Supplementary data from: Distinct mechanisms decommission redundant enhancers to facilitate phenotypic evolution

The evolutionary loss of morphological traits is often driven by changes
in gene regulation. Many developmental genes are controlled by multiple,
redundant enhancers, raising the question of how robust regulatory systems
can be dismantled to permit phenotypic transitions. We show that the loss
of larval trichomes in Drosophila sechellia resulted from the independent
inactivation of four embryonic enhancers of the shavenbaby gene. Each
enhancer was extinguished by a distinct mechanism: (1) a large deletion
that removed essential sequences, (2) the loss of activator sites and gain
of repressor sites, (3) the acquisition of a long-range silencer, and (4)
the unmasking of pre-existing repression. Notably, three of these
mechanisms relied on repression, pointing to repression as a rapid route
for the evolutionary loss of robust regulatory elements. These results
show that robustness in gene regulation does not prevent morphological
change but instead provides multiple opportunities for mutations to reduce
enhancer activity, giving selection many paths to reshape form.