Evolutionary genomics lab



Professor Naoko TAKEZAKI
TEL/FAX +81-87-891-2419
Email takezaki@med.kagawa-u.ac.jp
AddressIkenobe 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, JAPAN
Life Science Research Center, Kagawa University.

Naoko TAKEZAKI (Professor)

Research interests

  1. Genome evolution
  2. Vertebrate phylogeny/ vertebrate evolution
  3. Human evolution
  4. Phylogeny construction
  5. Molecular clock
  1. Application for the Doctorial Program
  2. @@@@ @
  3. Postdoctoral Fellowship
  4. CV
  5. Academic Society Activity
  6. Publication list
  7. Software Distribution
  8. Software for analyzing polymorphic data
Doctor Course Students Kagawa University, School of Medicine (Doctor Course)
Please contact above.


April 1978 - March 1984
B. Ed.,University of Tokyo,Tokyo, Japan
September 1989 - June 1991
M. S..in Anthropology, University of Utah, Salt Lake City, UT
August 1991 - May 1996
Ph. D. in Genetics, Pennsylvania State University, University Park, PA Thesis: Phylogenetic inference from molecular data. Advisor: Dr. Masatoshi Nei


April 1984 - March 1989
Computer engineer at Fujitsu Co., Tokyo, Japan
August 1991 | May 1996
Research assistant to Dr. Nei
September 1996 | March 1999
Research assistant in National Institute of Genetics, Mishima, Japan
April 1999 - August 2000
Instructor at Graduate University for Advanced Studies, Hayama, Japan
September 2000 | October 2003
Staff researcher at Max-Planck Institute fuer Biologie
October 2003 | August 2004
Researcher for Science and Technology at Center for Information Biology and DNA Data Bank of Japan at National Institute of Genetics
September 2004 | March 2007
Professor at Information Technology Center in Kagawa University

April 2007 | present
Professor at Life Science Research Center in Kagawa University

Postdoctoral Training

September 1996 - March 1999 Postdoctoral Fellow, Laboratory of DNA Analysis, Center for Information Biology at National Institute of Genetics, Mishima, Japan

Academic Society Activity

Genetics Society of Japan
Society for Molecular Biology and Evolution
Associate Editor of Molecular Biology and Evolution

