Starting from scratch: adaptation to variable environments after an extreme bottleneck

Project code: WE 2897/4-2

Fig. 1

Inflorescences from the self-fertilizing Capsella rubella (left) and the outcrossing ancestor Capsella grandiflora (right)

While new species are usually formed through a gradual evolutionary process, they can also arise almost instantaneously, through events that involve severe genetic bottlenecking and loss of variability. Despite a very narrow genetic basis, such species can be remarkably successful. An important question is therefore how they manage to diversify and adapt to new habitats. We aim to address this problem by studying two very young plant species that underwent such bottlenecks: Arabidopsis suecica is in the same genus as the model plant Arabidopsis thaliana and originated as an interspecific hybrid between A. thaliana and A. arenosa. Capsella rubella, which belongs to a genus that is closely related to Arabidopsis, arose as a self-fertilizing form of an outcrossing ancestor. We use modern sequencing technologies to elucidate the patterns of variability in these species, both at the level of genomic DNA polymorphisms and in the transcribed portion of the genome, and compare it to the ancestral species. In addition, we perform functional and fitness studies. Taken together, our data will allow us to address important questions related to the evolutionary role of selfing and allopolyploidy.

Fig. 2

Whole genome resequencing of Capsella rubella individuals from throughout the range of the species identifies different populations based on overall genetic distance (lighter: more closely related; darker: more distantly related).

Publications related to the project

  • Lee, C. R., Svardal, H., Farlow, A., Exposito-Alonso, M., Ding, W., Novikova, P., Alonso-Blanco, C., Weigel, D., Nordborg, M. (2017). On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Commun 8:14458.
    Weblink Weblink 
  • The 1001 Genomes Consortium (2016). 1,135 genomes reveal the global of polymorphism in Arabidopsis thaliana. Cell 166(2):481-91.  Weblink Weblink
  • Grimm, D. G., Roqueiro, D., Salome, P., Kleeberger, S., Greshake, B., Zhu, W., Liu, C., Lippert, C., Stegle, O., Scholkopf, B., Weigel, D., Borgwardt, K. (2017). easyGWAS: A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies. Plant Cell 29(1):5-19.  Weblink Weblink
  • Seren, Ü., Grimm, D. G., Fitz, J., Weigel, D., Nordborg, M., Borgwardt, K. M., Korte, A. (2016). A public database for Arabidopsis thaliana phenotypes. Nucl Acids Res 45(D1): D1054-D1059.  Weblink Weblink
  • Novikova, P. Y., J Hohmann, N., Nizhynska, V., Tsuchimatsu, T., Ali, J., Muir, G., Guggisberg, A., Paape, T., Schmid, K., Fedorenko, O. M., Holm, S., Sall, T., Schlotterer, C., Marhold, K., Widmer, A., Sese, J., Shimizu, K. K., Weigel, D., Kramer, U., Koch, M. A., Nordborg, M. (2016). Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat Genet 48(9):1077-82.  Weblink Weblink
  • Kawakatsu, T., Huang, S. S., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R., Nery, J. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C. R., Wang, C., Bemm, F., Becker, C., O'Neil, R., O'Malley, R. C., Quarless, D. X., Genomes Consortium, Schork, N. J., Weigel, D., Nordborg, M., Ecker, J. R. (2016). Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell 166(2):492-505.  Weblink Weblink
  • Weigel, D. and Nordborg, M. (2015). Population Genomics for Understanding in Wild Plant Species. Annu Rev Genet 49:315-38.  Weblink Weblink
  • Steige, K. A., Reimegard, J., Koenig, D., Scofield, D. G., Slotte, T. (2015). Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella. Mol Biol Evol 32(10):2501-14.  Weblink Weblink
  • Seymour, D. K., Koenig, D., Hagmann, J., Becker, C., Weigel, D. (2014). Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet 10: e1004785.  Weblink Weblink



  • Detlef Weigel
    Prof. Dr. Detlef Weigel
    Principal Investigator
    MPI for Developmental Biology, Tübingen
    Office: +49 (0)7071 / 601-1411
    send email
  • Jörg Hagmann, Ph. D. student
    Researcher in SPP1529
    Office: +49 (0)7071 / 601-1416
    send email
  • Dr. Daniel Koenig
    Collaborating Scientist
    Office: +49 (0)7071 / 601-1419
    Lab: +49 (0)7071 / 601-1405
    send email 
  • Hülya Wicher
    Office: +49 (0)7071 / 601-1411
    send email

Linked Projects

  • PI Magnus Nordborg
    Gregor Mendel Institute, Vienna
    NO 942/1-1
  • PI Barbara Neuffer
    University of Osnabrück
    NE 314/11-2