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Balancing selection shapes density-dependent foraging behaviour

Abstract

The optimal foraging strategy in a given environment depends on the number of competing individuals and their behavioural strategies. Little is known about the genes and neural circuits that integrate social information into foraging decisions. Here we show that ascaroside pheromones, small glycolipids that signal population density, suppress exploratory foraging in Caenorhabditis elegans, and that heritable variation in this behaviour generates alternative foraging strategies. We find that natural C. elegans isolates differ in their sensitivity to the potent ascaroside icas#9 (IC-asc-C5). A quantitative trait locus (QTL) regulating icas#9 sensitivity includes srx-43, a G-protein-coupled icas#9 receptor that acts in the ASI class of sensory neurons to suppress exploration. Two ancient haplotypes associated with this QTL confer competitive growth advantages that depend on ascaroside secretion, its detection by srx-43 and the distribution of food. These results suggest that balancing selection at the srx-43 locus generates alternative density-dependent behaviours, fulfilling a prediction of foraging game theory.

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Figure 1: Ascaroside pheromones suppress exploratory foraging behaviour.
Figure 2: Natural genetic variation in pheromone sensitivity.
Figure 3: The roam-1 QTL includes the icas#9 receptor SRX-43.
Figure 4: Population genetics of the roam-1 locus and icas#9 sensitivity.
Figure 5: Bidirectional competitive selection at the roam-1 locus.

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Acknowledgements

We thank E. Andersen for sharing the unpublished CeNDR database; the Caenorhabditis Genetics Center (NIH P40 OD010440) and the Million Mutation Project for strains; S. Flavell and A. Lopez for advice and insight; and P. Sengupta, M. O’Donnell, X. Jin and A. Sordillo for comments on the manuscript. R.A.B. and X.Z. were supported by the Research Corporation for Science Advancement (Cottrell Scholar Award, 22844). P.T.M. was supported by NIH grant R01GM114170 and the Ellison Medical Foundation. J.S.G. was supported by the NIH grant F30 MH101931-03. C.I.B. is an investigator of the HHMI. This work was supported by the Ellison Medical Foundation.

Author information

Authors and Affiliations

Authors

Contributions

J.S.G. designed and performed the genetic, molecular biology, and behavioural experiments, together with M.B. for RIL analyses and I.G.I. for competition experiments. M.D. performed calcium imaging experiments. E.Z.M. discovered the effect of pheromones on foraging. X.Z. and R.A.B. analysed pheromone production and synthesized pure pheromones. D.J.C. and P.T.M. performed population genetic analysis. J.S.G, P.T.M. and C.I.B. analysed and interpreted data. J.S.G. and C.I.B. wrote the manuscript, with input from all authors.

Corresponding author

Correspondence to Cornelia I. Bargmann.

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The authors declare no competing financial interests.

Additional information

Reviewer Information Nature thanks E. Haag, S. Lockery and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Figure 1 Roaming and dwelling states in the presence of ascarosides.

a, Roaming and dwelling behaviours scored from video analysis. n = 102–214 tracks per data point. b, c, Cumulative distribution of roaming (b) and dwelling (c) state durations for animals in a. ***P < 0.001 by log-rank test; ns, not significant. d, e, Scatter plot of average speed and angular speed (a measure of turning rate) in 10 s intervals taken from 1.5-h-long video recordings of wild-type animals in control (d) and icas#9 (e) conditions. Roaming animals move quickly and turn infrequently compared with dwelling animals. Note the bimodal distribution defining distinct behavioural states. Control, 161 tracks; icas#9, 102 tracks. f, g, Speed following a reversal (f) and the reversal rate (g) for roaming or dwelling animals. Roaming speed is slightly slower in ascarosides (e, f). Data presented as mean ± s.e.m. *P < 0.05, ***P < 0.001 by ANOVA with Dunnett correction; ns, not significant.

