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Department of Biological Sciences
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Laboratories
Molecular Neuroscience
Developmental Biology
Cellular Genetics
Molecular Genetics
Plant Development and Physiology
Cellular Biochemistry
Neurobiology
Evolutionary Genetics
Plant Environmental Responses
Environmental Microbiology
Animal Ecology
Plant Ecology
Systematic Zoology
Systematic Botany
Photosynthetic Microbial Consortia
Photo Evolutionary Genetics Laboratory
Our research interests are the genetic basis of biological evolution and speciation. We use a variety of approaches ranging from field work to bioinformatic analyses as well as laboratory experiments.
Faculty
Koichiro Tamura e-mail
Aya Takahashi e-mail
Masafumi Nozawa e-mail
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 of DNA Sequences and Bioinformatics
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Bioinformatics for DNA sequence data
Genome sequencing projects have produced large amounts of DNA sequence data. Analyzing these data together with our original sequence data by computational and bioinformatic techniques, we are studying how DNA sequences, genes and genomes evolve. We are also developing new theoretical methods and computer software for molecular evolutionary and phylogenetic analyses.
Molecular bases of speciation in Drosophila
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Experimental approaches using fruitflies
Studying the underlying molecular bases of speciation is one of the fundamental theme in evolutionary biology. Our aim is to understand the genetic changes that occur during the speciation event in Drosophila species. One of our current projects focuses on association between pigmentation intensity and sexual behavior in individuals from natural populations of D. melanogaster. We are also interested in analyzing the genomic features of transcriptome that could potentially influence the species isolation process. We take both experimental and bioinformatics approaches to tackle these questions.
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Genome-wide transciptome analyses using next generation sequencers
Evolutionary process of sex chromosomes in Drosophila
Sex chromosomes have repeatedly and independently emerged in many organisms during long history of life. After the emergence of sex chromosomes, however, Y chromosomes (or W chromosomes in the ZW sex-determining system) are degenerated in many cases, which would potentially be deleterious to males (or females in the ZW system). Then, how organisms have acquired and maintained the sex chromosomes under such a potential disadvantage? In our laboratory, we are tackling this issue using Drosophila miranda, D. albomicans, and D. americana, who recently acquired sex chromosomes. These young sex chromosomes are expected to be in the transient stages from ordinary autosomes to sex chromosomes, which is an ideal system to clarify the detailed processes of becoming sex chromosomes.

We also study the evolutionary mechanisms of miRNA-involved gene regulatory networks. Next Generation Sequencing (or NGS, e.g., DNA-seq, RNA-seq, ChIP-seq, smallRNA-seq, CLIP-seq, etc.) and bioinformatics are keywords for both projects.
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Drosophila species with young sex chromosomes
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An empirical approach of studying evolution of miRNA-target pairs
Recent Publications
  1. Igawa T, Nozawa M, Suzuki DG, Reimer JD, Norov AR, Wang Y, Henmi Y, Yasui K*. (2017) Evolutionary history of the extant amphioxus lineage with shallow-branching diversification. Sci. Rep. (in press)
  2. Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang T-H, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Palfalvi G, Pollard ST, Rozas J, Sanchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M*. (2017) Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecol. Evol. 1:0059.
  3. Kudo A, Shigenobu S, Kadota K, Nozawa M, Shibata FT, Ishikawa Y, Matsuo T*. (2017) Comparative analysis of the brain transcriptome in a hyper-aggressive fruit fly, Drosophila prolongata. Insect Biochem. Mol. Biol. 82:11-20.
  4. Okamiya H*, Igawa T, Nozawa M, Sumida M, Kusano T. (2017) Development and Characterization of 23 Microsatellite Markers for the Montane Brown Frog (Rana ornativentris) Curr. Herpetol. 36:63-68.
  5. Nozawa M*, Onizuka K, Fujimi M, Ikeo K, Gojobori T. (2016) Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nat. Commun. 7:13659.
  6. Komaki S, Lin S-M, Nozawa M, Oumi S, Sumida M, Igawa T*. (2016) Fine-scale demographic processes resulting from multiple overseas colonization events of the Japanese stream tree frog, Buergeria japonica. J Biogeogr. 12922.
  7. Ishikawa M, Shimizu H, Nozawa M, Ikeo K, Gojobori T*. (2016) Two-Step Evolution of Endosymbiosis between Hydra and Algae. Mol. Phyl. Evol. 103:19-25.
