Dr. Masatoshi Nei (1931-2023)
SAITOU Naruya
National Institute of Genetics
Mishima, Japan
Dr. Nei Masatoshi was born on January 2nd, 1931 in Miyazaki, Japan, and passed
away on May 18th, 2023, at the age of 92 in Philadelphia, USA. I would like to givemy personal obituary for him as one of his Ph.D. students. Many factual mattersabourt him given in this obituary owe to Nei (2020), his autobiography.
Dr. Nei studied at Naka Elementary School in Miyazaki during 1937-1943. He
then took Higher Education Part at Naka Elementary School during 1943-1944. He
continued to attend two different schools; Miyazaki Agriculture Middle School
during 1945-1948 and Ohyodo High School during 1948-1949. He then entered
School of Agriculture at Miyazaki University at the age of 18 in 1949. After
graduating from Miyazaki University, he entered Graduate School of Agriculture in
Kyoto University in 1953. He rst received M.S. degree in 1955, then proceeded todoctoral course of that Graduate School. He received Ph.D. in 1959.
Dr. Nei became assistant professor at Kyoto University in 1958 before
nishing the Ph.D. course there. Dr. Nei became Rockfeller fellow in 1960, andstayed in USA for two years. In 1961, he became head of the Department ofPopulation Genetics, National Institute of Radiological Sciences, Chiba, Japan. Thisinstitute was af liated with Ministry of Heath of Japan. Dr. Nei conducted boththeoretical works (e.g., Nei [1965]) and data analyses (Nei and Imaizumi [1966a],[1966b]) while he worked in Chiba. After he left there to become professor at Brown
University in U.S.A., Dr. YASUDA Norikazu got that position. When I was mastercourse student in University of Tokyo, I and KANEKO Ryuichi, one year junior tome, visited Dr. YASUDA every week to learn Crow and Kimura’s (1971)“Introduction to Population Genetics Theory”. Dr. KANEKO later became Vice
Director of National Institute of Population and Social Security Research, Japan.
Dr. Nei moved to Houston from Brown University in Providence in 1972.
Around that time, he devised Nei’s genetic distance (Nei [1972]), and applied thisnew measure to protein polymorphism data of human populations (Nei andRoychoudhury [1972, 1974]). It should be noted that he rst considered genetic
distance between different species without considering polymoprhim (Nei 1971).

fifi15fifiObituaryiDarwin volume 3, pages 15-19
Published on June 15, AS0023 (2023 AD)

