TOKYO METROPOLITAN UNIVERSITY
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Koichiro Tamura
Professor
Ph, D (Tokyo Metropolitan University, 1991)
Tel:
0426-77-1111(ext. 3725)
Email:
Adaptation to temperate 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.
Comparative Genomics for Molecular Evlution in Drosophila
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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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MEGA X Software
Recent Publications
  1. Patel R, Sanderford MD, Lanham TR, Tamura K, Platt A, Gilksberg BS, Dudley JT, Xu K, Scheinfeldt LB, Kumar S (2018) Adaptive landscape of protein variation in human exomes. Mol. Biol. Evol. 35:2015–2025.
  2. Battistuzzi FU, Tao Q, Jones L, Tamura K, Kumar S (2018). RelTime relaxes the strict molecular clock throughout the phylogeny. Genome Biol. Evol. 10:1631–1636.
  3. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 35:1547–1549.
  4. Tamura K, Tao Q, Kumar S. (2018) Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates. Mol. Biol. Evol. 35:1770–1782.
  5. Noyszewski AK, Liu YC, Tamura K, Smith AG. (2017) Polymorphism and structure of style-specific arabinogalactan proteins as determinants of pollen tube growth in Nicotiana. BMC evolutionary biology 17:186.
  6. Loh SYM, Ogawa Y, Kawana S, Tamura K, Lee HK. (2017) Semi-automated quantitative Drosophila wings measurements. BMC bioinformatics 18:319.
  7. Fraimout A, Debat V, Fellous S, Hufbauer RA, Foucaud J, Pudlo P, Marin J-M, Price DK, Cattel J, Chen X, Deprá M, Duyck PF, Guedot C, Kenis M, Kimura MT, Loeb G, Loiseau A, Martinez-Sañudo I, Pascual M, Richmond MP, Shearer P, Singh N, Tamura K, Xuéreb A, Zhang J, Estoup A. (2017) Deciphering the routes of invasion of Drosophila suzukii by means of ABC random forest. Mol. Biol. Evol. 34:980-996.
  8. Mello B, Tao Q, Tamura K, Kumar S. (2017) Fast and accurate estimates of divergence times from big data. Mol. Biol. Evol. 34:45-50.
  9. Kumar S, Stecher, G, Tamura K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 33:1870-1874.
  10. Satomura K, Tamura K. (2016) Ancient male recombination shaped genetic diversity of neo-Y chromosome in Drosophila albomicans. Mol. Biol. Evol. 33:367-374.
  11. Liu L, Tamura K, Sanderford M, Gray VE, Kumar S. A (2016) Molecular Evolutionary Reference for the Human Variome. Mol. Biol. Evol. 33:245-254.
  12. Ohta S, Seto Y, Tamura K, Ishikawa Y, Matsuo T. (2015) Comprehensive identification of odorant-binding protein genes in the seed fly, Delia platura (Diptera: Anthomyiidae). Applied Entomology and Zoology 50:457-463.
  13. Filipski A, Tamura K, Billing-Ross P, Murillo O, Kumar S. (2015) Phylogenetic placement of metagenomic reads using the minimum evolution principle. BMC Genomics 16:1-9.
  14. 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.
  15. 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. 31:1622-1624.
  16. 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.
  17. Ohta S, Seto Y, Tamura K, Ishikawa Y, Matsuo T. (2014) Identification of odorant-binding protein genes expressed in the antennae and the legs of the onion fly, Delia antiqua (Diptera: Anthomyiidae). Appl. Entomol. Zool. 49:89-95.
  18. 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.
  19. 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.
  20. 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.
  21. Tamura K, Battistuzzi FU, Billing-Ross P, Kumar S. (2012) Estimating Divergence Times in Large Molecular Phylogenies. Proc. Nat. Acad. Sci. USA 109:19333-19338.
  22. Kumar S, Stecher G, Peterson D, Tamura K. (2012) MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis program for automated and iterative data analysis. Bioinformatics 28: 2685-2686. 2012.
  23. Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. (2012) Statistics and Truth in Phylogenomics. Mol Biol. Evol. 29:457-472.
  24. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 28:2731-2739.
  25. Gao J, Hu Y, Toda MJ, Katoh T, Tamura K. (2011) 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.
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