Tissue-specific transcriptomics uncovers novel craniofacial genes underlying jaw divergence in specialist pupfishes

The regulation of gene expression is one of the key evolutionary processes
driving phenotypic divergence among species. Here, we investigate the
tissue-specific gene expression of a non-model adaptive radiation
of Cyprinodon pupfishes, characterized by their
divergent dietary niches and exceptionally fast rates of craniofacial
evolution. By comparing tissue-specific gene expression in the most
morphologically divergent skeletal structure, the oral jaws, with the
relatively morphologically conserved caudal tail region, we identified
genes that were differentially expressed exclusively in the developing
jaws of each of the three trophic specialists at hatching (8 dpf) and not
in any other species. We then assessed their overlap (as
transcriptionally-regulated genes) with adaptive regulatory variants
identified in previous genomic studies. Our analysis
identified pycr3 and atp8a1 as the
most promising for craniofacial evolution in the scale-eaters, both genes
with no known previous craniofacial function. We functionally confirmed
the craniofacial expression of these genes by in situ mRNA
hybridization chain reaction and demonstrated their species-specific
expression in branchial and muscle tissues between sister species of this
young radiation. Our work underscores the power of integrating
tissue-specific transcriptomics with speciation genomics to identify novel
craniofacial candidate genes controlling divergent morphogenesis in a
natural ‘evolutionary mutant’ system.