Publication list

  1. Tateno, Y., N. Takezaki, and M. Nei. 1994. Relative efficiencies of the maximum likelihood, neighbor-joining, and maximum parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11:261-277.
  2. Nei, M. and N. Takezaki. 1994. Estimation of genetic distances and phylogenetic trees from DNA analysis.
  3. Proc. 5th World Cong. Genet. Appl. Livestock Prod. 21:405-412.
  4. Takezaki, N. and M. Nei. 1994. Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant. J. Mol. Evol. 39:210-218.
  5. Tajima, F. and N. Takezaki. 1994. Estimation of evolutionary distance for reconstructing molecular phylogenetic trees. Mol. Biol. Evol. 11:278-286.
  6. Redd, A. J., N. Takezaki, S. T. Sherry, S. T. McGarvey, A. M. M. Sofro, and M. Stoneking. 1995. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific. Mol. Biol. Evol. 12:604-615.
  7. Russo, C., N. Takezaki, and M. Nei. 1995. Molecular phylogeny and divergence time of drosophilid species. Mol. Biol. Evol. 12:391-404.
  8. Nei, M., N. Takezaki, and T. Sitnikova. 1995. Assessing molecular phylogenies. Science 267:253-254.
  9. Takezaki, N., A. Rzhetskey, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:823-833.
  10. Nei, M. and N. Takezaki. 1996. The root of the phylogenetic tree of human populations. Mol. Biol. Evol. 13:170-177.
  11. Russo, C., N. Takezaki, and M. Nei. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.
  12. Takezaki, N. and M. Nei. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389-399.
  13. Nei, M. and N. Takezaki. 1996. Reconstruction of phylogenetic trees from microsatellite (STR) loci. Animal Genetics 27:1-16.
  14. Takezaki, N. 1998. Tie trees generated by distance methods of phylogenetic reconstruction. Mol. Biol. Evol 15:727-737.
  15. Takezaki, N. and T. Gojobori. 1999. Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol. Biol. Evol 15:727-37
  16. Suzuki, H., K. Tsuchiya and N. Takezaki. 2000. A molecular phylogenetic framework for the Ryukyu endemic rodents Tokusdaia osimensis and Diplothrix legata. Molecular Phylogenetics and Evolution 15:15-24.
  17. Nagl, S., H. Tichy, W. E. Mayer, N. Takezaki, N. Takahata, J. Klein. 2000. The origin and age of haplochromine fishes in Lake Victoria, east Africa. Proc R Soc Lond B Biol Sci. 267:1049-61.
  18. Figueroa F., W. E. Mayer, H. Sultmann, C. O'hUigin, H. Tichy, Y. Satta, N. Takezaki, N. Takahata, J. Klein. 2000. Mhc class II B gene evolution in East African cichlid fishes. Immunogenetics 51: 556-75.
  19. Sultman, H., A. Sato, B. W. Murray, N. Takezaki, R. Geisler, G. Rauch, and J. Klein. 2000. Conservation of Mhc Class II Region Synteny between zebrafish and human as determined by radiation hybrid mapping. Journal of Immunology 165:6984-6993.
  20. Takezaki, N., Z. Zaleska-Rutczynska, and F. Figueroa. 2002. Sequencing of amphioxus PSMB5/8 gene and phylogenetic position of agnathan sequences. Gene 282:179-187.
  21. Uinuk-Ool, T. S., N. Takezaki, R. I. Sukernik, S. Nagl, and J. Klein. 2002. Origin and affinities of indigenous Siberian populations as revealed by HLA class II gene frequencies. Hum. Genet. 110: 209-226.
  22. Takezaki, N., F. Figueroa, Z. Zaleska-Rutczynska, and J. Klein. 2003. Molecular phylogeny of early vertebrates: Monophyly of the agnathans as revealed by sequences of 35 genes. Mol. Biol. Evol. 20:287-292.
  23. Sato, A. , N. Takezaki, H. Tichy, F. Figueroa, W. E. Mayer, and J. Klein. 2003. Origin and speciation of Haplochromine fishes in East African crater lakes investigated by the analysis of their mtDNA, Mhc Genes, and SINEs. Mol. Biol. Evol. 20:1448-62.
  24. Uinuk-Ool, T. S., W. E. Mayer, A. Sato, N. Takezaki, L. Benyon, M. D. Cooper, and J. Klein. Identification and characterization of a TAP-family gene in the lamprey. 2003. Immunogenetics 55(1):38-48.
  25. Sato, A., T. S. Uinuk-Ool, N. Kuroda, W. E. Mayer, N. Takezaki, R. Dongak, F. Figueroa, M. D. Cooper, and J. Klein. Macrophage migration inhibitory factor (MIF) of jawed and jawless fishes: implications for its evolutionary origin. 2003. Dev. Comp. Immunol. 27:401-12.
