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How genetic information is modified to generate phenotypic variation within a species is one of the central questions in evolutionary biology. Here we focus on the striking intraspecific diversity of >200 aposematic elytral (forewing) colour patterns of the multicoloured Asian ladybird beetle,  Harmonia axyridis , which is regulated by a tightly linked genetic locus  h . Our loss-of-function analyses, genetic association studies, de novo genome assemblies, and gene expression data reveal that the GATA transcription factor gene  pannier  is the major regulatory gene located at the  h  locus, and suggest that repeated inversions and  cis -regulatory modifications at  pannier  led to the expansion of colour pattern variation in  H. axyridis . Moreover, we show that the colour-patterning function of  pannier  is conserved in the seven-spotted ladybird beetle,  Coccinella septempunctata , suggesting that  H. axyridis ’ extraordinary intraspecific variation may have arisen from ancient modifications in conserved elytral colour-patterning mechanisms in ladybird beetles.

Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles