Masatoshi Nei
Encyclopedia
is Evan Pugh Professor of Biology at Pennsylvania State University
and Director of the Institute of Molecular Evolutionary Genetics since 1990. 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 evolution
ary biologist. Acting alone or working with his students, he has continuously developed new statistical theories of molecular evolution taking into account frontier knowledge of molecular biology. He has also made several conceptual developments of evolutionary theory.
interaction natural selection
always tends to enhance the linkage intensity between genetic loci or maintain the same linkage relationship. 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 finding of linkage modification by natural selection. Recent molecular data indicate that many sets of interacting genes such as Hox genes, immunoglobulin genes, and histone genes often exist as gene clusters for a long evolutionary time. This observation can also be explained by his principle of maintenance of linkage of interacting genes. 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. 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). This prediction was ignored for many years but later vindicated when many multigene families and pseudogenes were discovered in the 1980s. 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. This distance measure was attacked by many cladists but is still widely used in molecular population genetics and molecular ecology. Later, he developed another distance measure called DA, which is appropriate for finding the topology of a phylogenetic tree. He also developed statistics of measuring the extent of population differentiation for any types of mating system using GST measure. In 1975, he and collaborators presented a mathematical formulation of population bottleneck effects and clarified the genetic meaning of bottleneck effects. In 1979, he developed a mathematical theory for studying genetic variation in terms of restriction enzymes. In collaboration with Takeo Maruyama and Chung-I Wu, he also developed a theory of evolution of reproductive isolation using various models of incompatibility of genes between two isolated populations. This model is still controversial but now appears applicable to the evolution of cis-regulatory elements and transcription factors.
. He also trained many graduate students and postdoctorals who have become leading figures in molecular evolution including Margaret Kidwell, Wen-Hsiung Li
, Ranajit Chakraborty, Shozo Yokoyama, Aravinda Chakravarti, Dan Graur
, Fumio Tajima, Chung-I Wu, Naoyuki Takahata, Takashi Gojobori
, Pekka Pamilo, Austin Hughes, Andrey Rzhetsky, Jianzhi (George) Zhang, and Sudhir Kumar.
Pennsylvania State University
The Pennsylvania State University, commonly referred to as Penn State or PSU, is a public research university with campuses and facilities throughout the state of Pennsylvania, United States. Founded in 1855, the university has a threefold mission of teaching, research, and public service...
and Director of the Institute of Molecular Evolutionary Genetics since 1990. He was born in 1931 in Miyazaki Prefecture
Miyazaki Prefecture
is a prefecture of Japan located on the island of Kyushu. The capital is the city of Miyazaki.- History :Historically, after the Meiji Restoration, Hyūga Province was renamed Miyazaki Prefecture....
, on Kyūshū
Kyushu
is the third largest island of Japan and most southwesterly of its four main islands. Its alternate ancient names include , , and . The historical regional name is referred to Kyushu and its surrounding islands....
Island, Japan. He was associate professor and professor of biology at Brown University from 1969 to 1972 and professor of population genetics
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...
at the Center for Demographic and Population Genetics, University of Texas at Houston, from 1972 to 1990. He is a theoretical population geneticist and evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary biologist. Acting alone or working with his students, he has continuously developed new statistical theories of molecular evolution taking into account frontier knowledge of molecular biology. He has also made several conceptual developments of evolutionary theory.
Theoretical studies
He is the first to show mathematically that in the presence of geneGene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
interaction natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
always tends to enhance the linkage intensity between genetic loci or maintain the same linkage relationship. 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 finding of linkage modification by natural selection. Recent molecular data indicate that many sets of interacting genes such as Hox genes, immunoglobulin genes, and histone genes often exist as gene clusters for a long evolutionary time. This observation can also be explained by his principle of maintenance of linkage of interacting genes. 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. 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). This prediction was ignored for many years but later vindicated when many multigene families and pseudogenes were discovered in the 1980s. 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. This distance measure was attacked by many cladists but is still widely used in molecular population genetics and molecular ecology. Later, he developed another distance measure called DA, which is appropriate for finding the topology of a phylogenetic tree. He also developed statistics of measuring the extent of population differentiation for any types of mating system using GST measure. In 1975, he and collaborators presented a mathematical formulation of population bottleneck effects and clarified the genetic meaning of bottleneck effects. In 1979, he developed a mathematical theory for studying genetic variation in terms of restriction enzymes. In collaboration with Takeo Maruyama and Chung-I Wu, he also developed a theory of evolution of reproductive isolation using various models of incompatibility of genes between two isolated populations. This model is still controversial but now appears applicable to the evolution of cis-regulatory elements and transcription factors.
