Convergence in cichlid lower pharyngeal jaw transcriptomes

Similar to whole genome divergence, gene expression divergence could be strongly influenced by the geographic setting in which species evolve. To contrast patterns of allopatric and sympatric speciation scenarios, we compared transcriptomes of the ecologically important lower pharyngeal jaws of six closely related cichlid fish species pairs (two sympatrically and four allopatrically diverged species pairs) to ask how molecular mechanisms underlying similar phenotypes differ between geographic settings. Not only were different genes used among the species, but the average expression level of differentially expressed genes were higher in allopatrically diverged species pairs compared to sympatric pairs. Genes differentially expressed between sympatric pairs had higher differences in expression suggesting that gene expression divergence evolves faster and to greater extend when gene flow is present. Large gene expression divergence between sympatric species could provide an important role for gene expression differences for local adaptation and speciation, via barriers to gene flow.