Evolutionary genetics of pathogens (led by Daniel Croll)

Our research aims to understand how pathogenic fungi evolve to cause disease on plants. For this, we analyze populations of major crop pathogens and identify how the pathogens managed to circumvent the immune system of plants. Plant pathogens are among the most fascinating cases of rapid evolution observable in nature. We are particularly interested in the processes of rapid adaptation to resist new fungicides, cause disease on a new crop variety or tolerate different environmental conditions. For this, we use primarily genome-wide association studies (GWAS) to link variation in phenotypes to specific loci in the genome. We also analyze complete genome to understand the mechanisms creating major changes in chromosomal sequences. Such rearrangements were often tightly linked to adaptation of the pathogen. In our work, we combine field work with experiments in the lab and genome-scale analyses.

For more information about Daniel’s research please see here.


Systematics, Taxonomy and Biogeography of Plants (led by Jason Grant)

Our research focuses on the taxonomy, systematics, speciation, biogeography and natural history of North and South American plants using macro and micro-morphology, and molecular systematics. Currently researched groups include the flowering plant families Gentianaceae (gentians; Macrocarpaea, Symbolanthus), Brassicaceae (Parrya), Bromeliaceae (Alcantarea, Vriesea, and Werauhia), Loganiaceae (Bonyunia), and the fern family Ophioglossaceae (Botrychium). Geographical regions where I largely conduct my research include the Andes in South America (Venezuela, Colombia, Ecuador, Peru, and Bolivia), and Arctic and boreal regions of North America and Asia.

Neotropical studies

Evaluation of historical patterns of speciation of plants in montane South America. Speciation and biogeography are especially important for studying genetic variation by using model organisms to interpret patterns that can be used in the assessment of general biodiversity, and threats that may lead to recommendations for conservation.

Arctic studies

Evaluation of dispersals of plants from Asia to North America. The genus Parrya (Brassicaceae) is primarily distributed in the Himalaya and other mountainous regions of Asia. My studies concentrate on the American radiation. The fern genus Botrychium (Ophioglossaceae) is widely distributed in North America, but is especially speciose in Alaska and the Pacific Northwest. In 2002 I described a new species from Alaska, Botrychium alaskense.


Speciation and genome dynamics (Christian Parisod and François Felber)

Species diversification requires both genetic variation and reproductive isolation. We thus need to better understand the origin and the spread of genetic changes until populations are stably differentiated. Transposable Elements (TEs) – or jumping genes – are shaping genome architecture of most species, inducing mutations and restricting recombination. TEs might thus be major speciation triggers. In our research, we assess the impact of TEs on the evolution of plant genome organization and reproductive isolation. Such research is important for fundamental science and plant improvement.

Genome dynamics and reproductive isolation in the buckler mustard (led by Christian Parisod)

We adopt an ecological genomics approach to associate the main processes driving plant genome evolution – polyploidy, retrotransposition and genome silencing – with the evolution of reproductive isolation. We address the impact of TEs on speciation and ecological radiation in the buckler mustard (Biscutella laevigata; Brassicaceae), because this taxon is formed of diverging diploid and recent autopolyploid lineages having radiated in a range of alpine habitats following environmental changes. It thus offers a suitable model to understand the mechanisms underlying chromosomal speciation at the diploid level and ecological speciation at the polyploid level.

Genome evolution and gene flow in the wheat group (led by Christian Parisod and François Felber)

One of the most intriguing barriers to hybridization between species is the activation of TEs when merging divergent genomes, which leads to hybrid failure and restrict interspecific gene flow. We use wild wheats (Aegilops spp; Poaceae) as a model to address the impact of TEs on barriers to gene flow, because this complex is formed of species clusters with high TE loads that differentially hybridize in the wild.