Harvard University
Department of Organismic & Evolutionary Biology

Gene network evolution in Arabidopsis arenosa

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 by network connections to additional genes that we found in our genome scan to be differentiated between populations. This suggests that these genes may be adaptating to changes elsewhere in the genome rather than to habitat per se. We are currently exploring this with a large population resequencing study of both diploid and tetraploid A. arenosa with which we hope to trace the signatures of selection in these genes at different levels of divergence. This will hopefully give us an idea of the age of selection and the circumstances in which it may have happened (e.g. species divergence, genome duplication, local adaptation and/or neutral divergence). We are currently trying also to design follow-up experiments to test whether these apparently coevolved interactions are important for module function (e.g. are the interactions among apparently selected alleles synergistic, additive, compensatory, etc...?).


As a first step, we are taking a population resequencing approach to study the dynamics of gene regulatory network evolution comparing species, the A. arenosa cytotypes, and populations within cytotypes. We are doing this with low-pass sequencing of several hundred plants from 20 populations. This includes diploids and tetraploids, and plants growing in different habitats. This will hopefully give us new insights into how interacting genes might co-evolve or adapt to one another as highly conserved genetic processes must adapt in response to genome change.



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 (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, and DNA repair and recombination genes.