It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and transcript processing would be unlikely to evolve in parallel with a new gene function. We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5-3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes. The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5' regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.

The sea lamprey is a basal, jawless vertebrate that possesses many neural crest derivatives, but lacks jaws and sympathetic ganglia. This raises the possibility that the factors involved in sympathetic neuron differentiation were either a gnathostome innovation or already present in lamprey, but serving different purposes. To distinguish between these possibilities, we isolated lamprey homologues of transcription factors associated with peripheral ganglion formation and examined their deployment in lamprey embryos. We further performed DiI labeling of the neural tube combined with neuronal markers to test if neural crest-derived cells migrate to and differentiate in sites colonized by sympathetic ganglia in jawed vertebrates. Consistent with previous anatomical data in adults, our results in lamprey embryos reveal that neural crest cells fail to migrate ventrally to form sympathetic ganglia, though they do form dorsal root ganglia adjacent to the neural tube. Interestingly, however, paralogs of the battery of transcription factors that mediate sympathetic neuron differentiation (dHand, Ascl1 and Phox2b) are present in the lamprey genome and expressed in various sites in the embryo, but fail to overlap in any ganglionic structures. This raises the intriguing possibility that they may have been recruited during gnathostome evolution to a new function in a neural crest derivative.

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