Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola

Understanding the genetic basis of species differences is a major goal in evolutionary biology. Pigmentation divergence between Drosophila species often involves genetic changes in pigmentation candidate genes that pattern the body and wings, but it remains unclear how these changes affect pigmentation evolution in multiple body parts between the same diverging species. Drosophila elegans and D. gunungcola show pigmentation differences in the thorax, legs, and wings, with D. elegans exhibiting male-specific wing spots and D. gunungcola lacking wing spots with intensely dark thoraces and legs. Here, we performed QTL mapping to identify the genetic architecture of these differences. We find a large effect QTL on the X chromosome for all three body parts. QTL on Muller Element E were found for thorax pigmentation in both backcrosses but were only marginally significant in one backcross for the legs and wings. Consistent with this observation, we isolated the effects of the Muller Element E...