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Masato YAMAMICHI, Ph.D.



  • Program-Specific Assistant Professor of Hakubi Center for Advanced Research/Center for Ecological Research, Kyoto University



In Tongariro crossing, New Zealand, 2006

Research Interests:

  • Eco-evolutionary dynamics in communities and ecosystems
  • Population genetics of speciation, adaptation, and polymorphism
  • Time-series analysis of ecological interactions

Education:


Research Positions:


Publications:

Peer-reviewed Articles

  1. Yamamichi M, Hoso M (2017Roles of maternal effects in maintaining genetic variation: Maternal storage effect. Evolution 71(2): 449-457 [PDF] [Supplement] DOI: 10.1111/evo13118
  2. Toju H, Yamamichi M, Guimarães PR Jr, Olesen JM, Mougi A, Yoshida T, Thompson JN (2017) Species-rich networks and eco-evolutionary synthesis at the metacommunity level. Nature Ecology & Evolution 1: 0024 [PDF] [Supplement] DOI: 10.1038/s41559-016-0024  
  3. Adachi T, Costa D, Robinson P, Peterson S, Yamamichi M, Naito Y, Takahashi A (2017) Searching for prey in a three-dimensional environment: hierarchical movements enhance foraging success in northern elephant seals. Functional Ecology 31(2): 361-369 [PDF] [Supplement] DOI: 10.1111/1365-2435.12686 [FE Spotlight]
  4. Yamamichi M, Ellner SP (2016) Antagonistic coevolution between quantitative and Mendelian traits. Proceedings of the Royal Society B: Biological Sciences 283(1827): 20152926 [PDF] [Supplement] [Dryad] DOI: 10.1098/rspb.2015.2926
  5. Yen JDL, Cabral RB, Cantor M, Hatton I, Kortsch S, Patrício J, Yamamichi M (2016) Linking structure and function in food webs: maximization of different ecological functions generates distinct food-web structures. Journal of Animal Ecology 85(2): 537-547 [PDF] [Supplement] DOI: 10.1111/1365-2656.12484
  6. Sato NJ, Tanaka KD, Okahisa Y, Yamamichi M, Kuehn R, Gula R, Ueda K, Theuerkauf J (2015) Nestling polymorphism in a cuckoo-host system. Current Biology 25(24): R1164-R1165 [PDF] [Supplement] DOI: 10.1016/j.cub.2015.11.028
  7. Yamamichi M, Miner BE (2015) Indirect evolutionary rescue: prey adapts, predator avoids extinction. Evolutionary Applications 8(8): 787-795 [PDF] [Supplement] [Institutional Repository] DOI: 10.1111/eva.12295
  8. Yamamichi M, Meunier CL, Peace A, Prater C, Rúa MA (2015) Rapid evolution of a consumer stoichiometric trait destabilizes consumerproducer dynamics. Oikos 124(7): 960-969 [PDF] [Supplement] DOI: 10.1111/oik.02388 [Oikos blog]
  9. Kasada M, Yamamichi M, Yoshida T (2014) Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator–prey system. Proceedings of the National Academy of Sciences of the United States of America 111(45): 16035-16040 [PDF] [Supplement] [Institutional Repository] DOI: 10.1073/pnas.1406357111 (Cover Article)
    http://www.pnas.org/content/111/45.cover-expansion
  10. Tezuka A, Kasagi S, van Oosterhout C, McMullan M, Iwasaki WM, Kasai D, Yamamichi M, Innan H, Kawamura S, Kawata M (2014) Divergent selection for opsin gene variation in guppy (Poecilia reticulata) populations of Trinidad and Tobago. Heredity 113(5): 381-389 [PDF] [Supplement] DOI: 10.1038/hdy.2014.35
  11. Yamamichi M, Yoshida T, Sasaki A (2014) Timing and propagule size of invasion determine its success by a time-varying threshold of demographic regime shift. Ecology 95(8): 2303-2315 [PDF] [Supplement] [Institutional Repository] DOI: 10.1890/13-1527.1
  12. Yamamichi M, Sasaki A (2013) Single-gene speciation with pleiotropy: Effects of allele dominance, population size, and delayed inheritance. Evolution 67(7): 2011-2023 [PDF] [Supplement] DOI: 10.1111/evo.12068
  13. Yamamichi M, Innan H (2012) Estimating the migration rate from genetic variation data. Heredity 108(4): 362-363 [PDF] DOI: 10.1038/hdy.2011.83
  14. Yamamichi M, Gojobori J, Innan H (2012) An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Molecular Biology and Evolution 29(1): 145-156 [PDF] [Supplement] DOI: 10.1093/molbev/msr172
  15. Yamamichi M, Yoshida T, Sasaki A (2011) Comparing the effects of rapid evolution and phenotypic plasticity on predator-prey dynamics. The American Naturalist 178(3): 287-304 [PDF] [Supplement] DOI: 10.1086/661241
  16. Matthews B, Narwani A, Hausch S, Nonaka E, Peter H, Yamamichi M, Sullam KE, Bird KC, Thomas MK, Hanley TC, Turner CB (2011) Toward an integration of evolutionary biology and ecosystem science. Ecology Letters 14(7): 690-701 [PDF] DOI: 10.1111/j.1461-0248.2011.01627.x

