Supergene evolution via gain of autoregulation

Development requires the coordinated action of many genes across space and time, yet numerous species are able to develop multiple discrete, alternate phenotypes. Such polymorphisms are often controlled by supergenes, sets of tightly-linked loci that function together to control development of a polymorphic phenotype. Although theories of supergene evolution are well established, the functional genetic differences between supergene alleles have been difficult to identify. The doublesex supergene controls mimicry polymorphism in several Papilio swallowtail butterflies, where divergent dsx alleles switch between discrete mimetic or non-mimetic female wing patterns. Here we show that the Papilio alphenor supergene evolved via recruitment of five new cis-regulatory elements (CREs) that control allele-specific dsx expression. Most dsx CREs, including three of the five new CREs, are bound by the DSX transcription factor itself. Additionally, DSX differentially binds a small number of unlinked..., Complete methodological details can be found in the associated publication and/or within the Dryad repository itself. , , # Supergene evolution via gain of autoregulation

[Access this dataset on Dryad](https://doi.org/10.5061/dryad.tx95x6b75)

## Abstract

This repository contains data files and R projects required to recapitulate and further explore the data presented in this paper. It includes four tarballs that perform different analyses for the paper. These tarballs contain the genome sequences and annotation for mimetic and non-mimetic *P. alphenor* (`genomes.tgz`); data and R project for analyzing ATAC-seq data (`atac.tgz`); data and R project for analyzing DSX and H3K4me3 CUT&RUN data (`cutnrun.tgz`); and data and R project for re-analyzing RNA-seq data generated in [VanKuren et al. (2023)](https://academic.oup.com/mbe/article/40/9/msad196/7260046) and updated to use these latest genomes (`rnaseq.tgz`). All analyses performed for the paper can be re-run using these data and projects. However, we provide several intermediate or summary files that you can immediately dive into to extract relevant inf...,