He started to have Ph.D. students in Houston. I rst met him in the campus ofTokyo Metropolican University in 1980 or so, when he gave an invited lecture there.
He was already famous for his many works including Nei’s genetic distance, as wellas his textbook (Nei, 1975). That book was not available when I wanted to buy acopy, so I xerox-copied the whole book, and studied that book carefully. Much later
when I visited Houston in 1988, Dr. Nei gave me a precious copy of that book.
I wanted to study in U.S.A., and got Fulbright Scholarship. I chose Dr. Nei assupervisor, and I bcame his eighth Ph.D. student at the University of Texas Health
Science Center at Houston, during 1982-1986. Dan Graur was one year senior to me,and Fumio Tajima was nishing his Ph.D. thesis at that time, and Dr. Takashi
Gojobori and Dr. Joel Claiborne Stephens were post-doctoral fellows in Nei
Laboratory. Drs. Wen-Hsiung Li and Ranajit Chakraborty were associate professors
at CDPG (Center for Demographic and Population Genetics), and Dr. William Jack
Schull was director of CDPG.
Based on the symposium held in 1982 in Stony Brook, Dr. Nei and Dr. Richard
K. Koehn coedited a book (Nei and Koehn 1983). Meanwhile, Dr. Arun. K.
Roychoudhury often visited Houston to prepare “Human polymorphic genes: worlddistribution” that was eventually published in 1988 (Roychoudhury and Nei 1988).
I was lucky to come up with a simple algorithm to construct a phylogenetictree, while I was in Houston. In 1985 Dr. Joseph Felsenstein proposed to use thebootsrap probability as the indicator of branch credibility in a phylogenetic tree. Dr.
Nei reviewed that paper, and mentioned in lab meeting that exclusively
multifurcating tree is the null tree for that method. I started to think about analgorithm based on this comment by Dr. Nei, and reached a simple algorithm toconstruct unrooted phylogenetic trees from distance matrix data very rapidly inDecember 1985. We named this method as “the neighbor-joining (NJ) method” andpublished the paper in 1987. Fortunately, many people even now use this neighborjoining method. As of May 29, 2023, the total number of citation of Saitou and Nei’s(1987) NJ paper was 68,906. I hope the citations will exceed 70,000 within this year.
He was also busy in creating new journal, Molecular Biology and Evolution with Dr.
Walter Fitch after a great success of the symposium held in Stony Brook. I rememberthat once “Molecular Evolutionary Genetics” was considered as the journal title, but
its abbreviation, MEG, was somehow not good, and nally MBE was chozen. He
later used this unused journal title for his book.
Dr. Nei started to write “Molecular Evolutionary Genetics” at that time, and it
was published in 1987 (Nei [1987]). At that time I was already in Japan, and Dr.
Takashi Gojobori and I asked Dr. Nei to let us translate this book into Japanese. Thistranslation was published in 1990 from Baifukan, Tokyo.
Dr. Nei left Houston in 1990, and became director of newly created Institute of
Molecular Evolutionary Genetics at Pennsylvania State University. When he was infififi16Houston, he produced nine Ph.D. including Martin Tracey, Wen-Hsiung Li, Margaret
Kidwell, Yoshio Tateno, Aravinda Chakravarti, Fumio Tajima, Dan Graur, Li Jin, andmyself. At the PennState, he produced 14 Ph.D. including Tatsuya Ota, ClaudiaRusso, Sudhir Kumar, Naoko Takezaki, Jianzhi Zhang, Helen Piontiklvska, Hao Li,
and Sayaka Miura. There were more than 20 post-doctoral fellows who studied in NeiLaboratory. They include Arun. K. Roychoudhury, Ranajit Chakraborty, Paul Fuerst,
Shozo Yokoyama, Takashi Gojobori, Ching-I Wu, Naoyuki Takahata, Joel Claiborne
Stephens, Pekka Pamilo, Austin Hughes, Yasuo Ina, Koichiro Tamura, AndreyRzhetsky, Ziheng Yang, Ingrid Jakobsen, Takeshi Ito, Yoshiyuki Suzuki, Kazuharu
Misawa, Galina Glazko, Yoshihito Niimura, Masafumi Nozawa, and Hielim Kim.
These former Ph.D. students and postdocs also produced many students of molecularevolution.
We should not forget about his two other great contributions to the eld of
molecular evolution. One is creation of society called “Society for Molecular Biologyand Evolution” (SMBE) in 1993. The rst SMBE meeting was hosted by Walter M.
Fitch, rst president of SMBE. Dr. Nei became the second SMBE president.
Another great contribnution is creation of a user-friendly software MEGA
(molecular evolutionary genetics analysis). First MEGA version 1.0 was released in
1993 by Drs. Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei, and thecorresponding publication was one year later (Kumar et al. 1994). MEGA grew
constantly, and the latest version is MEGA 11 (Tamura et al, 2021). A textbook onmolecular phylogeny (Nei and Kumar 2000) was related to this MEGA activity. This
book was traslated into Japanese by Tatsuya Ota and Naoko Takezaki.
Another, and essentially the last scien tic book Dr. Nei published was“Mutation-driven evolution (Nei 2013). Dr. Nei claimed that “perhaps somewhat
controvercially, driving force behind evolution is mutation, with natural selection
being of only secondary importance”. This is essentially the neutral theory expanded
to phenotypic evolution from the molecular level. It was traslated into Japanese by
Yoshiyuki Suzuki and Masafumi Nozawa.
Dr. Nei received numerous prizes and honors. Major ones are Japan Society for
Human Genetics Prize in 1977, Kihara Prize in 1990 from Genetics Society of Japan,
Member, National Academy of Science USA in 1997, International Prize for Biology
in 2002 from Japan Society for Promortion of Science, Thomas Hunt Morgan Medalin 2006 from Genetics Society of America, and Kyoto Prize in 2013 from Inamori
Foundation.
Dr. Nei published his autobiography in 2020, from Temple University (Nei[2020]). Cover of this book was designed by his son, Keitaro Nei. I was happy when I
found my photo in that book as well as frequent mention about me. Motoo Kimuraalso appeared in that book often.