Peer-reviewed Articles (in Japanese)

  1. Yamamichi M (2013) Statistical inference in phylogeography and future perspectives. In: Ikeda H, Koizumi I (eds.), Phylogeography: Plant Species Biology 36: 261-293, Bun-ichi Sogo Shuppan Co. Ltd., Tokyo
  2. Yamamichi M, Hiraiwa-Hasegawa M (2012) Research object biases in Japanese Journal of Conservation Ecology. Japanese Journal of Conservation Ecology 17(2): 199-210
  3. Yamamichi M, Kadoya T (2009) An introduction to parameter estimation of simulation models by Bayesian calibration. Japanese Journal of Ecology 59(2): 207-216

Non-reviewed Articles (in Japanese)

  1. Shikayama D, Itaki Y, Yamamichi M (2015) Why are there a few popular and many unpopular comics? Distribution predictions of comic series periods by using the popularity-vote model. Research Institute for Mathematical Sciences Kokyuroku 1966: 34-40
  2. Yamamichi M, Innan H (2012) An introduction to ecogenomics (7) Future perspectives of ecogenomics studies. Japanese Journal of Ecology 62(1): 95-109
  3. Yamamichi M (2011) The effects of rapid evolution and phenotypic plasticity on population dynamics. Research Institute for Mathematical Sciences Kokyuroku 1751: 140-147
  4. Yamamichi M, Innan H (2011) An introduction to ecogenomics (6) Detecting the signatures of natural selection (2). Japanese Journal of Ecology 61(2): 237-249
  5. Yamamichi M, Innan H (2010b) An introduction to ecogenomics (5) Detecting the signatures of natural selection (1). Japanese Journal of Ecology 60(2): 293-302
  6. Yamamichi M, Innan H (2010a) An introduction to ecogenomics (4) The theory and analysis of DNA polymorphism data (2). Japanese Journal of Ecology 60(1): 137-148
  7. Yamamichi M, Innan H (2009b) An introduction to ecogenomics (3) The theory and analysis of DNA polymorphism data (1). Japanese Journal of Ecology 59(3): 339-349
  8. Yamamichi M, Innan H (2009a) An introduction to ecogenomics (2) Genome-wide association mapping. Japanese Journal of Ecology 59(1): 105-113
  9. Yamamichi M, Innan H (2008) An introduction to ecogenomics (1) Local adaptation and the divergence of phenotypic traits. Japanese Journal of Ecology 58(3): 241-247
  10. Yamamichi M (2008) Hierarchical Bayes and its application to reaction-diffusion model. Newsletter of the Japanese Society for Mathematical Biology 56: 10-15
  11. Yamamichi M (2007) What we can learn from long-term surveys of citizens' participation using hierarchical Bayes model. Bird Research News 4(12): 2
Google Scholar Citations; Researchmap; ResearchGate; University Database; ORCID


Presentations:

Invited Talks

  1. Yamamichi M. "Timing and propagule size of invasion determine its success by a time-varying threshold of demographic regime shift". Plenary Symposium B: Scaling from Life History Traits to the Population Dynamics (organized by William A. Nelson & Takehiko Yamanaka). 30th Annual Meeting of the Society of Population Ecology. Tsukuba, Japan. October 10-12, 2014.
  2. Yamamichi M. "Rapid evolution of phenotypic plasticity in a predator-prey system". MS21: Modeling the interactions between ecological and evolutionary processes: fast, slow, and everything in between (organized by Michael Cortez). SMB2013. Tempe, Arizona, U.S.A. June 10-13, 2013.
  3. Yamamichi M, Sasaki A. "Single-gene speciation revisited: Allele dominance and pleiotropy". SMBE 2011. Kyoto, Japan. July 26-30, 2011. (Selected as Oral Presentation)
  4. Yamamichi M, Innan H. "No genetic evidence for complex speciation of humans and chimpanzees". Annual Meeting of the Society for Molecular Biology and Evolution: SMBE 2008. Barcelona, Spain. June 5-8, 2008. (O-136) (Selected as Oral Presentation)

