Data from: The transcriptomics of crushing jaw convergence in cichlid fishes: comparative gene expression in recent sympatric versus older allopatric trophic adaptations

How gene expression diverges during adaptation might be strongly influenced by the geographic setting and timeframe over which species evolve. To contrast transcriptomic patterns of replicate trophic adaptations that evolved convergently during both allopatric and sympatric contexts, we conducted RNA-seq on the trophically important lower pharyngeal jaws of two sympatrically and four allopatrically diverged species pairs of cichlid fishes. We first show that all of these species pairs have convergently diverged along a crushing trophic axis and that the sympatric pairs are as phenotypically divergent as the allopatric pairs. Then, we found that distinct sets of genes were differentially expressed in the jaws of sympatrically diverging pairs as compared to jaws in older allopatric species pairs. The genes that were differentially expressed in the jaws of allopatric pairs also were more highly expressed on average than in the sympatric pairs. Finally, for genes that were differentially expressed, the magnitude of differences in expression between the jaws were greater for sympatrically diverging species pairs. The particular genes, their expression levels, and the magnitude of expression differences between sympatrically originating adaptations might all play an important role in generating and maintaining boundaries to gene flow during the rapid ecological divergence that often characterizes sympatric speciation.