M Nei

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. ncbi Ultraconserved coding regions outside the homeobox of mammalian Hox genes
    Zhenguo Lin
    Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 8:260. 2008
  2. ncbi Molecular origin of species
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802-5301, USA
    Science 282:1428-9. 1998
  3. ncbi Selectionism and neutralism in molecular evolution
    Masatoshi Nei
    Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA
    Mol Biol Evol 22:2318-42. 2005
  4. ncbi Concerted and birth-and-death evolution of multigene families
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Genet 39:121-52. 2005
  5. ncbi Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, 328 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 98:2497-502. 2001
  6. ncbi Purifying selection and birth-and-death evolution in the ubiquitin gene family
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 97:10866-71. 2000
  7. ncbi The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species
    Masatoshi Nei
    Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    J Hered 93:157-64. 2002
  8. ncbi The new mutation theory of phenotypic evolution
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:12235-42. 2007
  9. ncbi The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:951-63. 2008
  10. ncbi Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University
    Genome Biol Evol 3:812-29. 2011

Research Grants

  1. Statistical Studies of Genomic Evolution
    Masatoshi Nei; Fiscal Year: 2009
  2. MOLECULAR EVOLUTIONARY GENETICS
    Masatoshi Nei; Fiscal Year: 2003
  3. THEORETICAL POPULATION GENETICS AND ITS APPLICATIONS
    Masatoshi Nei; Fiscal Year: 1993
  4. THEORETICAL POPULATION GENETICS AND ITS APPLICATIONS
    Masatoshi Nei; Fiscal Year: 1991
  5. MOLECULAR EVOLUTIONARY GENETICS
    Masatoshi Nei; Fiscal Year: 1999

Detail Information

Publications72

  1. ncbi Ultraconserved coding regions outside the homeobox of mammalian Hox genes
    Zhenguo Lin
    Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
    BMC Evol Biol 8:260. 2008
    ..In this study, we used comparative genomic methods to infer possible functional elements in the coding regions of mammalian Hox genes...
  2. ncbi Molecular origin of species
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802-5301, USA
    Science 282:1428-9. 1998
  3. ncbi Selectionism and neutralism in molecular evolution
    Masatoshi Nei
    Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA
    Mol Biol Evol 22:2318-42. 2005
    ..It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels...
  4. ncbi Concerted and birth-and-death evolution of multigene families
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Annu Rev Genet 39:121-52. 2005
    ..Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters...
  5. ncbi Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, 328 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 98:2497-502. 2001
    ..3 billion years ago, respectively. However, estimates of ancient divergence times are subject to a substantial amount of error caused by uncertainty of the molecular clock, horizontal gene transfer, errors in sequence alignments, etc...
  6. ncbi Purifying selection and birth-and-death evolution in the ubiquitin gene family
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 97:10866-71. 2000
    ..These observations suggest that the members of this gene family evolve almost independently by silent nucleotide substitution and are subjected to birth-and-death evolution at the DNA level...
  7. ncbi The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species
    Masatoshi Nei
    Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    J Hered 93:157-64. 2002
    ..0 MY ago, respectively. In this case the use of two calibration points, that is, the divergence time (13 MY ago) between humans and orangutans and between primates and artiodactyls (90 MY ago) gave essentially the same estimates...
  8. ncbi The new mutation theory of phenotypic evolution
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:12235-42. 2007
    ..It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance...
  9. ncbi The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 9:951-63. 2008
    ..It seems that mutation by gene duplication and inactivation has important roles in both the adaptive and non-adaptive evolution of chemosensation...
  10. ncbi Roles of mutation and selection in speciation: from Hugo de Vries to the modern genomic era
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University
    Genome Biol Evol 3:812-29. 2011
    ..Some authors emphasized the importance of natural selection to speed up speciation, but mutation is crucial in speciation because reproductive barriers cannot be generated without mutations...
  11. ncbi The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802 5301, USA
    Proc Natl Acad Sci U S A 95:12390-7. 1998
    ....
  12. ncbi The neutral theory of molecular evolution in the genomic era
    Masatoshi Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Annu Rev Genomics Hum Genet 11:265-89. 2010
    ..However, because phenotypic evolution is controlled by the interaction of many genes, the study of natural selection ought to take such interactions into account. Experimental studies of evolution will also be crucial...
