TOKYO METROPOLITAN UNIVERSITY
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Koichiro Tamura
Professor
Ph, D (Tokyo Metropolitan University, 1991)
Tel:
0426-77-1111(ext. 3725)
Email:
ktamura@tmu.ac.jp
Molecular Evolution and Comparative Genomics in Drosophila
Drosophila melanogaster has been a canonical model organism to study genetics, development, behavior, physiology, evolution, and population genetics for nearly a century. Despite this emphasis and the completion of its nuclear genome sequence, the timings of major speciation events leading to the origin of this fruit fly remain elusive because of the paucity of extensive fossil records and biogeographic data. Our analysis of 2977 pairwise sequence comparisons from 176 nuclear genes reveals timings of the landmark speciation events. The inferred temporal pattern of fruit fly evolution shows correspondence with the cooling patterns of paleoclimate changes and habitat fragmentation in the Cenozoic. We are also interested in machanisms of molecular evolution of genes and genomes in Drosophila.
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Evolutionary Time Scale of Drosophila Speciation
Theoretical Studies on Nucletide Substitution between DNA Sequences
The number of nucleotide substitutions between DNA sequences is one of the most important parameters in the study of molecular evolution. This measure of evolutionary distance is routinely used to infer phylogenetic trees and estimate divergence times among genes, individuals, populations, and species. Using a comprehensive approach including real data analyses, mathematical modelings, and computer simulations, we are studying the rate and pattern of evolutionary changes among DNA sequences and developing the statistical methods to estimate the number of nucleotide substitutions.
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Distribution of Synonymous Substitution for 3789 Genes between Human and Mouse
Bioinformatics for Molecular Evolutionary Genetics Analyses
With its theoretical basis firmaly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and infering the nature and extent of selective forces shaping the evolution of genes and genomes. As a response to the demand for easy-to-use computer programs for such analyses, we have produced Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of DNA and protein sequence variations from an evolutionary perspective.
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MEGA4 Software
Publications
  1. Katoh T, Nakaya D, Tamura K, Aotsuka T. Phylogeny of the Drosophila immigrans Species Group(Diptera: Drosophilidae) Based on Adh andGpdh Sequences. Zool. Sci. 24:913-921. 2007.
  2. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol. 24:1596-1599. 2007.
  3. Nozawa M, Kumagai M, Aotsuka T, Tamura K. Unusual evolution of interspersed repeat sequences in the Drosophila ananassae subgroup. Mol. Biol. Evol. 23:981-987. 2006.
  4. Nozawa M, Aotsuka T, Tamura K. A novel chimeric gene, siren, with retroposed promoter sequence in the Drosophila bipectinata complex. Genetics 171: 1719-1727. 2005.
  5. Saito S, Tamura K, Aotsuka T. Replication origin of mitochondrial DNA in insects. Genetics 171: 1695-1705. 2005.
  6. Tamura K, Nei M, Kumar S. Prospects for Inferring Very Large Phylogenies Using the Neighbor-Joining Method. Proc. Nat. Acad. Sci. USA 101: 11030-11035. 2004.
  7. *Kumar S, *Tamura K, Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinformatics 5:150-163. 2004. (*Joint first author)
  8. Tamura K, Subramanian S, Kumar S. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21:36-44. 2004.
  9. Tamura K, Kumar S. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol. 19:1727-1736. 2002.
  10. Kumar S, Tamura K, Jakobsen IB, Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245. 2001.
  11. Tamura K. On the estimation of the rate of nucleotide substitution for the control region of human mitochodrial DNA. Gene 259:189-197. 2000.
  12. Kobayashi N, Shirai Y, Tsurusaki N, Tamura K, Aotsuka T, Katakura H. Two Cryptic Species of the Phytophagous Ladybird Beetle Epilachna vigintioctopunctata (Coleoptera: Coccinellidae) Detected by Analyses of Mitochondria DNA and Karyotypes, and Crossing Experiments. Zool. Sci. 17:1159-1166. 2000.
  13. Katoh T, Tamura K, Aotsuka T. Phylogenetic position of the subgenus Lordiphosa of the genus Drosophila (Diptera: Drosophilidae) inferred from alcohol dehydrogenase (Adh) gene sequences. J Mol. Evol. 51:122-30. 2000.
  14. Purdom PW Jr, Bradford PG, Tamura K, Kumar S. Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformatics 16:140-151. 2000.
  15. Kobayashi N, Tamura K, Aotsuka T. PCR Error and Molecular Population Genetics. Biochemical Genetics 37:317-321. 1999.
  16. Kobayashi N, Tamura K, Aotsuka T, Katakura H. Molecular Phylogeny of Twelve Asian Species of Epilachnine Ladybird Beetles (Coleoptera, Coccinellidae) with Notes on the Direction of Host Shift. Zool. Sci. 15: 147-151. 1998.
  17. Tamura K, Toba G, Park J, Aotsuka T. Origin of Hawaiian drosophilids inferred from alcohol dehydrogenase gene sequences. Current Topics on Molecular Evolution 9-18. 1995. (Proceedings of the US-Japan Workshop, edited by M. Nei and N. Takahata. The Pennsylvania State University, USA, Graduate School for Advanced Studies, Hayama, Japan.)
  18. Kumar S, Tamura K, Nei M. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. CABIOS 10:189-191. 1994.
  19. Tamura K. Model selection in the estimation of the number of nucleotide substitutions. Mol. Biol. Evol. 11:154-157. 1994.
  20. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526. 1993.
  21. Tamura K. The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol. Biol. Evol. 9:814-825. 1992.
  22. Tamura K. Estimation of the number of nucleotide substitutions when there are strongtransition-transversion and G+C-content biases. Mol. Biol. Evol. 9:678-687. 1992.
  23. Hedges SB, Kumar S, Tamura K, Stoneking M. Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739. 1992.
  24. Tamura K, Aotsuka T, Kitagawa O. Mitochondrial DNA polymorphisms in the two subspecies of Drosophila sulfurigaster: relationship between geographic structure of population and nucleotide diversity. Mol. Biol. Evol. 8:104-114. 1991.
  25. Tamura K, Aotsuka T. Rapid isolation method of animal mitochondrial DNA by thealkaline lysis procedure. Biochemical Genetics. 26:815-819. 1988.
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