Deep cis-regulatory homology of the butterfly wing pattern groundplan

Butterfly wing patterns derive from a deeply conserved developmental
groundplan, yet are highly diverse and evolve rapidly. It is poorly
understood how gene regulatory architectures can accommodate both deep
homology and adaptive change. To address this, we characterized the
cis-regulatory evolution of the groundplan gene WntA in nymphalid
butterflies. Comparative ATAC-seq and in vivo knockouts of 46
Cis-Regulatory Elements (CREs) across five species revealed extensive
sequence homology of groundplan CREs, except in monarch butterflies. Most
CRE perturbation assays showed effects spanning multiple elements and
encoding both positive and negative regulatory functionality. Our results
provide little support for models predicting rapid turnover of
single-trait enhancers and suggest morphological change within a tissue is
achieved by tuning deeply conserved and highly sensitive networks of
interdependent CREs.