- Population genomics
- Evolution of meiosis
- Gene network evolution
- Mechanisms of habitat adaptation and morphological evolution
The overarching interest of the lab is to understand the molecular mechanisms of genome evolution and adaptation. Most of our work currently focuses on Arabidopsis arenosa. This lovely relative of A. thaliana is an obligate outcrosser, tetraploid through most of its range, and widely distributed in Europe. There are three main areas we are interested in pursuing with this species:
(1) Adaptation to whole genome duplication. Arabidopsis arenosa is autotetraploid through most of its central and northern European range. It is obligately outcrossing. We are capitalizing on the availability of extant diploids and tetraploids to ask how A. arenosa adapted to having double the number of chromosomes. We are using a combination of genomics, transcriptomics, molecular genetics and cytology (cytology is mainly being done by our collaborators James Higgins and Chris Franklin at the University of Birmingham in the UK) to address how meiosis and other key cellular processes may have evolved in tetraploid evolution. We are also beginning to analyze the molecular evolution of meiosis-related genes in diploid and tetraploid A. arenosa and initiating functional studies of a key subset of genes that are strongly differentiated between diploids and tetraploids.
(2) Biogeography and Habitat adaptation. Arabidopsis arenosa autotetraploids have adapted to a wide range of habitats, ranging from the apparently ancestral shaded limestone outcrop habitat to silicaceous outcrops, serpentine, railways, acid bogs, beaches, and heavy metal contaminated mine tailings. We are using RADseq markers and low pass population resequencing to study the evolutionary history of diploid and tetraploid A. arenosa populations and how these might have colonized their present range and habitats. We have found that tetraploid populations found in distinct habitats (railways versus outcrops) show striking differences in flowering time, vernalization responsiveness, perenniality and plant architecture.
Within the scope of an NSF-funded study, we are using a combination of genetic mapping, transcriptome analyses and phenotyping to better characterize these differences molecularly and phenotypically. We have begun to map flowering time and plant architecture traits in segregating F2 populations (focusing at least initially on the contrast of shaded outcrops versus exposed drought-prone railways). We are also beginning studies of the potential role of epigenetic regulation in natural variation for flowering and vernalization responsiveness.
(3) Gene Network evolution. One striking observation from our genome scan is that signatures of selection are often seen in genes whose products are known to interact. These are also often connected in networks to additional genes that are differentiated between populations. This suggests that these genes may be adaptating to the genome rather than to habitat. We are currently exploring this with a large population resequencing study and follow-up experiments to test functional modules of related genes.