  13. ncbi Bottlenecks, genetic polymorphism and speciation
    Masatoshi Nei
    Institute of Molecular and Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, 16801, USA
    Genetics 170:1-4. 2005
  14. ncbi Phylogenetic analysis in molecular evolutionary genetics
    M Nei
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Annu Rev Genet 30:371-403. 1996
    ..Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct...
  15. ncbi Color vision of ancestral organisms of higher primates
    M Nei
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 14:611-8. 1997
    ....
  16. ncbi Evolution by the birth-and-death process in multigene families of the vertebrate immune system
    M Nei
    Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 94:7799-806. 1997
    ..We found little evidence that interlocus gene conversion plays an important role in the evolution of MHC and Ig multigene families...
  17. ncbi Molecular phylogeny and divergence times of drosophilid species
    C A Russo
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 12:391-404. 1995
    ..melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events...
  18. ncbi Evolution of immunoglobulin kappa chain variable region genes in vertebrates
    T Sitnikova
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 15:50-60. 1998
    ....
  19. ncbi Evolution of Antennapedia-class homeobox genes
    J Zhang
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Genetics 142:295-303. 1996
    ....
  20. ncbi Evolution of olfactory receptor genes in the human genome
    Yoshihito Niimura
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 100:12235-40. 2003
    ..These observations can be explained by the assumption that several chromosomal rearrangements have occurred at the regions of OR gene clusters and the OR genes contained in different genomic clusters are shuffled...
  21. ncbi An unusual form of purifying selection in a sperm protein
    A P Rooney
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 17:278-83. 2000
    ..The driving force for arginine-rich selection appears to be the DNA-binding function of protamine P1 and an interaction with a protein kinase in the fertilized egg...
  22. ncbi Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes
    Li Hao
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Gene 347:149-59. 2005
    ..The rate of expansion of this gene family seems to be one of the highest among all hominoid gene families. The KIR gene family is also subject to birth-and-death evolution...
  23. ncbi Evolutionary change of the numbers of homeobox genes in bilateral animals
    Jongmin Nam
    Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, USA
    Mol Biol Evol 22:2386-94. 2005
    ..We conclude that both gain and loss of homeobox genes were important for the evolutionary change of phenotypic characters in bilateral animals...
  24. ncbi Antiquity and evolution of the MADS-box gene family controlling flower development in plants
    Jongmin Nam
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA
    Mol Biol Evol 20:1435-47. 2003
    ..Our study supports the idea that there are two main evolutionary lineages (type I and type II) of MADS-box genes in plants and animals...
  25. ncbi MEGA2: molecular evolutionary genetics analysis software
    S Kumar
    Department of Biology, Arizona State University, Tempe, AZ 85287 1501, USA
    Bioinformatics 17:1244-5. 2001
    ..AVAILABILITY: http://www.megasoftware.net. CONTACT: s.kumar@asu.edu..
  26. ncbi Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers
    Sabyasachi Das
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 105:16647-52. 2008
    ..These rearrangements have resulted in interspecific variation of the genomic lengths of the IGL loci and the number and order of IGL constituent genes, but the overall organization of the IGL loci has not changed...
  27. ncbi Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    Yoshiyuki Suzuki
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 99:16138-43. 2002
    ..These results indicate that bootstrap probabilities are more suitable for assessing the reliability of phylogenetic trees than posterior probabilities and that the mammalian and plant phylogenies may not have been fully resolved...
  28. ncbi Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice
    Yoshihito Niimura
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Gene 346:13-21. 2005
    ..These observations suggest that the greater OR gene repertoire in mice has been generated mainly by tandem gene duplication within each genomic cluster...
  29. ncbi Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms
    Jongmin Nam
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 101:1910-5. 2004
    ..Furthermore, the higher rate of birth-and-death evolution in type I genes appeared partly due to a higher frequency of segmental gene duplication and weaker purifying selection in type I than in type II genes...
  30. ncbi A new method of inference of ancestral nucleotide and amino acid sequences
    Z Yang
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Genetics 141:1641-50. 1995
    ..84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences...
