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Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In  Caenorhabditis elegans , the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in  Pristionchus pacificus  revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains´ pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene  dauerless  controls dauer formation by copy number variation. The Ohioan strain has one  dauerless  copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers.  dauerless  is exclusively expressed in CAN neurons, and both CAN ablation and  dauerless  mutations increase dauer formation. Strikingly,  dauerless  underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor  daf-12 . We identified the novel or fast-evolving gene  dauerless  as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest  daf-12  as major target for dauer regulation. We discuss the consequences of the novel  vs.  fast-evolving nature of orphans for the evolution of developmental networks and their role in natural variation and intraspecific competition.

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation