Wing patterning in Heliconius butterflies is a longstanding example of both 
Müllerian mimicry and phenotypic radiation under strong natural selection. The 
loci controlling such patterns are "hotspots" for adaptive evolution with great 
allelic diversity across different species in the genus. We characterise 
nucleotide variation, genotype-by-phenotype associations, linkage 
disequilibrium, and candidate gene expression at two loci and across multiple 
hybrid zones in Heliconius melpomene and relatives. Alleles at HmB control the 
presence or absence of the red forewing band, while alleles at HmYb control the 
yellow hindwing bar. Across HmYb two regions, separated by approximately 100 kb, 
show significant genotype-by-phenotype associations that are replicated across 
independent hybrid zones. In contrast, at HmB a single peak of association 
indicates the likely position of functional sites at three genes, encoding a 
kinesin, a G-protein coupled receptor, and an mRNA splicing factor. At both HmYb 
and HmB there is evidence for enhanced linkage disequilibrium (LD) between 
associated sites separated by up to 14 kb, suggesting that multiple sites are 
under selection. However, there was no evidence for reduced variation or 
deviations from neutrality that might indicate a recent selective sweep, 
consistent with these alleles being relatively old. Of the three genes showing 
an association with the HmB locus, the kinesin shows differences in wing disc 
expression between races that are replicated in the co-mimic, Heliconius erato, 
providing striking evidence for parallel changes in gene expression between 
Müllerian co-mimics. Wing patterning loci in Heliconius melpomene therefore show 
a haplotype structure maintained by selection, but no evidence for a recent 
selective sweep. The complex genetic pattern contrasts with the simple genetic 
basis of many adaptive traits studied previously, but may provide a better model 
for most adaptation in natural populations that has arisen over millions rather 
than tens of years.