Convergent evolution of gene expression in two high-toothed stickleback populations

Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus). Are convergently evolved cis and/or trans changes in gene expression associated with convergently evolved morphological evolution? Do cis or trans regulatory changes contribute more to the evolutionary gain of a morphological trait? Transcriptome data from dental tissue of ancestral low-toothed and two derived high-toothed stickleback populations reveal significantly shared gene expression changes that have convergently evolved in the two independently derived founded high-toothed populations. Comparing cis and trans regulatory changes using phased gene expression data from F1 hybrids, we find that trans regulatory changes are predominant and are more likely to be shared among both high-toothed populations. In contrast, while cis regulatory changes have evolved in both high-toothed populations, overall these changes are distinct and not shared among high-toothed populations. These data indicate that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar trans regulatory environments.

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