Contributed Talks

  1. Yamamichi M, Hairston Jr. NG, Ellner SP. "Rapid evolution affects how populations respond to environmental fluctuations". 102nd ESA Annual Meeting. Portland, Oregon, U.S.A. August 6-11, 2017.
  2. Hairston NG, Schaffner LR, Miner BE, Bonner E, Spaak P, Yamamichi M, Ellner SP. "Daphnia eco-evolutionary process meets the clear water phase: seasonal plankton dynamics when the consumer evolves". ASLO 2017 Aquatic Sciences Meeting. Honolulu, Hawaii, U.S.A. February 26-March 3, 2017. [abstract]
  3. Yamamichi M, Kazama T, Tokita K, Katano I, Doi H, Yoshida T, Hairston Jr. NG, Urabe J. "A shady phytoplankton paradox: Why phytoplankton increases under low light". 101st ESA Annual Meeting. Fort Lauderdale, Florida, U.S.A. August 7-12, 2016. (COS 29-3) [abstract]
  4. Yamamichi M, Ellner SP. "Antagonistic coevolution between quantitative and Mendelian traits". American Society of Naturalists Conference 2016. Asilomar, California, U.S.A. January 10-14, 2016.
  5. Yamamichi M. "Modeling adaptation processes in eco-evolutionary feedbacks". Experimental Evolution and Community Dynamics (EECD) Minisymposium 2015. Hanko, Finland. October 13-15, 2015.
  6. Yamamichi M, Hoso M. "Effects of genetic architectures on polymorphism dynamics under negative frequency-dependent selection". Mathematical Models in Ecology and Evolution (MMEE) 2015. Paris, France. July 8-10, 2015. [abstract]
  7. Yamamichi M. "Feedbacks between ecology and evolution in predator-prey systems". 4th Taiwan-Japan Ecology Workshop. Hualien, Taiwan. November 15-17, 2014.
  8. Adachi T, Costa D, Robinson P, Yamamichi M, Naito Y, Takahashi A. "Searching prey in 3D environment: hierarchical foraging behaviour of northern elephant seals". The 5th International Bio-logging Science Symposium. Strasbourg, France. September 22-27, 2014. (OB-02)
  9. Yamamichi M, Ellner SP. "Coevolution mediated by continuous predator and discrete prey traits". JSMB/SMB 2014 Meeting. Osaka, Japan. July 28-August 1, 2014. (CS 13)
  10. Yamamichi M, Yoshida T, Sasaki A. "Introduction timing of genetic diversity in eco-evolutionary dynamics". 98th ESA Annual Meeting. Minneapolis, Minnesota, U.S.A. August 4-9, 2013. (COS 128-2) [abstract]
  11. Yamamichi M, Sasaki A. "Single-gene speciation with functional pleiotropy: effects of allele dominance, population size, and maternal effect". Evolution Ottawa: 1st Joint Congress on Evolutionary Biology. Ottawa, Ontario, Canada. July 6-10, 2012.
  12. Yamamichi M, Yoshida T, Sasaki A. "Invasion timing determines settlement success in an endogenously oscillating system". 96th ESA Annual Meeting. Austin, Texas, U.S.A. August 7-12, 2011. (COS 71-7) [abstract]
  13. Yamamichi M, Yoshida T, Sasaki A. "The effects of rapid evolution and phenotypic plasticity on aquatic predator-prey dynamics". 95th ESA Annual Meeting. Pittsburgh, Pennsylvania, U.S.A. August 1-6, 2010. (COS 116-4) [abstract]
  14. Fujita G, Yoshio M, Miyashita T, Yamamichi M, Tatsuta H. "When landscape genetics meets population ecology: an integrative study of population expansion patterns of sika deer on the Boso peninsula". The 23rd Symposium of the Society of Population Ecology: Spatial structure and dynamics of ecological system. Sapporo, Japan. October 19-21, 2007.