Protein polymorphism and neutral theory
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 students 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., could not reject the null hypothesis of neutral evolution though a large amount of data for various genes from diverse groups of species were examined. The only exception was the major histocompatibility complex (MHC) loci, which show an extraordinarily high degree of polymorphism. He also showed that pseudogenes may represent a paradigm of neutral evolution without any selection. For these reasons, he accepted the neutral theory of evolution.Human evolution
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, which was in agreement with the results published by R. C. Lewontin in the same year. Nei and Roychoudhury then estimated that Europeans and Asians diverged about 55,000 years ago and these two populations diverged from Africans about 115,000 years ago. This conclusion was supported by many later studies using larger numbers of genes and populations, and the estimates are still widely used. This study was a forerunner of the out of Africa theory of human origin by Allan Wilson.Molecular phylogenetics
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. At present, the neighbor-joining method is most widely used in molecular phylogenetics, though some theoreticians advocate the likelihood and the Bayesian methods. 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.MHC loci and positive Darwinian selection
Nei’s group invented a statistical method for detecting positive Darwinian selection by comparing the numbers of synonymous nucleotide substitutions and nonsynonymous nucleotide substitutions. Applying this method, they showed that the exceptionally high degree of sequence polymorphism at MHC loci is caused by overdominant selection. Although various statistical methods for this test have been later developed, their original methods are still widely used. He maintains that the Bayesian method of inferring positively selected amino acid sites tends to give false-positives and experimental tests are necessary for confirmation of these sites.Birth-and-death evolution and neomutationism
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. In some gene families this process is very fast and 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 genetic changes and natural selection is merely a force eliminating less fit genotypes (neomutationism). He conducted statistical analyses of the evolution of genes controlling phenotypic characters such as olfactory reception and obtained evidence supporting his neomutationism.New journal, new society, and students
He founded the journal Molecular Biology and Evolution in 1983 and the Society for Molecular Biology and Evolution in 1993, together with Walter M. FitchWalter M. Fitch
Walter M. Fitch . Until his death he was professor of molecular evolution at the University of California, Irvine. He was also a member of the National Academy of Sciences, the American Philosophical Society, and the American Association for the Advancement of Science, and was a Foreign Member of...
. He also trained many graduate students and postdoctorals who have become leading figures in molecular evolution including Margaret Kidwell, Wen-Hsiung Li
Wen-Hsiung Li
Wen-Hsiung Li is a Taiwanese American scientist working in the fields of molecular evolution, population genetics, and genomics...
, Ranajit Chakraborty, Shozo Yokoyama, Aravinda Chakravarti, Dan Graur
Dan Graur
Dan Graur is an American scientist working in the fields of molecular evolution. He is currently the John and Rebecca Moores Professor at the University of Houston. He is coauthor along with Wen-Hsiung Li of Fundamentals of Molecular Evolution.-Biography:...
, Fumio Tajima, Chung-I Wu, Naoyuki Takahata, Takashi Gojobori
Takashi Gojobori
a Japanese molecular biologist, is Vice-Director of the National Institute of Genetics and Professor at Center for Information Biology and DNA Data Bank of Japan in NIG, Mishima, Japan...
, Pekka Pamilo, Austin Hughes, Andrey Rzhetsky, Jianzhi (George) Zhang, and Sudhir Kumar.
Recognition
- 1977 Japan Society of Human Genetics Award
- 1990 Fellow, American Academy of Arts and Sciences
- 1990 Kihara Prize, Genetics Society of Japan
- 1997 Member, National Academy of Sciences, USA
- 2002 International Prize for Biology, Japan Society of the Promotion of Sciences
- 2003 Barbara Bowman AwardBarbara T. BowmanBarbara Taylor Bowman is an award-winning early childhood education expert/advocate, professor, and author. Her areas of expertise include early childhood care/education, educational equity for minority and low-income children, as well as intergenerational family support and roles...
, Texas Geneticist Society - 2006 Thomas Hunt Morgan Medal, Genetics Society of America
See also
- Molecular evolutionMolecular evolutionMolecular evolution is in part a process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology and population genetics sought to understand recent discoveries on the structure...
- MutationismMutationismMutationism refers to the theory emphasizing mutation as a creative principle and source of discontinuity in evolutionary change, particularly associated with the founders of modern genetics....
- Nucleotide diversityNucleotide diversityNucleotide diversity is a concept in molecular genetics which is used to measure the degree of polymorphism within a population.One commonly used measure of nucleotide diversity was first introduced by Nei and Li in 1979...
- Neighbor-joiningNeighbor-joiningIn bioinformatics, neighbor joining is a bottom-up clustering method for the creation of phenetic trees , created by Naruya Saitou and Masatoshi Nei...
Books
- Nei, M., and S. Kumar (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
- 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.