TOKYO METROPOLITAN UNIVERSITY
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Koichiro Tamura
Professor
Ph, D (Tokyo Metropolitan University, 1991)
Tel:
0426-77-1111(ext. 3725)
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Molecular basis of adaptive evolution in Drosophila
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Drosophila flies on slime fluxes
1. Molecular evolution of anti-microbial peptide genes in Drosophila
Fruit flies (Drosophila) adapt to various environmets, which gives us opportunity to study molecular mechanisms of environmental adaptation of organisms. We currently focus on anti-microbial reptides (AMPs). Drosophila speices live in fermented fruits, slime fluxes, decaying bark, etc. where various microbes live. To protect themselves from the infection of environmental microbes, Drosophila rely on AMPs. Therefore, AMPs are key molecules for their environmental adaptation. We are studying the molecular evolution of AMPs and its connection to the adaptation to microbe-rich environments.

2. Adaptation to template climate by a tropical species, D. albomicans
The distribution of D. albomicans was limited in tropics in Southeast Asia until the mid-1980. Since then, however, the distribution has been extended toward north to west Japan to date. In our study, we found that the cold tolerance of this species has been improved in Japanese population with higher response to cold acclimation. This suggests that the improved cold tolerance is attributable to gene expression changes in response to the cold acclimation. Using RNA-seq method, we found many candidate genes responsible for the improvement of cold tolerance. We are trying to identify the causative genes among these genes by artificially modifying gene expression using GAL4/UAS system in D. melanogaster.
Molecular Evolution and Comparative Genomics in Drosophila
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Evolutionary Time Scale of Drosophila Speciation
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.
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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MEGA6 Software
Publications
  1. Filipski A, Murillo O, Freydenzon A, Tamura K, Kumar S. (2014) Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Mol. Biol. Evol. 31:2542-2550.
  2. Takezaki N, Nei M, Tamura K. (2014) POPTREEW: Web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities. Mol. Biol. Evol., msu093.
  3. Stecher G, Liu L, Sanderford M, Peterson P, Tamura K, Kumar S. (2014) MEGA-MD: Molecular Evolutionary Genetics Analysis software with mutational diagnosis of amino acid variation. Bioinformatics 30:1305-1307.
  4. Isobe K, Takahashi A, Tamura K. (2013) Cold tolerance and metabolic rate increased by cold acclimation in Drosophila albomicans from natural populations. Genes Genet. Syst. 88:289-300.
  5. Ohta S, Seto Y, Tamura K, Ishikawa Y, Matsuo T. (2013) Identification of odorant-binding protein genes expressed in the antennae and the legs of the onion fly, Delia antiqua (Diptera: Anthomyiidae). Applied Entomology and Zoology, 1-7.
  6. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol. Evol. 30:2725-2729.
  7. Seto Y, Tamura K. (2013) Extensive Differences in Antifungal Immune Response in Two Drosophila Species Revealed by Comparative Transcriptome Analysis. Int. J. Genomics 2013:Article ID 542139.
  8. Tamura K, Battistuzzi FU, Billing-Ross P, Kumar S. Estimating Divergence Times in Large Molecular Phylogenies. Proc. Nat. Acad. Sci. USA 109:19333-19338. 2012.
  9. Kumar S, Stecher G, Peterson D, Tamura K. MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis program for automated and iterative data analysis. Bioinformatics 28: 2685-2686. 2012.
  10. Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. Statistics and Truth in Phylogenomics. Mol Biol. Evol. 29:457-472. 2012.
  11. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol. Evol. 28:2731-2739. 2011.
  12. Gao J, Hu Y, Toda MJ, Katoh T, Tamura K. Phylogenetic relationships between Sophophora and Lordiphosa, with proposition of a hypothesis on the vicariant divergences of tropical lineages between the Old and New Worlds in the family Drosophilidae. Mol. Phyl. Evol. 60:98–107. 2011.
  13. Kobayashi N, Kumagai M, Minegishi D, Tamura K, Aotsuka T, Katakura H. Molecular population genetics of a host-associated sibling 1 species complex of 2 phytophagous ladybird beetles (Coleoptera: Coccinellidae: Epilachninae). J. Zool. Syst. Evol. Res. 49:16-24. 2011.
  14. Takezaki N, Nei M, Tamura K. POPTREE2: Software for Constructing Population Trees from Allele Frequency Data and Computing Other Population Statistics with Windows Interface. Mol. Biol. Evol. 27:747-752. 2010.
  15. Kumar S, Nei M, Dudley J, Tamura K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 9:299-306. 2008.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. Saito S, Tamura K, Aotsuka T. Replication origin of mitochondrial DNA in insects. Genetics 171: 1695-1705. 2005.
  21. 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.
  22. *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)
  23. Tamura K, Subramanian S, Kumar S. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21:36-44. 2004.
  24. Tamura K, Kumar S. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol. 19:1727-1736. 2002.
  25. Kumar S, Tamura K, Jakobsen IB, Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245. 2001.
  26. Tamura K. On the estimation of the rate of nucleotide substitution for the control region of human mitochodrial DNA. Gene 259:189-197. 2000.
  27. 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.
  28. 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.
  29. 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.
  30. Kobayashi N, Tamura K, Aotsuka T. PCR Error and Molecular Population Genetics. Biochemical Genetics 37:317-321. 1999.
  31. 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.
  32. 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.)
  33. Kumar S, Tamura K, Nei M. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. CABIOS 10:189-191. 1994.
  34. Tamura K. Model selection in the estimation of the number of nucleotide substitutions. Mol. Biol. Evol. 11:154-157. 1994.
  35. 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.
  36. Tamura K. The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol. Biol. Evol. 9:814-825. 1992.
  37. 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.
  38. Hedges SB, Kumar S, Tamura K, Stoneking M. Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739. 1992.
  39. 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.
  40. 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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