Adaptive significance of regulatory changes in association with plant speciation

Clarifying the adaptive importance of changes in gene regulation is an important aim in evolutionary biology. In this project, we aim to 1) test whether there is evidence for adaptive regulatory evolution in association with plant speciation, and 2) quantify the long-term impact of natural selection on regulatory regions in plants. Our main focus is on the emerging plant model system Capsella. This system offers an excellent opportunity for testing hypotheses on regulatory evolution in a setting where the timeframe of speciation and phenotypic evolution is clearly defined. This project involves generation and analysis of massively parallel sequence data sets with a focus on allele-specific gene expression and population genetic analysis. The project greatly benefits from the completion of the Capsella rubella reference sequence and the close relationship between Capsella and Arabidopsis thaliana, which facilitates annotation and interpretation of genomic data. This project was funded by a grant from the Swedish Research Council.

The evolutionary consequences of dominance at the Brassicaceae self-incompatibility locus

The existence of dominance modifiers, genetic elements that modify levels of dominance, has been debated for nearly a century. Selection for dominance modifiers can be efficient at loci that are under strong balancing selection, such as the self-incompatibility locus (S-locus) in plants. In this project we investigate the genetic basis of S-locus dominance and its consequences at the sequence and phenotypic level in the crucifer genus Capsella, an emerging model for the study of mating system evolution. To this end, we use a combination of targeted sequencing of entire S-locus haplotypes, gene expression studies and controlled crosses. The project utilises a variety of massively parallel sequencing techniques, and a strong component of bioinformatics and evolutionary genomics analyses. This project was funded by the Swedish Research Council.

Testing the utility of massively parallel sequencing on ancient sediments

In this collaborative project with the groups of Barbara Wohlfarth (Department of Geological Sciences, Stockholm University) and Laura Parducci (Department of Plant Ecology and Evolution, Uppsala University) we aim to retrieve and analyze metagenomic data sets from environmental DNA from 11,000-16,000-year old lake sediments. Ancient lake sediments store a wealth of biological, chemical and physical information that allow reconstructing past climatic and environmental conditions in great detail. Recent advances in environmental DNA analyses that make use of new large-scale sequencing technologies now offer the unprecedented opportunity to unravel a complementary spectrum of ancient faunal and floral remains than those identified by micro- or macrofossil analyses. As such, aDNA analysis can provide a completely new understanding of how ecosystems responded to dramatic climatic changes. This project was funded by the Faculty of Science, Stockholm University.