Examine individual changes

'{{Infobox scientist |name = Masatoshi Nei |image = Masatoshi Nei - 2013.jpg |alt = |caption = |birth_date = January 2, 1931 |birth_place = [[Miyazaki Prefecture]], Japan |death_date = |death_place = |residence = |citizenship = |nationality = |ethnicity = |fields = [[molecular evolution]]<br>[[molecular phylogenetics]] |workplaces = [[Pennsylvania State University]] |alma_mater = [[University of Miyazaki]](1953)<br>[[Kyoto University]] |doctoral_advisor = |academic_advisors = |doctoral_students = |notable_students = |known_for = statistical theories of molecular evolution and development of the theory of mutation-driven evolution |author_abbrev_bot = |author_abbrev_zoo = |influences = |influenced = |awards = {{no wrap|Member, [[United States National Academy of Sciences|National Academy of Sciences]] (1997)<br>[[International Prize for Biology]] (2002)<br>[[Thomas Hunt Morgan Medal]] (2006)<br>[[Kyoto Prize]] (2013)}} }} {{nihongo|'''Masatoshi Nei'''|根井正利|Nei Masatoshi}} is Evan Pugh Professor of Biology at [[Pennsylvania State University]] and Director of the [http://imeg.psu.edu/ 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 developed several new concepts of evolutionary theory and proposed the theory of mutation-driven evolution. ==Work in population genetics== ===Theoretical studies=== 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.<ref>{{cite journal | last=Nei | first=Masatoshi | year=1967 | title=Modification of linkage intensity by natural selection | journal=Genetics | volume=57 | pages=625–641 | pmid=5583732 | issue=3 | pmc=1211753}}</ref> 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.<ref>{{cite journal | last=Nei | first=Masatoshi | year=1968 | title=Evolutionary change of linkage intensity | journal=Nature | volume=218 | pages=1160–1161 | doi=10.1038/2181160a0 | pmid=5656638 | issue=5147 }}</ref> 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|R. A. Fisher’s]] argument, deleterious mutations can accumulate rather quickly on the Y chromosome or duplicate genes in finite populations.<ref>Nei, M. (1970) Accumulation of nonfunctional genes on sheltered chromosomes. ''Am. Nat.'' 104:311-322</ref><ref>Nei, M. and A. K. Roychoudhury (1973) Probability of fixation of nonfunctional genes at duplicate loci. ''Am. Nat.'' 107:362-372</ref> 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]]).<ref>Nei, M. (1969) Gene duplication and nucleotide substitution in evolution. ''Nature'' 221:40-42</ref> 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.<ref>Nei, M. (1972) Genetic distance between populations. ''Am. Nat.'' 106:283-292</ref> He later developed another distance measure called D_A, which is appropriate for finding the topology of a phylogenetic tree of populations.<ref>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.</ref> He also developed statistics of measuring the extent of population differentiation for any types of mating system using G_ST measure.<ref>Nei, M. (1973) Analysis of gene diversity in subdivided populations. ''Proc. Natl. Acad. Sci. USA'' 70:3321-3323.</ref> In 1975, he and collaborators presented a mathematical formulation of population bottleneck effects and clarified the genetic meaning of bottleneck effects.<ref>Nei, M., T. Maruyama and R. Chakraborty (1975) The bottleneck effect and genetic variability in populations. ''Evolution'' 29:1-10</ref> In 1979, he proposed a statistical measure called [[nucleotide diversity]],<ref>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,</ref> 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 <ref>Nei, M. T. Maruyama, and C. I. Wu (1983) Models of evolution of reproductive isolation. ''Genetics'' 103:557-579.</ref><ref>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.</ref> ===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 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.<ref name=Nei83> Nei, M. (1983) Genetic polymorphism and the role of mutation in evolution (P. K. Koehn and M. Nei, eds.) ''Evolution of Genes and Proteins.'' Sinauer Assoc., Sunderland, MA, pp. 165-190.</ref> <ref name=Nei87>Nei, M. (1987) ''Molecular Evolutionary Genetics.'' Columbia University Press, New York.</ref> 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.<ref name=Nei87/><ref>Li, W. H., T. Gojobori, and M. Nei (1981) Pseudogenes as a paradigm of neutral evolution. ''Nature'' 292:237-239.</ref> ==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. 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.<ref>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.</ref><ref>Nei, M. and A. K. Roychoudhury (1982) Genetic relationship and evolution of human races. ''Evol. Biol.'' 14:1-59.</ref> 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|out-of-Africa theory]] of human origins. ==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.<ref>Saitou, N. and M. Nei (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. ''Mol. Biol. Evol.'' 4:406-425.