Life is fifthdimension.

This site is evolutionary biologist Akifumi S. Tanabe's official web site. I may be contacted at the following.

Research interest

Molecular phylogenetics, its applications to evolutionary ecology research, and evolution of insects, molluscs and vertebrates.

Profile

Position: Postdoctoral fellow
Affiliation: National Research Institute of Fisheries Science, Fisheries Research Agency, Japan
Specialized field: Evolutionary biology; Ecology; Phylogenetics; Phylogeography; and related field
Membership: Ecological Society of Japan; Society of Evolutionary Studies, Japan; The Japanese Society of Limnology; Japan Association for Quaternary Research

Biography

Nov. 26, 1980: Born in Hisai city, Mie prefecture, Japan
Apr., 1987: Enrolled in Seishi city-run elementary school
Mar., 1993: Graduated from Seishi city-run elementary school
Apr., 1993: Enrolled in Takada junior high and senior high school
Mar., 1999: Graduated from Takada junior high and senior high school
Apr., 1999: Enrolled in Department of Biology, Geology and Environmental sciences, Faculty of Science, Shizuoka University
Mar., 2003: Graduated from Department of Biology, Geology and Environmental sciences, Faculty of Science, Shizuoka University
Apr., 2003: Enrolled in master's cource of Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University
Mar., 2005: Completed master's cource of Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University
Apr., 2005: Enrolled in doctoral cource of Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University
Sep., 2008: Completed doctoral cource of Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University
Oct., 2008: Accepted as postdoctoral research associate of Laboratory of Community and Ecosystem Ecology, Division of Ecology and Evolutionary Biology, Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University
Mar., 2009: Left postdoctoral research associate of Laboratory of Community and Ecosystem Ecology, Division of Ecology and Evolutionary Biology, Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University
Apr., 2009: Accepted as postdoctoral research associate of Institute of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba
Mar., 2011: Left postdoctoral research associate of Institute of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba
Apr., 2011: Accepted as junior assistant professor of Institute of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba
Aug., 2011: Left junior assistant professor of Institute of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba
Sep., 2011: Accepted as postdoctoral fellow of Graduate School of Science, Kyoto University
Mar., 2012: Left postdoctoral fellow of Graduate School of Science, Kyoto University
Apr., 2012: Accepted as postdoctoral fellow of Graduate School of Global Environmental Studies, Kyoto University
Jan., 2013: Left postdoctoral fellow of Graduate School of Global Environmental Studies, Kyoto University
Feb., 2013: Accepted as research fellow of National Research Institute of Fisheries Science, Fisheries Research Agency

Ph.D. dissertation

Tanabe, A. S., 2008, "How to walk in the misty forest: new approaches to decode the tree of life", Ph.D. dissertation, Tohoku University, Sendai, Japan.

Publications

in English

Toju, H., Tanabe, A. S., Notsu, Y., Sota, T. and Fukatsu, T., 2013, "Diversification of endosymbiosis: replacements, co-speciation and promiscuity of bacteriocyte symbionts in weevils", The ISME Journal, in press.
Toju, H., Tanabe, A. S., Yamamoto, S. and Sato, H., 2012, "High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples", PLoS ONE, 7, e40863, doi:10.1371/journal.pone.0040863.
Okuyama, Y., Tanabe, A. S. and Kato, M., 2012, "Entangling ancient allotetraploidization in Asian Mitella: An integrated approach for multilocus combinations", Molecular Biology and Evolution, 29, 429-439, doi:10.1093/molbev/msr236.
Tanabe, A. S., 2011, "Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data", Molecular Ecology Resources, 11, 914-921, doi:10.1111/j.1755-0998.2011.03021.x.
Makino, W. and Tanabe, A. S., 2009, "Extreme population genetic differentiation and secondary contact in the freshwater copepod Acanthodiaptomus pacificus in the Japanese Archipelago", Molecular Ecology, 18, 3699-3713, doi:10.1111/j.1365-294X.2009.04307.x.
Schmidt-Rhaesa, A., Nishi, H., Tanabe, A. S. and Urabe, M., 2009, "New records of hairworms (Nematomorpha, Gordiida) from Japan", Species Diversity, 14, 131-135.
Tanabe, A. S., 2007, "Kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data", Molecular Ecology Notes, 7, 962-964, doi: 10.1111/j.1471-8286.2007.01807.x.

in Japanese

Tanabe, A. S. and Honda, M., 2010, "Methods of phylogenetic reconstruction based on DNA sequences and their applications to herpetological studies", Bulletin of the Herpetological Society of Japan, 2010, 144-156.
Takeuchi, H. and Tanabe, A. S., 2001, "ATOK13/14/MS-IME98/2000 and Life Science Dictionary", Life Science Dictionary, revised edition (Kaneko, S., ed.), 82-92, Yodosha, Tokyo.
Takeuchi, H. and Tanabe, A. S., 2001, "Personal Dictionary (PDIC) for Win32", Life Science Dictionary, revised edition (Kaneko, S., ed.), 112-125, Yodosha, Tokyo.
Takeuchi, H. and Tanabe, A. S., 2001, "DDwin", Life Science Dictionary, revised edition (Kaneko, S., ed.), 126-134, Yodosha, Tokyo.
Takeuchi, H. and Tanabe, A. S., 2001, "Usage of Life Science Dictionary on Zaurus", Life Science Dictionary, revised edition (Kaneko, S., ed.), 135-149, Yodosha, Tokyo.

