Evan Pugh Professor of Biology & Director, Institute of Molecular Evolutionary Genetics
Molecular Evolutionary Genetics

Evolutionary studies of DNA sequence data
DNA sequence data provide important information on the evolution of genes and populations. We are, therefore, analyzing sequence data that are available from GenBank and recent publications to understand the mechanism of evolution and the history of genes. Currently, our work is concerned with multigene families, especially immune system genes (MHC, immunoglobulin, T-cell receptors, etc.) that form a complex gene superfamily. Statistical properties of amino acid and nucleotide substitution in active centers are also being studied for various proteins such as ribonuclease and influenza virus hemagglutinin genes.

Human evolution at the molecular level
To understand the process and pattern of human evolution, we are studying the genetic relationship among various human populations at the molecular data level. For this purpose, we have collected allele frequency data for a large number of electrophoretic, immunological, and DNA marker loci. Using these data and statistical methods we developed, we are trying to reconstruct the evolutionary history of human populations.

• B.S., Miyazaki University, 1953
• M.S., Kyoto University, Japan, 1955
• Ph.D., Kyoto University, Japan, 1959

Nei, M., P. Xu, and G. Glazko (2001) Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proceedings of the National Academy of Sciences USA 98:2497-2502. [Supplemental Table 3] [Supplemental Table 4]

Su, C. and M. Nei (2001) Evolutionary dynamics of the T-cell receptor VB gene family as inferred from the human and mouse genomic sequences. Molecular Biology and Evolution 18:503-513.

Suzuki, Y., T. Gojobor, and Nei, M (2001) ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics 17:660-661.

Kumar, S. K. Tamura, I. Jakobsen, and M. Nei (2000) MEGA: Molecular Evolutionary Genetics Analysis, Ver. 2., Pennsylvania State University, University Park.

Nei, M. and S. Kumar (2000) Molecular Evolution and Phylogenetics, Oxford University Press, Oxford.

Nei, M., I. B. Rogozin, and H. Piontkivska. (2000) Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proceeding of the National Academy Science USA 97:10866-1087.

Ota, T., T. Sitnikova, and M. Nei (2000) Evolution of vertebrate immunologlobulin variable gene segments. Curr. Top. Microbiol. Immunol. 248:221-245.

Rooney, A. P., J. Zhang, and M. Nei. (2000) An unusual form of purifying selection in a sperm protein. Molecular Biology and Evolution 17:278-283.

Takahshi and M. Nei (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Molecular Biology and Evolution 17:1251-1258.

Takahashi, K., A. P. Rooney, and M. Nei (2000) Origins and divergence times of mammalian class II MHC gene clusters. Journal of Heredity 91:198-204.

Zhang, J. and M. Nei (2000) Positive selection in the evolution of mammalian interleukin-2 genes. Molecular Biology Evolution 17:1413-1416.

Gu, X. and M. Nei (1999) Locus specificity of polymorphic alleles and evolution by a birth-and-death process in mammalian MHC genes. Molecular Biology and Evolution 16:147-156.

Su, C., I. Jakobsen, X. Gu and M. Nei (1999) Diversity and evolution of T-cell receptor variable region genes in mammals and birds. Immunogenetics 50:301-308.

Su, C. and M. Nei (1999) Fifty-million-year-old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage. Proceedings of the National Academy of Science USA 96: 9710-9715.

Nei, M. (1998) Genetic studies on the origin of modern humans. In The Origins and Past of Modern Humans - Towards Reconciliation (K. Omoto and P. V. Tobias, eds.), pp. 27-41. World Scientific, Singapore and London.

Nei, M., S. Kumar and K. Takahashi (1998) The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proceedings of the National Academy of Science USA 95: 12390-12397.

Nei, M. and J. Zhang (1998) Molecular origin of species. Science 282: 1428-1429.

Sitnikova, T. and M. Nei (1998) Evolution of immunoglobulin kappa chain variable region genes in vertebrates. Molecular Biology and Evolution 15: 50-60.

Zhang, J., H.F. Rosenberg and M. Nei (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proceedings of the National Academy of Science USA 95:3708-3713

Sitnikova, T. and M. Nei (1998) Evolution of immunoglobulin kappa chain variable region genes in vertebrates. Molecular Biology and Evolution 15:50-60.

Roychoudhury, A. K. and M. Nei (1997) The emergence and dispersal of mongoloids. J. Indian Anthrop. Soc. 32:1-49

Zhang, J., S. Kumar and M. Nei (1997) Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Molecular Biology and Evolution 14:1335-1338.

Zhang, J. M. Nei (1997) Accuracies of ancestral amino acid sequences inferred by parsimony, likelihood, and distance methods. Journal of Molecular Evolution 44:S139-S146.

M. Nei, X. Gu, and T. Sitnikova (1997) Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proceedings of the National Academy of Science USA, 94: 7799-7806

M. Nei, J. Zhang, and S. Yokoyama (1997) Color vision of ancestral organisms of higher primates. Molecular Biology and Evolution 14: 611-618.

M. Nei (1996) Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genetics 30:371–403.

N. Takezaki and M. Nei (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389–399.

Russo, C. A. M., N. Takezaki and M. Nei (1996) Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Molecular Biology and Evolution 13:525-536

J. Zhang and M. Nei (1996) Evolution of antennapedia-class homeobox genes. Genetics 142:295–303.

M. Nei and N. Takezaki (1996) The root of the phylogenetic tree of human populations. Molecular Biology and Evolution 13:170–177.

Maintained by Joyce White. Send reprint requests to jlw7@psu.edu.

Last update: July 30, 2001.

Search the MEDLINE database at PubMed for articles by Articles by M. Nei.

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