</ref> <ref>Rzhetsky, A. and M. Nei (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. ''Mol. Biol. Evol.'' 10:1073-1095.</ref> At present, the neighbor-joining method is most widely used in molecular phylogenetics, though some theoreticians advocate the likelihood and the Bayesian methods.<ref>Nei, M., and S. Kumar (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.</ref> 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 [http://www.megasoftware.net/ MEGA].<ref>Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis. Ver. 1.02, The Pennsylvania State University, University Park, PA.</ref> ==MHC loci and positive Darwinian selection== 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. .<ref>Nei, M. and T. Gojobori (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. ''Mol. Biol. Evol.'' 3:418-426.</ref> Applying this method, they showed that the exceptionally high degree of sequence polymorphism at MHC loci is caused by overdominant selection.<ref>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.</ref> Although various statistical methods for this test have been developed later, their original methods are still widely used.<ref name=Nei2013>Nei, M. (2013) ''Mutation-Driven Evolution.'' Oxford University Press, Oxford.</ref> ==New evolutionary concepts== 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.<ref>Nei, M. and A. P. Rooney (2005) Concerted and birth-and-death evolution of multigene families.</ref> 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 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).<ref name=Nei87/><ref name=Nei2013/> He conducted statistical analyses of evolution of genes controlling phenotypic characters such as immunity and olfactory reception and obtained evidence supporting this theory.<ref name=Nei2013/> ==New journal, new society, and students== He founded the journal [http://mbe.oxfordjournals.org/ ''Molecular Biology and Evolution''] in 1983 and the Society for Molecular Biology and Evolution in 1993, together with [[Walter M. Fitch]]. He also trained many graduate students and postdoctorals who later became leading figures in molecular evolutionary biology including [[Wen-Hsiung Li]], Margaret Kidwell, Ranajit Chakraborty, Shozo Yokoyama, Aravinda Chakravarti, [[Dan Graur]], Fumio Tajima, Naruya Saitou, Chung-I Wu, Naoyuki Takahata, [[Takashi Gojobori]], 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 T. Bowman|Barbara Bowman Award]], Texas Geneticist Society * 2006 [[Thomas Hunt Morgan Medal]], [[Genetics Society of America]] * 2013 [[Kyoto Prize|Kyoto Prize for Basic Science]], Inamori Foundation ==See also== * [[Genetic distance]] * [[Molecular evolution]] * [[Mutationism]] * [[Nucleotide diversity]] * [[Neighbor-joining]] * [[Neutral theory of molecular evolution]] ==References== {{Reflist|2}} ==Books== * Nei, M.(2013) ''Mutation-Driven Evolution.'' Oxford University Press, Oxford. * 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. ==External links== * [http://www.personal.psu.edu/nxm2/ '''Masatoshi Nei'''’s home page] * [https://www.youtube.com/watch?v=m6CCVeeRPo8 Masatoshi Nei's 2013 Kyoto Prize Commemorative Lecture] * [http://www.bio.psu.edu/people/faculty/nei/Lab/2006-Weir%20TMA.pdf Weir, B. (2006) The 2006 Thomas Hunt Morgan Medal. Genetics 172:719-720.] * [http://science.psu.edu/news-and-events/2003-news/Nei1-2003.htm Penn State's Masatoshi Nei International Prize for Biology article] * [http://science.psu.edu/news-and-events/2013-news/Nei6-2013 Penn State's Masatoshi Nei Kyoto Prize article] * [http://www.kyoto-u.ac.jp/contentarea/ja/issue/research_activities/documents/2013/vol3no2/RA2013-2-05.pdf International Recognition of Kyoto University Research] * [http://discovermagazine.com/2014/march/12-mutation-not-natural-selection-drives-evolution March 2014 Discover Magazine: Mutation, Not Natural Selection, Drives Evolution] {{Authority control|VIAF=64080210}} {{Persondata <!-- Metadata: see [[Wikipedia:Persondata]]. --> | NAME =Nei, Masatoshi | ALTERNATIVE NAMES = | SHORT DESCRIPTION = American geneticist | DATE OF BIRTH = January 2, 1931 | PLACE OF BIRTH =[[Miyazaki Prefecture]], Japan | DATE OF DEATH = | PLACE OF DEATH = }} {{DEFAULTSORT:Nei, Masatoshi}} [[Category:Japanese geneticists]] [[Category:Japanese molecular biologists]] [[Category:American geneticists]] [[Category:Statistical geneticists]] [[Category:Living people]] [[Category:Pennsylvania State University faculty]] [[Category:Brown University faculty]] [[Category:University of Texas at Houston faculty]] [[Category:1931 births]] [[Category:People from Miyazaki Prefecture]] [[Category:Kyoto University alumni]] [[Category:Members of the United States National Academy of Sciences]] [[Category:Evolutionary biologists]] [[Category:Population geneticists]] [[Category:Japanese emigrants to the United States]] [[Category:American people of Japanese descent]] [[Category:American academics of Japanese descent]] [[Category:American scientists of Japanese descent]]'