Hybrid misexpression in multiple developing tissues within a recent adaptive radiation ofCyprinodonpupfishes

Genetic incompatibilities constitute the final stages of reproductive isolation and speciation, but little is known about incompatibilities that occur within recent adaptive radiations among closely related diverging populations. Crossing divergent species to form hybrids can break up coadapted variation, resulting in genetic incompatibilities within developmental networks shaping adaptive traits. We crossed two closely related sympatric Cyprinodon pupfish species – a dietary generalist and a specialized molluscivore – and measured expression levels in their F 1 hybrids to identify regulatory variation underlying the novel craniofacial morphology found in this recent microendemic adaptive radiation. We extracted mRNA from eight day old whole-larvae tissue and from craniofacial tissues dissected from 17-20 day old larvae to compare gene expression between a total of seven F 1 hybrids and 24 individuals from parental species populations. We found 3.9% of genes differentially expressed between generalists and molluscivores in whole-larvae tissues and 0.6% of genes differentially expressed in craniofacial tissue. We found that 2.1% of genes were misexpressed in whole-larvae hybrids at 8 dpf whereas 19.1% of genes were misexpressed in hybrid craniofacial tissue at 17-20 dpf, after correcting for sequencing biases. We also measured allele specific expression across 15,429 phased heterozygous sites to identify regulatory mechanisms underlying differential expression between generalists and molluscivores. Together, our results highlight the importance of considering misexpression as an early indicator of genetic incompatibilities in the context of rapidly diverged morphology and suggests that wide-spread compensatory regulatory divergence drives hybrid misexpression in developing tissues that give rise to novel craniofacial traits.