The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus. Arabidopsis

We generated F1 hybrids of each of the sister species A. lyrata and A. halleri with their outgrouprelative A. thaliana and monitored allele-specific levels of expression in standard growth conditions,during dehydration or in response to cold exposure. This data allowed us to draw a genome-widedistribution of cis-regulatory mutations active in three distinct environments reflecting divergentadaptations of the two species. Because the sister species were both crossed to an outgroup species, itwas possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed inonly one of the two hybrids were liekly to be derived, whereas those observed in both hybrids eitherpredate the split between the two species or arose along the A. thaliana lineage. By contrasting thedistribution of cis-regulatory mutations derived in the A. lyrata vs A. halleri lineages, we can establishrelative rates of cis-acting evolution across polygenic molecular functions and detect those, whichprovided a polygenic response to divergent natural selection in each lineage.