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Background  Protein-coding change is one possible genetic mechanism underlying the evolution of adaptive wing colour pattern variation in  Heliconius  butterflies. Here we determine whether 38 putative genes within two major  Heliconius  patterning loci,  HmYb  and  HmB , show evidence of positive selection. Ratios of nonsynonymous to synonymous nucleotide changes (ω) were used to test for selection, as a means of identifying candidate genes within each locus that control wing pattern.    Results  Preliminary analyses using 454 transcriptome and Bacterial Artificial Chromosome (BAC) sequences from three  Heliconius  species highlighted a cluster of genes within each region showing relatively higher rates of sequence evolution. Other genes within the region appear to be highly constrained, and no ω estimates exceeded one. Three genes from each locus with the highest average pairwise ω values were amplified from additional  Heliconius  species and races. Two selected genes,  fizzy-like  ( HmYb ) and  DALR  ( HmB ), were too divergent for amplification across species and were excluded from further analysis. Amongst the remaining genes,  HM00021  and  Kinesin  possessed the highest background ω values within the  HmYb  and  HmB  loci, respectively. After accounting for recombination, these two genes both showed evidence of having codons with a signature of selection, although statistical support for this signal was not strong in any case.    Conclusions  Tests of selection reveal a cluster of candidate genes in each locus, suggesting that weak directional selection may be occurring within a small region of each locus, but coding changes alone are unlikely to explain the full range of wing pattern diversity. These analyses pinpoint many of the same genes believed to be involved in the control of colour patterning in  Heliconius  that have been identified through other studies implementing different research methods.

Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species