproductive isolation. Genetics 103:557-579.
  12. ^ Nei, M., and M. Nozawa (2011) Roles of Mutation and Selection in Speciation: From Hugo de Vries to the modern genomic era. Genome Biol Evol 3:812-829.
  13. ^ Nei, M. (1983) Genetic polymorphism and the role of mutation in evolution (M. Nei and P. K. Koehn, eds.) Evolution of Genes and Proteins. Sinauer Assoc., Sunderland, MA, pp. 165-190.
  14. ^ a b c Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
  15. ^ Li, W. H., T. Gojobori, and M. Nei (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292:237-239.
  16. ^ Nei, M. and A. K. Roychoudhury (1974) Genic variation within and between the three major races of man, Caucasoids, Negroids, and Mongoloids. Am. J. Hum. Genet. 26:421-443.
  17. ^ Nei, M. and A. K. Roychoudhury (1982) Genetic relationship and evolution of human races. Evol. Biol. 14:1-59.
  18. ^ Saitou, N. and M. Nei (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  19. ^ Rzhetsky, A. and M. Nei (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10:1073-1095.
  20. ^ Nei, M., and S. Kumar (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
  21. ^ Yoshida, Ruriko; Nei, Masatoshi (2016-06-01). "Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes". Molecular Biology and Evolution. 33 (6): 1618–1624. doi:10.1093/molbev/msw042. PMID 26929244.
  22. ^ Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis. Ver. 1.02, The Pennsylvania State University, University Park, PA.
  23. ^ Nei, M. and T. Gojobori (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
  24. ^ Hughes, A. L. and M. Nei (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
  25. ^ a b c Nei, M. (2013) Mutation-Driven Evolution. Oxford University Press, Oxford.
  26. ^ Nei, M. and A. P. Rooney (2005) Concerted and birth-and-death evolution of multigene families.
  27. ^ Nei, Masatoshi (2014-06-01). "My memory of Walter Fitch (1929-2011) and starting molecular biology and evolution". Molecular Biology and Evolution. 31 (6): 1329–1332. doi:10.1093/molbev/msu133. PMC 4032136. PMID 24723418.
  28. ^ Du, Zong-Jun; Miao, Ting-Ting; Rooney, Alejandro P.; Liu, Qian-Qian; Chen, Guan-Jun (2013-05-01). "Neiella marina gen. nov., sp. nov., isolated from the sea cucumber Apostichopus japonicus". International Journal of Systematic and Evolutionary Microbiology. 63 (Pt 5): 1597–1601. doi:10.1099/ijs.0.043448-0. PMID 22904222.


  • Nei, M.(2013) Mutation-Driven Evolution. Oxford University Press, Oxford.
  • Nei, M., and S. Kumar (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
  • National Research Council, (1996) The Evaluation of DNA Forensic Evidence. National Academies Press, Washington D.C.
  • Roychoudhury, A. K., and M. Nei (1988) Human Polymorphic Genes: World Distribution. Oxford University Press, Oxford and New York.
  • Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
  • Nei, M., and R. K. Koehn (eds). (1983) Evolution of Genes and Proteins. Sinauer Assoc., Sunderland, MA.
  • Nei, M. (1975) Molecular Population Genetics and Evolution. North-Holland, Amsterdam and New York.

External links[edit]