Tim Paape

Link to Research Group page (Prof. Dr. Kentaro K. Shimizu)

Research Interests

Molecular evolution and whole genome duplication in plants: mating system evolution (self-incompatibility), ecological genomics, transcriptomics of polyploids, population genetics, adaptive evolution of plants and microbes.


Education and Professional Positions

2018 - present Oberassistent / Senior Teaching and Research Assistant, Population Genomics, University of Zurich, Switzerland
2012 - 2018 Senior Postdoctoral Associate, Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland. Adaptive evolution and metal hyperaccumulation in allopolyploid plants
2013 - 2015 Plant Fellows Researcher
2009 - 2012 Postdoctoral Associate, Plant Biology, Univ. of Minnesota, St. Paul, MN, USA. Medicago Hapmap Project
2004 - 2009 Ph.D. Ecology, Behavior and Evolution, Univ. of California San Diego, CA, USA Thesis: Evolutionary genetics of gemetophytic self-incompatibility (SI) in Solancaceae and Papaveraceae
2003 - 2004 Research Associate, Univ. of Minnesota, St. Paul, MN, USA. Medicago truncatula plant-microbe interactions; plant defensins
2002 B.Sc. (with Honors) Biology, Fort Lewis College, Durango, Colorado, USA

Selected Publications

  • Paape T., Briskine RV., Lischer HEL., Halstead-Nussloch G., Shimizu-Inatsugi R., Hatakeyama M., Tanaka K., Nishiyama T., Sabirov R., Sese J., Shimizu KK. (2018). Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica. Nature Communications 9: 3909. DOI: 10.1038/s41467-018-06108-1
  • Paape T., Hatakeyama M., Shimizu-Inatsugi R., Cereghetti T., Onda Y., Tanaka K., Sese J., Shimizu K. (2016). Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allopolyploid Arabidopsis kamchatica. Molecular Biology and Evolution, 33:2781–2800. DOI: 10.1093/molbev/msw141
  • Briskine R., Paape T., Shimizu-Inatsugi R., Nishiyama T., Akama S., Sese J., Shimizu KK. (2016). Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12604
  • Kubo K., Paape T., Hatakeyama M., Entani T., Akie Takara., Kajihara K., Shimizu-Inatsugi R., Shimizu K. & Takayama S. (2015). Evolution of non-self-recognition through gene duplication and genetic exchange in S-RNase based self-incompatibility. Nature Plants 1, Article number: 14005. DOI: 10.1038/nplants.2014.5
  • Paape T., Bataillon T., Briskine R., Zhou P., Young ND., Tiffin PL. (2013). Selection, genome wide fitness effects, and evolutionary rates in the model legume Medicago truncatula. Molecular Ecology, 22: 3525–3538. DOI: 10.1111/mec.12329
  • Paape T., Briskine R., Zhou P., Young ND., Tiffin PL. (2012). Fine scale population recombination rates, hotspots and spatial correlates in the Medicago truncatula genome. Genome Biology and Evolution, 4: 726-737. DOI: 10.1093/gbe/evs046