  26. Tozaki, T., N. Takezaki, T. Hasegawa, N. Ishida, M. Kurosawa, M. Tomita, N. Saitou, and H. Mukoyama. 2003. Microsatellite variation in Japanese and Asian horses and their phylogenetic relationship using a European horse outgroup. J. Hered. 94 :374-80.
  27. T.S. Uinuk-ool, N. Takezaki, N. Kuroda, F. Figueroa, A. Sato, I. E. Samonte, W. E. Mayer and J. Klein. 2003. Phylogeny of antigen processing enzymes: Cathepsins of a cephalochordate, an agnathan and a bony fish. Scand. J. Immunol. 58 :436-48.
  28. Terai, Y. , N. Takezaki, W. E. Mayer, H. Tichy, N. Takahata, J. Klein, and N. Okada. 2004. Phylogenetic relationships among East African haplochromine fishes as revealed by short interspersed elements (SINEs). J. Mol. Evol. 54: 64-78.
  29. Uinuk-Ool, T.S., N. Takezaki, O. A. Derbeneva, N. V. Volodko, and R. I. Sukernik. 2004. Variation of HLA class II genes in the Nganasan and Ket, two aboriginal Siberian populations. Eur. J. Immunogenet. 31: 43-51.
  30. Takezaki, N., F. Figueroa, Z. Zaleska-Rutczynska, N. Takahata, and J. Klein. 2004. The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of 44 nuclear genes. Mol. Biol. Evol. 21:1512-1523.
  31. Sato, A., R. Dongak, L. Hao, N. Takezaki, S. Shintani, T. Aoki, and J. Klein. 2006. Mhc class I genes of the cichlid fish Oreochromis niloticus. Immunogenetics. 58(11): 917-928.
  32. Nonaka, I., K. Minaguchi, and N. Takezaki. 2007. Y-chromosomal binary haplogroups in the Japanese population and their relationship to 16 Y-STR polymorphisms. Ann. Hum. Genet. 71(Pt 4):480-495.
  33. Tsuboi, K., N. Takezaki, and N. Ueda. 2007. The N-acylethanolamine-hydrolyzing acid amidase (NAAA). Chem. Biodivers. 4:1914-1925.
  34. Takezaki, N., and M. Nei. 2008. Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA. Genetics. 178:384-392.
  35. Maruyama S, Minaguchi K, Takezaki N, Nambiar P. 2008. Population data on 15 STR loci using AmpF/STR Identifiler kit in a Malay population living in and around Kuala Lumpur, Malaysia. Leg. Med. 10(3):160-162.
  36. Takezaki, N. and M. Nei. 2009. Genomic drift and evolution of microsatellite DNAs in human populations. Mol. Biol. Evol. 26:1835-1840.
  37. Takezaki, N., M. Nei, and K. Tamura. 2010. POPTREE2 : Software for constructing population trees from allele frequency data and computing other population statistics with Windows-interface. Mol. Biol. Evol. 27:747-752.
  38. Takezaki, N. Evolution of microsatellites. In. ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [DOI: 10.1002/9780470015902.a0022866]
  39. Takezaki, N., M. Nei, and K. Tamura. 2014. POPTREEW: web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities. Mol. Biol. Evol. 31:1622-1644.
  40. Takezaki, N. and H. Nishihara. 2016. Resolving the phylogenetic position of coelacanth: The closest relative Is not always the most appropriate outgroup. Genome Biol Evol 8:1208-1221.
  41. Takezaki, N. and H. Nishihara. 2017. Support for lungfish as the closest relative of tetrapods by using slowly evolving ray-finned fish as the outgroup. Genome Biol Evol 9:93-101.
  42. Takezaki, N. 2017. CNVs and microsatellite DNA polymorphism. In. N. Saitou, Edior, Evolution of the Human Genome I, Springer, Tokyo, Japan. pp 143 - 155.
  43. Takezaki, N. 2018. Global rate variation in bony vertebrates. Genome Biol Evol 10:1803-1815.

Software Distribution

  1. lintre
    • Program for making linearized trees (by re-estimating branch lengths under the assumption of constant rate of evolution) and testing the molecular clock for a given topology of a phylogenetic tree.
    • poptree
    • Poptree2
      • Software for construction of population trees from allele frequency data and computing other population statistics with Windows-interface
    • SENDBS
      • Program that computes average nucleotide substitutions within and between populations. The method is described in Nei and Jin (1989, MBE 6:290-300). However, note that sendbs computes standard errors of average nucleotide substitutions with a bootstrap method by resampling sites, which is different from Nei and Jin's method. Also, sensbs constructs a population tree with a neighbor-joining method.

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