Gene regulatory Divergence of lower pharyngeal jaw phenotypes in Lake Malawi cichlids

Patterns of regulatory evolution have been investigated in a few select model species, but studies on ecologically relevant traits of vertebrates are scarce. Trophic morphologies that diverged rapidly and in convergence across multiple taxa could offer a powerful system to broaden our understanding of how gene regulation influences morphological divergence, potentially contributing to speciation. We performed RNA-seq of lower pharyngeal jaws of two species of Lake Malawi cichlids (Mylochromis mola and Copadichromis borleyi) with distinct jaw morphologies and their F1 hybrids. By investigating allele specific expression in F1 hybrids, we determined regulatory elements involved in gene expression differences between parental species. Contrary to the prevailing assumption that cis-elements contribute mostly to interspecific gene expression differences, we find trans-regulatory elements to be the main contributors. Combining jaw transcriptomes of another 26 species we find 216 genes with convergent expression patterns associated with jaw morphologies. However, convergent expression patterns are likely to be governed by different regulatory elements among the different species.