  31. ncbi Genomic drift and copy number variation of chemosensory receptor genes in humans and mice
    M Nozawa
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA, USA
    Cytogenet Genome Res 123:263-9. 2008
    ....
  32. ncbi Diversity and evolution of T-cell receptor variable region genes in mammals and birds
    C Su
    Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park 16802, USA
    Immunogenetics 50:301-8. 1999
    ..This pattern is similar to that found for immunoglobulin variable region (IGV) genes...
  33. ncbi ADAPTSITE: detecting natural selection at single amino acid sites
    Y Suzuki
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Bioinformatics 17:660-1. 2001
    ..bio.psu.edu/adaptivevol.html and http://www.cib.nig.ac.jp/dda/yossuzuk/welcome.html. The package includes the source code written in C, binary files for UNIX operating systems, manual, and example files...
  34. ncbi Locus specificity of polymorphic alleles and evolution by a birth-and-death process in mammalian MHC genes
    X Gu
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, USA
    Mol Biol Evol 16:147-56. 1999
    ....
  35. ncbi Origin and evolution of the chicken leukocyte receptor complex
    Nikolas Nikolaidis
    Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 102:4057-62. 2005
    ....
  36. ncbi Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids
    Chen Su
    Institute of Molecular Evolutionary Genetics, Department of Biology, The Pennsylvania State University, Pennsylvania, USA
    Mol Biol Evol 19:205-15. 2002
    ..Our findings suggest that adaptive evolution has occurred in the functionally important sites of the V(H)H genes to maintain the normal immune function in the dimeric Ig...
  37. ncbi Evolutionary dynamics of the immunoglobulin heavy chain variable region genes in vertebrates
    Sabyasachi Das
    Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
    Immunogenetics 60:47-55. 2008
    ..Our results suggest that the evolution of IGHV multigene family is more complex than previously thought and that several factors may act synergistically for the development of antibody repertoire...
  38. ncbi The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution
    Zhenguo Lin
    Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
    Nucleic Acids Res 35:7591-603. 2007
    ..Our work presents an overall portrait of the evolution of these important genes in DNA metabolism and also provides further understanding about the early evolution of cellular organisms...
  39. ncbi Heterogeneous but conserved natural killer receptor gene complexes in four major orders of mammals
    Li Hao
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, 16802, USA
    Proc Natl Acad Sci U S A 103:3192-7. 2006
    ..Identification of putative NKC sequences in opossum and chicken genomes implies that the expansion of the NKC gene families might have occurred before the radiation of placental mammals but after the divergence of birds from mammals...
  40. ncbi Evolutionary dynamics of olfactory receptor genes in Drosophila species
    Masafumi Nozawa
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:7122-7. 2007
    ..The difference in evolutionary pattern between Drosophila and mammals can be explained partly by the differences of gene expression mechanisms and partly by the environmental and behavioral differences...
  41. ncbi Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
    Yoshiyuki Suzuki
    Institute of Molecular Evolutionary Genetics, Department of Biology, The Pennsylvania State University, University Park, 16802, USA
    Mol Biol Evol 19:1865-9. 2002
    ..These observations, together with those from previous studies, suggest that the positively selected sites inferred by the parsimony-based method are more reliable than those inferred by the likelihood-based method...
  42. ncbi Origins and evolution of the formin multigene family that is involved in the formation of actin filaments
    Dimitra Chalkia
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, USA
    Mol Biol Evol 25:2717-33. 2008
    ..Our results indicate the importance of gene duplication and domain acquisition in the evolution of the eukaryotic cell and offer insights into how a complex system, such as the cytoskeleton, evolved...
  43. ncbi Origin and evolution of the Ig-like domains present in mammalian leukocyte receptors: insights from chicken, frog, and fish homologues
    Nikolas Nikolaidis
    Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA, 16802, USA
    Immunogenetics 57:151-7. 2005
    ..Second, the mammalian LRC sequences are most closely related to the Fc receptor sequences and these two groups diverged before the separation of birds and mammals...
  44. ncbi Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods
    Yoshihito Niimura
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 102:6039-44. 2005
    ..All of these observations can be explained by the environmental change that organisms have experienced from the time of the common ancestor of all vertebrates to the present...
