- Population genomics
- Evolution of meiosis
- Gene network evolution
- Mechanisms of habitat adaptation and morphological evolution
Gene network evolution in Arabidopsis arenosa
One striking observation from our published genome scan (Hollister et al. 2012, PLoS Genetics) as well as our newer scan for differentiation between ploidies (Yant et al. 2013, Current Biology), is that signatures of selection are often seen in genes whose products are known or suspected to interact.
This suggests that these genes may be co-adapting - specifically that they are adaptating to changes in the interacting locus. We are thus very interested in exploring the evolution of interacting genes and asking whether "intragenomic adaptation" is important in these situations.
Currently we are examining two meiosis genes known to interact in A. thaliana, and showing evidence of selection in A. arenosa, in more detail as a test case. We are (1) studying patterns of evolution and co-evolution in a larger sample of individuals, and (2) testing whether effects of selected alleles are synergistic or additive, or whether effects of one require the changes found in the other.
In addition, we are generating a large population resequencing study of both diploid and tetraploid A. arenosa with which we hope to trace the age of the signatures of selection in species-level and population-level divergence and ask in a borader sample, which includes diploids, if the interacting proteins show evidence of evolutionary rate covariation.
Above is an example of a network of "high confidence" interactions from functional studies in A. thaliana. Highlighted in red are genes that show evidence of having been under selection in A. arenosa in Hollister et al 2012(many more than the genome rate of 1.6%!). This network contains genes involved in basal transcription around the core polymerase Pol II and includes DNA replication, chromatin remodeling, DNA repair, and recombination genes.