How genomic changes promote adaptation and speciation in Arabidopsis relatives and in tropical trees

Evolutionary Functional Genomics / Systems Biology

Darwin proposed the first conclusive theory to explain biodiversity with two principles: adaptation by natural selection, and speciation. However, little is known about the genes responsible for biodiversity, due to the split between laboratory molecular biologists and field evolutionists. The key to synthesize biology is genomics: specifically, evolutionary genomics.

We take interdisciplinary approaches to study the molecular basis of biodiversity, and helps start the University Research Priority Program of Systems Biology / Functional Genomics. One of the advantages of using plants is the feasibility of ecological studies since they are immobile. The plants we study include a model species Arabidopsis thaliana, an allopolyploid Arabidopsis kamchatica in East Asia, a species-rich genus Cardamine, and Dipterocarpaceae in Malaysia tropical forests.

Recent Publications

  • Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana
    Tsuchimatsu, T; Kakui, H; Yamazaki, M; Marona, C; Tsutsui, H; Hedhly, A; Meng, D; Sato, Y; Stadler, T;Grossniklaus, U; Kanaoka, MM; Lenhard, M; Nordborg, M; Shimizu, KK
    Nature Communications  8 June 2020., 10.1038/s41467-020-16679-7
  • Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses
    Hanya, Goro; Tackmann, Janko; Sawada, Akiko; Lee, Wanyi; Pokharel, Sanjeeta Sharma; et al.
    Microbial Ecology  DOI: 10.1007/s00248-020-01515-8 Early Access: APR 2020
  • Artificial selection reveals the role of transcriptional constraints in the maintenance of life history variation
    Pick, Joel L.; Hatakeyama, Masaomi; Ihle, Kate E.; Gasparini, Julien; Haussy, Claudy; et al.
    Evolution Letters  DOI: 10.1002/evl3.166  Early Access: APR 2020
  • Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq
    Tsujimoto, Michiaki; Araki, Kiwako S.; Honjo, Mie N.; Yasugi, Masaki; Nagano, Atsushi J.; et al.
    Aob Plants,  DOI: 10.1093/aobpla/plz080 Published: FEB 2020
  • Genetic relationships and linguistic diversity in present-day populations of South America
    Barbieri, Chiara; Barquera, Rodrigo; Arias, Leonardo; Sandoval, Jose R.; Acosta, Oscar; et al.
    American Journal Of Physical Anthropology Vol 171 Pages: 17-18 Supplement: 69 MAR 2020
  • The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast
    Barbieri, Chiara; Barquera, Rodrigo; Arias, Leonardo; Sandoval, Jose R.; Acosta, Oscar; et al.
    Molecular Biology And Evolution,  DOI: 10.1093/molbev/msz174, DEC 2019
  • Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence
    Izuno, Ayako; Wicker, Thomas; Hatakeyama, Masaomi; Copetti, Dario; Shimizu, Kentaro K.
    G3-genes Genomes Genetics, 10.1534/g3.119.400643
  • Transcriptional Variation in Glucosinolate Biosynthetic Genes and Inducible Responses to Aphid Herbivory on Field-Grown Arabidopsis thaliana
    Sato, Y; Tezuka, A; Kashima, M; Deguchi, A; Shimizu-Inatsugi, R; Yamazaki, M; Shimizu, KK; Nagano, AJ
    FRONTIERS IN GENETICS, 10 10.3389/fgene.2019.00787 SEP 11 2019
  • A stigmatic gene confers interspecies incompatibility in the Brassicaceae
    Fujii, S; Tsuchimatsu, T; Kimura, Y; Ishida, S; Tangpranomkorn, S; Shimosato-Asano, H; Iwano, M; Furukawa, S; Itoyama, W; Wada, Y; Shimizu, KK; Takayama, S
    NATURE PLANTS, 5 (7):731-741; 10.1038/s41477-019-0444-6 JUL 2019
  • Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana
    Sato, Y; Shimizu-Inatsugi, R; Yamazaki, M; Shimizu, KK; Nagano, AJ
    BMC PLANT BIOLOGY, 19 10.1186/s12870-019-1705-2 APR 27 2019
  • Molecular basis of flowering under natural long-day conditions in Arabidopsis
    Song, YH; Kubota, A; Kwon, MS; Covington, MF; Lee, N; Taagen, ER; Cintron, DL; Hwang, DY; Akiyama, R; Hodge, SK; Huang, H; Nguyen, NH; Nusinow, DA; Millar, AJ; Shimizu, KK; Imaizumi, T
    NATURE PLANTS, 4 (10):824-835; 10.1038/s41477-018-0253-3 OCT 2018
  • Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica
    Paape, T; Briskine, RV; Halstead-Nussloch, G; Lischer, HEL; Shimizu-Inatsugi, R; Hatakeyama, M; Tanaka, K; Nishiyama, T; Sabirov, R; Sese, J; Shimizu, KK
    NATURE COMMUNICATIONS, 9 10.1038/s41467-018-06108-1 SEP 25 2018
  • Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana
    Y Sato, R Shimizu-Inatsugi, M Yamazaki, KK Shimizu, AJ Nagano
    bioRxiv, 320903,  DOI: 10.1101/320903 2018
  • Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica
    Timothy Paape, Roman V Briskine, Heidi EL Lischer, Gwyneth Halstead-Nussloch, Rie Shimizu-Inatsugi, Masaomi Hatekayama, Kenta Tanaka, Tomoaki Nishiyama, Renat Sabirov, Jun Sese, Kentaro K Shimizu
    bioRxiv, 248195 2018 
  • The Nagoya Protocol could backfire on the Global South
    Deplazes-Zemp, A; Abiven, S; Schaber, P; Schaepman, M; Schaepman-Strub, G; Schmid, B; Shimizu, KK; Altermatt, F
    NATURE ECOLOGY & EVOLUTION, 2 (6):917-919; 10.1038/s41559-018-0561-z JUN 2018
  • Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica 
    Yew, Chow-Lih; Kakui, Hiroyuki; Shimizu, Kentaro K. 
    JOURNAL OF PLANT RESEARCH, 131 (2): 349-358, MAR 2018
  • Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop 
    Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; et al. 
    DNA RESEARCH, 25 (1): 39-47, FEB 2018
Kentaro Shimizu

Prof. Dr. Kentaro Shimizu
University of Zurich
Department of Evolutionary Biology and Environmental Studies
8008 Zurich

Tel: +41 (0)44 635 67 40

Research topics

  • Evolution of reproductive systems
  • Self-compatibility
  • Genome duplication (speciation)
  • Arabidopsis relatives
  • Tropical trees (Dipterocarpaceae)



  • Evolutionary and ecological functional genomics (EEFG)
  • Statistical genetics
  • Ecology
  • Molecular developmental genetics
  • Systems biology