Posters

  1. Yamamichi M, Sasaki A. "Ecological speciation via pleiotropy: fixation probability of the speciation gene". Joint Meeting of the 59th Annual Meeting of ESJ and the 5th EAFES International Congress. Otsu, Japan. March 17-21, 2012. (P2-160J) [abstract] (Excellent Poster Award)
  2. Yamamichi M, Sasaki A. "Ecological speciation of snails by right-handed snakes: Red queen or evolutionary stasis?". Evolution 2010. Portland, Oregon, U.S.A. June 25-29, 2010 (P1139)
  3. Yamamichi M, Yoshida T, Sasaki A. "The ecological and evolutionary stability of the plastic prey". International Forum for Ecosystem Management Applying to Ecosystem Adaptability Science I. Robustness and Stability of Organisms and Ecosystems. Sendai, Japan. February 21-24, 2010. (P4)

Workshop Participation:

  1. 2015: Kyoto Winter Research Program in Mathematical Biology Next Wave 2015 in Kyoto, Japan
  2. 2014: Woodstoich III in Sydney, Australia
  3. 2013: Complex Systems Summer School 2013 at Santa Fe Institute, U.S.A.
  4. 2012: NESCent Workshop "Evolutionary Quantitative Genetics" in Durham, U.S.A.
  5. 2011: OIST Summer School and Workshop "QECG2011: Linkage and Recombination in Genome Sequences" in Okinawa, Japan
  6. 2009: Eawag Ph.D. summer school "Interactions between ecological and evolutionary processes in aquatic systems" in Kastanienbaum, Switzerland


Awards and Honors:

  1. Best English Presentation Award (2017, The 64th Annual Meeting of the Ecological Society of Japan, Evolution section)
  2. Population Ecology Young Scientist Award (2016, Society of Population Ecology)
  3. Excellent English Presentation Award (2015, The 62nd Annual Meeting of the Ecological Society of Japan, Evolutionary Ecology of Animals section)
  4. Suzuki Award (ESJ Encouraging Award) (2015, Ecological Society of Japan)
  5. Inoue Research Award for Young Scientists (2015, Inoue Foundation for Science)
  6. Excellent Poster Award (2012, 28th Annual Meeting of the Society of Population Ecology)
  7. Excellent Poster Award (2012, Joint Meeting of the 59th Annual Meeting of the Ecological Society of Japan and the 5th EAFES International Congress, Evolution section)
  8. Best Poster Award (2012, Japan-Indonesia Academic Exchange Seminar by Indonesian Institute of Sciences (LIPI), Bogor Agricultural University (IPB), & The Graduate University for Advanced Studies)
  9. Sokendai President's Award (2010, The Graduate University for Advanced Studies)
  10. Excellent Poster Award (2010, The 57th Annual Meeting of the Ecological Society of Japan, Animal Population section)
  11. The Dean Award for Academic Excellence (2007, Faculty of Agriculture, The University of Tokyo)


Fellowships and Grants:

  1. Grant-in-Aid for Young Scientists B (2016-2019, JSPS)
  2. Grant-in-Aid for Scientific Research B (as a Co-Investigator, 2016-2019, JSPS)
  3. John Mung Program (2015-2016, Kyoto University)
  4. Grant-in-Aid for Scientific Research A (as a Co-Investigator, 2015-2018, JSPS)
  5. Hakubi Research Fellowship (2014-2019, Kyoto University)
  6. Postdoctoral Fellowship for Research Abroad (2012-2014, JSPS)
  7. Interdisciplinary Research Collaboration Grant (2012, The Graduate University for Advanced Studies)
  8. The Short-Stay Study Abroad Program (2011, The Graduate University for Advanced Studies)
  9. Excellent Young Researchers Overseas Visit Program (2010, JSPS)
  10. Research Fellowship for Young Scientists (Doctoral Course Students, DC1) (2009-2012, JSPS)
  11. JASSO Scholarship (2007-2009, JASSO)

Reviewer:

  • The American Naturalist (2), Ecological Complexity, Ecology (3), Ecology Letters (5)eLife, Evolution, Evolutionary Applications, Functional Ecology (2), Genetics Research, Interface FocusJournal of Animal Ecology, Journal of Complex Networks, Journal of Ecology, Journal of Mathematical Biology, Journal of Theoretical Biology (4)Mathematical BiosciencesMethods in Ecology and Evolution, Philosophical Transactions of the Royal Society B: Biological Sciences, Population Ecology (2), Proceedings of the Royal Society B: Biological Sciences (3), Trends in Ecology and EvolutionJapanese Journal of EcologyAxios Review (2)Book chapter (3)
  • DAAD Fellowship Application (Germany)

Publons


Teaching:

  • Advanced evolutionary biology (Co-Instructor, 2016-2017, Kyoto University)
  • Understanding life: From molecule to ecosystem (Co-Instructor, 2015, Kyoto University)
  • Ecological Science (Co-Instructor, 2015, Kyoto University)
  • Interdisciplinary Life Science Course (Co-Instructor, 2014-2016, Kyoto University)


Contact:

  • Center for Ecological Research, Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan
  • Email: yamamichi (a) ecology.kyoto-u.ac.jp

サブページ (1): Japanese