Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes

Abstract

Evolution can follow predictable genetic trajectories, indicating that discrete environmental shifts can select for reproducible genetic changes. Conspecific individuals are an important feature of an animal's environment, and a potential source of selective pressures. Here we show that adaptation of two Caenorhabditis species to growth at high density, a feature common to domestic environments, occurs by reproducible genetic changes to pheromone receptor genes. Chemical communication through pheromones that accumulate during high-density growth causes young nematode larvae to enter the long-lived but non-reproductive dauer stage. Two strains of Caenorhabditis elegans grown at high density have independently acquired multigenic resistance to pheromone-induced dauer formation. In each strain, resistance to the pheromone ascaroside C3 results from a deletion that disrupts the adjacent chemoreceptor genes serpentine receptor class g (srg)-36 and -37. Through misexpression experiments, we show that these genes encode redundant G-protein-coupled receptors for ascaroside C3. Multigenic resistance to dauer formation has also arisen in high-density cultures of a different nematode species, Caenorhabditis briggsae, resulting in part from deletion of an srg gene paralogous to srg-36 and srg-37. These results demonstrate rapid remodelling of the chemoreceptor repertoire as an adaptation to specific environments, and indicate that parallel changes to a common genetic substrate can affect life-history traits across species.

Figure 1

C. elegans cultivated in liquid are resistant to dauer pheromones. a, The developmental decision between reproductive growth and dauer larva formation is regulated by temperature, food, and population density. Population density is assessed by the release and sensation of ascarosides including C3, C5, C6, and C9. b, History of the C. elegans strains N2, LSJ1, LSJ2, and CC1 (see Methods). c, Dauer formation of N2, LSJ2, and CC1 in response to crude dauer pheromone or synthetic ascarosides. d, Dauer formation in response to synthetic C3 ascaroside. e, QTL mapping of C3 resistance. f, Schematic of near isogenic lines (NILs) with a small region from LSJ2 or CC1 introgressed into N2. g, Dauer formation in N2, LSJ2, and CX13249 strains. Error bars in all figures represent s.e.m.

Figure 2

Resistance to C3 ascaroside is caused by deletion of two srg genes. a, Genomic region surrounding srg-36 and srg-37 on X, deletion breakpoints in LSJ2 and CC1 strains, fragments used for transgenic rescue, and design of bicistronic fusion genes. b, Transgenic rescue of dauer formation in response to C3 ascaroside. NIL strains used as recipients for rescue are shown in Figure 1f. ASI promoter was srg-47 (Figure S3), AFD promoter was gcy-8, ASE promoter was flp-6. c, Expression of GFP from bicistronic fusion genes for srg-36 and srg-37 in L1 larvae, showing predominant expression in ASI sensory neurons.

Figure 3

The srg genes encode ascaroside receptors. a, Localization of SRG-36∷GFP to ASI cilia (L4 animal). b, Ascaroside avoidance behaviours of animals with ectopic expression of srg-36, srg-37, or CBG24690 (shown in Figure 4) in the ASH nociceptive neurons. c, Ascaroside-induced Ca⁺⁺ transients in ASH neurons that ectopically express C. elegans srg-36 or srg-37 or C. briggsae CBG24690 in ASH. Grey bars indicate the presence of C3 or C6 ascaroside, shading indicates s.e.m., n≥10 animals/condition. Ca⁺⁺ was monitored using the genetically-encoded calcium sensor GCaMP3.0. Δ/F, percentage fluorescence change (baseline fluorescence = 100%).

Figure 4

Evolutionary conservation of srg function. a, Rescue of C. briggsae dauer formation in response to partially purified dauer pheromone by genomic fragments containing the CBG24690 gene. CX13431 is a near isogenic line containing the CBG24690 deletion from DR1690 introgressed into the AF16 background. b, Schematic of genes closely related to srg-36 and srg-37 from C. elegans, C. briggsae, and C. remanei (adapted from). c, CBG24690 genomic region from the AF16 C. briggsae reference strain, and location of a large deletion in the DR1690 C. briggsae strain that was cultivated for an extended period in liquid axenic media.