  8. Ishikawa M, Yuyama I, Shimizu H, Nozawa M, Ikeo K, Gojobori T*. (2016) Different endosymbiotic interactions inof two hydra species reflect the evolutionary history of endosymbiosis. Genome Biol. Evol. 8:2155-2163.
  9. Nozawa M*, Fujimi M, Iwamoto C, Onizuka K, Fukuda N, Ikeo K, Gojobori T. (2016) Evolutionary transitions of microRNA-target pairs. Genome Biol. Evol. 8:1621-1633.
  10. Koga H*, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata TF, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. (2016) Experimental approach reveals the role of alx1 in the evolution of the echinoderm larval skeleton. PLOS One 11:e0149067.
  11. Nozawa M*, Kinjo S. (2016) Origin and evolution of non-coding RNAs. Encyclopedia for Evol. Biol. 3:130-135.
  12. Sunaga, S., Akiyama, N., Miyagi, R., and *Takahashi, A. Factors underlying natural variation in body pigmentation of Drosophila melanogaster. Genes Genet. Syst. (in press)
  13. Satomura K, Tamura K. (2016) Ancient male recombination shaped genetic diversity of neo-Y chromosome in Drosophila albomicans. Mol. Biol. Evol. 33:367-374.
  14. 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.
  15. 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.
  16. 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.
  17. Miyagi, R., Akiyama, N., Osada, N., and Takahashi, A. (2015) Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster. Mol. Ecol. 24: 5829-5841.
  18. Tanaka, K. M., Takahashi, A., Fuse, N., and Takano-Shimizu-Kouno, T. (2014) A novel cell death gene acts to repair patterning defects in Drosophila melanogaster. Genetics 197: 739-742.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. Takahashi A. (2013) Pigmentation and behavior: potential association through pleiotropic genes in Drosophila. Genes Genet. Syst. 88: 165-174.
  27. 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.
  28. 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.
  29. Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. (2012) Statistics and Truth in Phylogenomics. Mol Biol. Evol. 29:457-472.
  30. Nishimura A., Ishida Y., Takahashi A., Okamoto H., Sakabe M., Itoh M., Takano-Shimizu T., Ozaki M. (2012) Starvation-induced elevation of taste responsiveness and expression of a sugar taste receptor gene in Drosophila melanogaster. J. Neurogenet. 26: 206-15.
  31. Takahashi A, Fujiwara-Tsujii N, Yamaoka R, Itoh M, Ozaki M, Takano-Shimizu T. (2012) Cuticular hydrocarbon content that affects male mate preference of Drosophila melanogaster from West Africa. Int. J. Evol. Biol. 2012:278903.
  32. 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.
  33. 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.
  34. Kobayashi1 N, Kumagai M, Minegishi D, Tamura K, Aotsuka T, Katakura H (2011) 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.
  35. Takahashi A., Takano-Shimizu T. (2011) Divergent enhancer haplotype of ebony on inversion In(3R)Payne associated with pigmentation variation in a tropical population of Drosophila melanogaster. Mol. Ecol. 20: 4277-4287.
  36. Kitamura N, Fujiyama N, Katakura H, Aotsuka T (2010) Reproductive isolation between 2 karyotypes in natural populations of the leaf beetle Chrysolina aurichalcea. Journal of Heredity 101. 317-324.
  37. Fiedler GC, Rhyne AL, Segawa R, Aotsuka T, Schizas NV (2010) The evolution of euhermaphroditism in caridean shrimps: A molecular perspective of sexual systems and systematics. BMC Evol. Biol. 10:297.
  38. Okuno, J. and Fiedler, G.C. (2010). Lysmata lipkei, a new species of peppermint shrimp (Decapoda, Hippolytidae) from the warm temperate and subtropical waters of Japan In: C. H. J. M. Fransen, S. De Grave and P. K. L. Ng (eds.), Studies on Malacostraca: Lipke Bijdeley Holthuis Memorial Volume, Crustaceana Monograph, 14: 597-610.
  39. Takezaki N, Nei M, Tamura K (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.
  40. Sawamura K., Maehara K., Mashino S., Kagesawa T., Kajiwara M., Matsuno K., Takahashi A., Takano-Shimizu T. (2010) Introgression of Drosophila simulans Nup160 (nuclear pore protein 160) in Drosophila melanogaster alone does not cause inviability but does cause female sterility. Genetics 186: 669-676.
©2015 Department of Biological Sciences, Tokyo Metropolitan University