Presentations

in English

Tanabe, A. S. and Toju, H., 2012, "High accuracy and high precision taxonomic identification of host organisms of barcode DNA sequences", 2012 Aquatic Sciences Meeting of Association for the Sciences of Limnology and Oceanography in Otsu, Japan.
Tanabe, A. S., Inagaki, Y., Hashimoto, T., Tsuji, M. and Sato, M., 2011, "Effective bootstrapping: a new method for estimating accurate credibilities of splits on a phylogenetic tree", 2011 Annual Meeting of Society for Molecular Biology and Evolution in Kyoto, Japan.

in Japanese

Tanabe, A. S. and Toju, H. , 2012, "Claident: A taxonomic assignment system of host organisms of barcode DNA sequences", The 14th Annual Meeting of Society of Evolutionary Studies, Japan in Hachioji.
Tanabe, A. S. and Toju, H. , 2012, "Claident: A taxonomic assignment system of host organisms of barcode DNA sequences", The 2012 first regular meeting of Kinki Branch of Ecological Society of Japan in Otsu.
Tanabe, A. S. and Toju, H. , 2012, "A universal system for taxonomic assignment of barcode DNA sequences: Toward an exhaustive metagenomic barcoding", The 56th Annual Meeting of The Mycological Society of Japan in Gifu.
Tanabe, A. S., Inagaki, Y., Hashimoto, T., Tsuji, M. and Sato, M., 2011, "Effective bootstrapping: a new method for estimating accurate credibilities of splits on a phylogenetic tree", The 13th Annual Meeting of Society of Evolutionary Studies, Japan in Kyoto.
Tanabe, A. S., Inagaki, Y., Hashimoto, T., Tsuji, M. and Sato, M., 2011, "Quantifying bias of credibility indices of phylogenetic tree under the maximum likelihood criterion", The 58th Annual Meeting of Ecological Society of Japan in Sapporo.
Tanabe, A. S., 2010, "Incorporating gap informations to molecular phylogenetic inference: effects of multiple sequence alignment and trimming of ambiguously aligned sites", The 12th Annual Meeting of Society of Evolutionary Studies, Japan in Tokyo.
Tanabe, A. S., 2010, "Molecular phylogenetic inference and model selection for molecular evolution: comparison among nonpartitioned, proportional, and separate models", The 57th Annual Meeting of Ecological Society of Japan in Tokyo.
Tanabe, A. S., 2009, "Application of orthogenesis-like model to divergence time estimation and comparing with Brownian motion model", The 11th Annual Meeting of Society of Evolutionary Studies, Japan in Sapporo.
Tanabe, A. S., 2009, "The selection of Molecular Evolution Model, Likelihood Ratchet, and Detection of Rate Inconstancy of Molecular Evolution from Phylogenetic Tree", The Workshop of "Estimation and Applications of Molecular Phylogeny for Evolutionary Ecology" in The 56th Annual Meeting of Ecological Society of Japan in Morioka.
Tanabe, A. S., 2008, "Gap encoding problem revisited: a comparison study among 4 encoding algorithms and 3 evolution models at Bayesian phylogenetic analysis", The 10th Annual Meeting of Society of Evolutionary Studies, Japan in Tokyo.
Tanabe, A. S., 2008, "Development and implementation of a new method for estimating divergence times", The 55th Annual Meeting of Ecological Society of Japan in Fukuoka.
Tanabe, A. S., 2007, "The selection of nucleotide substitution model on multilocus and protein coding sequence data", The 9th Annual Meeting of Society of Evolutionary Studies, Japan in Kyoto.
Tanabe, A. S., 2006, "Molecular phylogeny of Trichopteran insects", The 53rd Annual Meeting of Ecological Society of Japan in Niigata.
Tanabe, A. S., 2005, "Applications of Local Clock model for topology selection and root point estimation", The 7th Annual Meeting of Society of Evolutionary Studies, Japan in Sendai.
Tanabe, A. S., 2005, "Phylogeny and speciation of Japanese Lepidostomatidae (Trichoptera)", The 52nd Annual Meeting of Ecological Society of Japan in Osaka.
Tanabe, A. S. and Kitamura, A., 2003, "The effect of glacial-interglacial climatic cycles to species stability - from morphological variations of Limopsis belcheli (bivalvia) in bathyal zone around Japan", 2003 Annual Meeting of Palaeontological Society of Japan in Shizuoka.

Products

Assams-assembler: A high-throughput long-read assembler based on overlap/layout/consensus framework
Claident: A software package for rapid sequence classification and accurate taxonomic identification of host organisms of sequences for metagenomic and barcoding studies
CombineTrees: Combining same topology trees with averaging branch lengths
DistCalc: Geographic distance calculator from longitude and latitude
Kakusan: Nucleotide substitution model selection script written in Perl language for multi-partitioned data set
Aminosan: Amino-acid substitution model selection script written in Perl language for multi-partitioned data set
MrBayes5D: A modified version of MrBayes to apply more amino-acid models
Phylogears: Flexible tools package for parallel and high-throuput phylogenetic tree reconstruction

Documents

in English

Tips for MrBayes

in Japanese

A Deskside Handbook for Molecular Phylogenetic Analysis (unfinished Japanese version only)
Textbook for the workshop of molecular phylogenetics at Tsukuba (Japanese version only)

Japanese Wiki (but nonwritable)

Life is fifthdimension. by Akifumi S. Tanabe is licensed under a Creative Commons Attribution-ShareAlike 2.1 Japan License.