Dominant morphs in the mimetic butterfly Papilio dardanus are characterised by highly divergent alleles of the transcription factor engrailed

The phylogenetic history of genes underlying phenotypic diversity can offer insight into the evolutionary origin of adaptive traits. This is especially true where single genes have large phenotypic effects, for example in determining polymorphic mimicry in butterflies. Here, we characterise the evolutionary history of two candidate genes for the mimicry switch in the polymorphic Batesian mimic Papilio dardanus coding for the transcription factors engrailed and invected. We show that in exon 1 of the engrailed gene is highly variable within P. dardanus, and that haplotypes associated with the dominant morphs f. poultoni and f. planemoides are highly divergent, in particular at non-synonymous sites. Some non-synonymous changes are shared between the two alleles suggesting either convergence or a shared ancestry. Gene trees for invected do not show this pattern. Despite their great divergence, all engrailed alleles of P. dardanus were monophyletic with respect to alleles of closely related species. Phylogenetic analyses therefore reveal no evidence for introgression from other species. A McDonald-Kreitman test conducted on a population sample from South Africa confirms a significant excess of intraspecific non-synonymous diversity in P. dardanus engrailed, suggesting long-term balanced polymorphism at this locus.