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Last year I was invited by Dr. Nei and visited his retirement house inPhiladelphia. He gave me about 120 books written in Japanese as well as about 150
book written in English kept at Temple University. I donated all these books toGenetics Museum at National Institute of Genetics. The attached photo was taken in
his retirement house.
References
Crow J. F. and Kimura M. (1970) Introduction to population genetics theory. Harper & Row, NewYork.
Kumar S., Tamura K., and Nei M. (1994) MEGA: molecular evolutionary genetic analysis software
for microcomputers. Bioinformatics, vol. 10, pp. 189–191.
Nei M. (1965) Variation and covariation of gene frequencies in subdivided populations. Evolution,
vol. 19, pp. 256–258.
Nei M. (1969) Gene duplication and nucleotide substitution in evolution. Nature, vol. 221, pp.
40-42.
Nei M. (1971) Interspeci c gene differences and evolutionary time estimated from electrophoretic
data on protein identity. American Naturalist, vol. 105, pp. 385–398.
Nei M. (1972) Genetic distances between populations. American Naturalist, vol. 106, pp. 283–292.
Nei M. (1975) Molecular population genetics and evolution. North-Holland, Amstredam.
Nei M. (1987) Molecular evolutionary genetics. Columbia University Press, New York.
Nei M. (2013) Mutation-driven evolution. Oxford University Press, New York.
Nei M. (2020) My life as a molecular evolutionist. Institute of Genomics and Evolutionary
Medicine, Temple University.
Nei M. and Richard K. Koehn eds. (1983) Evolution of genes and proteins. Sinaur Associates,Sunderland.
Nei M. and Imaizumi Y. (1966a) Genetic structure of human populations. I. Local differentiation ofblood group frequencies in Japan. Heredity, vol. 21, pp. 9-25.
Nei M. and Imaizumi Y. (1966b) Genetic structure of human populations. I. Differentiation of bloodgroup frequencies among isolated populations. Heredity, vol. 21, pp. 183-190.
Nei M. and Kumar S. (2000) Molecular evolution and phylogenetics. Oxford University Press, NewYork.
Nei M. and Roychoudhury A. K. (1972) Genetic differences between Caucasian, Negro, andJapanese. Science, vol. 177, pp. 434-436.
Nei M. and Roychoudhury A. K. (1974) Genetic variation within and between the three major racesof man, Caucasoids, Negroids, and Mongoloids. American Journal of Human Genetics, vol. 26,
pp. 421-443.
Roychoudhury A. K. and Nei M. (1988) Human polymorphic genes: world distribution. Oxford
University Press, New York.
Saitou N. and Nei M. (1986) Polymorphism and evolution of in uenza A virus genes. MolecularBiology and Evolution, vol. 3, pp. 57-74.
Saitou N. and Nei M. (1987) The neighbor-joining method: a new method for reconstructing
phylogenetic trees. Molecular Biology and Evolution, vol. 4, pp. 406-425.
Tamura K., Stecher G., and Kumar S. (2021) MEGA11: molecular evolutionary genetic analysisversion 11. Molecular Biology and Evolution, vol. 38, pp. 3022–3027.

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Photo taken at Dr. and Mrs. Nei’s retirement house on August 15th, 2022. From right to left: Saitou,Dr. Nei, Mrs. Nei, Keitaro Nei, Sayaka Miura, and her husband.
Edited by TAMURA Koichiro

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