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Significance Speciation is the basis of the origin of biodiversity in nature. Sympatric speciation (SS) is still a controversial model of the origin of new species, since first proposed by Darwin in 1859. Here, we complement earlier genomic evidence with new analyses of transcriptome profiling, DNA editing, and microRNA, examined in the blind subterranean rodent,Spalax galili , in the Galilee Mountains, Israel, all substantiating SS with gene flow. Gene ontology enrichment of differentially expressed genes, in the abutting soil populations, highlights evolving reproductive isolation, despite a few interpopulation recombinants. Because sharply divergent geological, edaphic, climatic, and biotic interfaces abound in nature, we conclude that SS may be a common model of the origin of new species, as envisaged by Darwin.

Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax