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Parallel evolution of gene expression commonly underlies convergent niche specialization, but parallel changes in expression could also underlie divergent specialization. We investigated divergence in gene expression and whole-genome genetic variation across three sympatric Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist and two derived specialists adapted to novel niches - a "scale-eater" and a "snail-eater." We sampled total mRNAdoi:10.1101/180190 fatcat:zlzvsf2rgvgg5p7yyanvam73cq