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.