We generated F1 hybrids of each of the sister species A. lyrata and A. halleri with their outgroup
relative 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-wide
distribution of cis-regulatory mutations active in three distinct environments reflecting divergent
adaptations of the two species. Because the sister species were both crossed to an outgroup species, it
was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in
only one of the two hybrids were liekly to be derived, whereas those observed in both hybrids either
predate the split between the two species or arose along the A. thaliana lineage. By contrasting the
distribution of cis-regulatory mutations derived in the A. lyrata vs A. halleri lineages, we can establish
relative rates of cis-acting evolution across polygenic molecular functions and detect those, which
provided a polygenic response to divergent natural selection in each lineage. Less...