  45. ncbi Birth-and-death evolution in primate MHC class I genes: divergence time estimates
    Helen Piontkivska
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA
    Mol Biol Evol 20:601-9. 2003
    ..The overall phylogenetic pattern observed among class I genes is consistent with the model of birth-and-death evolution...
  46. ncbi Purifying selection and birth-and-death evolution in the histone H4 gene family
    Helen Piontkivska
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, 328 Mueller Lab, University Park, PA 16802, USA
    Mol Biol Evol 19:689-97. 2002
    ....
  47. ncbi Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes
    Nikolas Nikolaidis
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA
    Mol Biol Evol 21:498-505. 2004
    ..Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene conversion-like events...
  48. ncbi Origins and evolution of microRNA genes in Drosophila species
    Masafumi Nozawa
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, USA
    Genome Biol Evol 2:180-9. 2010
    ..Therefore, once miR genes acquired their functions, they appear to have evolved very slowly, maintaining essentially the same structures for a long time...
  49. ncbi Origin and evolution of influenza virus hemagglutinin genes
    Yoshiyuki Suzuki
    Institute of Molecular Evolutionary Genetics and Department of Biology, 328 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Biol Evol 19:501-9. 2002
    ..Also, the A virus HA gene diverged from the B virus HA gene about 4,000 years ago and from the C virus HE gene about 8,000 years ago. These time estimates are much earlier than the previous ones...
  50. ncbi Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication
    Li Hao
    Department of Biology, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
    Immunogenetics 56:343-54. 2004
    ..A hypothesis was presented to explain the origin of the differential use of Ly49 and KIR genes in rodents and primates...
  51. ncbi A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes
    Jongmin Nam
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University University Park, PA 16802, USA
    Nucleic Acids Res 33:e12. 2005
    ..These results indicate that our statistical method may be useful for predicting protein regions that are likely to be functionally differentiated. These regions may be chosen for further experimental studies...
  52. ncbi Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species
    Sayaka Miura
    Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, USA
    Genome Biol Evol 3:129-39. 2011
    ..These results indicate that these regions can be a potential source of generating new target sites, which results in multiple target genes for each miR in animals...
  53. ncbi Evolutionary dynamics of the T-cell receptor VB gene family as inferred from the human and mouse genomic sequences
    C Su
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA
    Mol Biol Evol 18:503-13. 2001
    ..Our results show that the VB gene family is subject to evolution by a birth-and-death process rather than to concerted evolution...
  54. ncbi Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites
    Y Suzuki
    Institute of Molecular Evolutionary Genetics, Department of Biology, The Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 18:2179-85. 2001
    ..It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths of the phylogenetic tree are relatively small...
  55. ncbi Estimation of divergence times for major lineages of primate species
    Galina V Glazko
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
    Mol Biol Evol 20:424-34. 2003
    ....
  56. ncbi Phylogenetic test of the molecular clock and linearized trees
    N Takezaki
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
    Mol Biol Evol 12:823-33. 1995
    ..A linearized tree will then be constructed for a given topology for the remaining sequences under the assumption of rate constancy. We have used these methods to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences...
  57. ncbi Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages
    Yoshihito Niimura
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Gene 346:23-8. 2005
    ..Therefore, the two evolutionary hypotheses mentioned above are not mutually exclusive and both are nearly equally responsible for the difference in the number of OR genes between humans and mice...
  58. ncbi Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer
    Zhenguo Lin
    Department of Biology and the Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 103:10328-33. 2006
    ..These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes...
  59. ncbi Reliabilities of identifying positive selection by the branch-site and the site-prediction methods
    Masafumi Nozawa
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA
    Proc Natl Acad Sci U S A 106:6700-5. 2009
    ..The codon sites showing functional changes generally do not show a high omega value. To understand adaptive evolution, some form of experimental confirmation is necessary...
  60. ncbi Eighty percent of proteins are different between humans and chimpanzees
    Galina Glazko
    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802, USA
    Gene 346:215-9. 2005
    ..Still, the number of proteins responsible for the phenotypic differences may be smaller since not all genes are directly responsible for phenotypic characters...
