| Summary: | The positioning of wing pattern elements is controlled by pattern ‘switch’ loci which map to the same genomic regions in multiple species. Here two of these regions have been characterized in detail for the first time. Using fine scale recombinational mapping two pattern ‘switch’ loci of major effect, <i>HmYb </i>and <i>HmSb,</i> were cloned and sequenced. The region was annotated in detail using 454 generated EST data and BLAST homology. Microsynteny across the region is strongly conserved with the silk moth <i>Bombyx mor</i>i. Some candidate genes for regulation of this major phenotypic switch were identified, and a number of loci with complex patterns of alternative splicing. This work had laid the foundation for population genetic and comparative analysis of this genomic ‘hotspot’ for phenotypic evolution across the <i>Heliconius.</i> Wing pattern elements are coloured by two pigments types- ommochromes (red, yellow) and melanins (black, brown). The ommochrome pathway has been recruited from an ancient role in eye pigmentation to a novel role in butterfly wing pigmentation, and is likely to have played a key role in the development of aposematic wing patterning in the <i>Heliconius </i>lineage. Here all identified structural genes from the two pigmentation pathways in <i>H. melpomene. </i>From the ommochrome pathway <i>cinnabar </i>and <i>scarlet </i>gene expression are localized to the red forewing band. Analysis of the <i>cinnabar </i>locus shows that there have been multiple independent duplications in the <i>Heliconius </i>which are likely to affect both gene expression and pleiotropy. From the melanin pathway expression of the <i>ebony </i>gene is also spatially restricted to the forewing band in <i>H. melpomene</i>, consistent with a role in suppression of melanin formation in red pattern elements. The evolution of the arthropod <i>yellow </i>gene family genes was also characterized, and expression of novel lepidopteran <i>yellow </i>genes was assayed from developing <i>Heliconius </i>wings.
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