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 mutat..., , , # Supplementary data from: Distinct mechanisms decommission redundant enhancers to facilitate phenotypic evolution

Dataset DOI: [10.5061/dryad.s4mw6m9mh](https://doi.org/10.5061/dryad.s4mw6m9mh)

## Description of the data and file structure

**README**

**Dataset associated with:**\
*Distinct mechanisms decommission redundant enhancers to facilitate phenotypic evolution*

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**Overview**

This repository contains imaging data and supplementary materials associated with the manuscript.

The imaging datasets consist of maximum intensity projections of confocal z-stacks from stage 15 *Drosophila* embryos used for quantitative analyses in the main and supplementary figures.


**General Description of Imaging Datasets**

For each dataset (corresponding to a specific figure and enhancer construct set):

* n = 10 embryos per genotype were analyzed quantitatively.
* No em...,