  61. ncbi Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees
    Kazuharu Misawa
    Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    J Mol Evol 57:S290-6. 2003
    ..s tree, which largely depends on Bayesian posterior probability, may not be correct...
  62. ncbi Genomic drift and copy number variation of sensory receptor genes in humans
    Masafumi Nozawa
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 104:20421-6. 2007
    ..We therefore conclude that genomic drift plays an important role for generating intra- and interspecific CNVs of sensory receptor genes. Similar results were obtained when all annotated genes were analyzed...
  63. ncbi Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts
    Takeshi Itoh
    Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 99:12944-8. 2002
    ..Rather, the elevated evolutionary rate appears to be mainly due to enhanced mutation rate, although the possibility of relaxation of purifying selection cannot be ruled out...
  64. ncbi Prospects for inferring very large phylogenies by using the neighbor-joining method
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, 85287-4501, USA
    Proc Natl Acad Sci U S A 101:11030-5. 2004
    ..Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies...
  65. ncbi False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus
    Yoshiyuki Suzuki
    Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Japan
    Mol Biol Evol 21:914-21. 2004
    ..For this reason, parsimony-based methods rarely produce false positives and are safer than ML-based methods for detecting positive selection at individual codon sites, although a large number of sequences are necessary...
  66. ncbi Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates
    Yoshihito Niimura
    Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
    J Hum Genet 51:505-17. 2006
    ..It appears that the number and types of genes in chemosensory receptor gene families have evolved in response to environmental needs, but they are also affected by fortuitous factors...
  67. ncbi MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
    Sudhir Kumar
    Life Sciences A 351, The Biodesign Institute, Tempe, AZ 85287 4501, USA
    Brief Bioinform 5:150-63. 2004
    ..This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA...
  68. ncbi Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA
    Naoko Takezaki
    Life Science Research Center, Kagawa University, Japan
    Genetics 178:385-92. 2008
    ..To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 individuals are required when DA distance is used...
  69. ncbi Molecular evolution of the nontandemly repeated genes of the histone 3 multigene family
    Alejandro P Rooney
    Department of Biological Sciences, Mississippi State University, P O Box GY, Mississippi State, MS 39762, USA
    Mol Biol Evol 19:68-75. 2002
    ..Further analyses of the structure of H3 proteins revealed that the histones of higher eukaryotes might have evolved from a replication-independent-like H3 gene...
  70. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
    ..The current version of MEGA is available free of charge at (http://www.megasoftware.net)...
  71. ncbi MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir Kumar
    Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
    Brief Bioinform 9:299-306. 2008
    ..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods...
  72. ncbi The 2006 Thomas Hunt Morgan Medal. Masatoshi Nei
    Bruce Weir
    Genetics 172:719-20. 2006

Research Grants18

  1. Statistical Studies of Genomic Evolution
    Masatoshi Nei; Fiscal Year: 2009
    ..In these studies, most DNA and protein sequences to be used will be obtained by homology search from the genome sequences of various model organisms. ..
  2. MOLECULAR EVOLUTIONARY GENETICS
    Masatoshi Nei; Fiscal Year: 2003
    ..g., ubiquitin, histone, and globins) to understand whether the highly conserved proteins are due to concerted evolution or to purifying selection or combinations of several factors. ..
  3. THEORETICAL POPULATION GENETICS AND ITS APPLICATIONS
    Masatoshi Nei; Fiscal Year: 1993
    ..will also be studied with the aim of understanding the coevolution of host immune system genes (MHC, T-cell receptor, immunoglobulins, etc.) and antigenic genes of parasites...
  4. THEORETICAL POPULATION GENETICS AND ITS APPLICATIONS
    Masatoshi Nei; Fiscal Year: 1991
    ..In addition to the above studies, statistical analysis of polymorphic DNA sequences will be made to investigate the mechanism of maintenance of DNA polymorphism...
  5. MOLECULAR EVOLUTIONARY GENETICS
    Masatoshi Nei; Fiscal Year: 1999
    ..A theoretical study will also be conducted on the general mechanism of maintenance of the immunoglobulin. MHC, and T-cell receptor gene diversity and their evolution. ..