Extended Data Figure 2 Roaming and dwelling behaviour of MY14.

a, Fraction of time that MY14 animals spend roaming or dwelling in control, ascr#8, and icas#9 conditions; n = 66–109 tracks per data point. Assays were conducted in 8% O2. b, c, Cumulative distribution of roaming (b) and dwelling (c) state durations for MY14 animals scored in a. Roaming states are significantly shorter in the presence of ascr#8 (t½ = ~150 s, versus ~220 s in controls), but are not significantly affected by icas#9 (t½ = ~190 s). Roaming states may also be longer at baseline in MY14 than in N2 (see Extended Data Fig. 1). ***P < 0.001 by log-rank test.

Extended Data Figure 3 Ascarosides produced by wild-type strains.

a, b, LC–MS/MS analysis of ascarosides secreted by N2, CX12311 and MY14 strains grown on OP50 (a) or HB101 (b) bacteria. icas#9 is produced at similar levels by icas#9-sensitive and icas#9-resistant strains. n = 2 (a) or 3 (b) culture extracts per genotype.

Extended Data Figure 4 Covariate analysis of 94 RILs.

a, b, Covariate analysis controlling for the roam-1 genotype, testing for additive (a) or interactive (b) QTLs at other loci. The horizontal line denotes the P < 0.05 genome-wide significance threshold. LOD, log likelihood ratio.

Extended Data Figure 5 Signal transduction by SRX-43.

a, Expression of Psrx-43::srx-43::SL2::GFP bicistronic reporter transgenes bearing N2 (top) or MY14 (bottom) srx-43 sequences. Arrows indicate cell bodies of ASI sensory neurons. Scale bars, 50 μm. b, ASH sensory neurons are insensitive to multiple ascarosides. ASH calcium imaging with GCaMP3 in control animals that do not express the srx-43 transgene, isolated as non-transgenic siblings of transgenic animals tested in Fig. 3f (n = 19). Ascarosides tested at 10 nM. c, SRX-43 from MY14 confers icas#9 sensitivity on ASH neurons. Compare SRX-43 from N2 in Fig. 3f. d, icas#9 decreases daf-7::GFP expression in ASI neurons of N2 but not roam-1MY14 adults. Bars indicate mean fluorescence intensity ± s.e.m. *P < 0.05 by ANOVA with Tukey’s multiple comparisons test. e, Responses to icas#9 of daf-7(lf) mutants are attenuated in N2 but not in roam-1MY14 genetic backgrounds. Modified exploration assays were conducted on strains including daf-3(lf) alleles (see methods). *P < 0.05 by t-test. Data presented as mean ± s.e.m. f, Time course for icas#9 response in exploration assay. Pheromone response expressed as mean ± s.e.m. for 2, 4, 6, 10, and 14 h following initiation of exploration assay. ***P < 0.001 by t-test with Bonferonni correction comparing squares entered in control plates versus 10 nm icas#9 plates; n = 12 for all time points.

Extended Data Figure 6 Alternative roam-1 alleles have high sequence variability.

a, The roam-1 QTL region (top). roam-1 SNPs are SNPs, when compared to the N2 reference genome, that are shared by JU360, MY2, MY14, ED3021, JU1171, MY16 and MY6 and not by any other strains, according to the Million Mutation Project. This defines the roam-1MY14 haplotype. Other SNPs denote all other SNPs with respect to the N2 reference genome found in any of the 40 wild isolates in the Million Mutation Project. b, Polymorphisms of the srx-43 promoter and coding region revealed by Sanger sequencing. Despite the high rate of polymorphism, there are only four non-synonymous mutations in the MY14 coding sequence detected by Sanger sequencing; three of these four were detected by the Million Mutation Project (Extended Data Table 1). We confirmed that the MY14 and N2 sequences are alleles of the same gene by examining sequence reads of the MY14-like strain MY23 in the CeNDR data set (http://www.elegansvariation.org) and aligning each read to N2 and MY14 sequence for the srx-43 region as determined by Sanger sequencing. We observed that 7,272 of the MY23 (MY14) reads better matched the MY14 Sanger sequence and 4 of the reads better matched the N2 reference sequence, as would be expected if MY14 and N2 each bear one alternative allele of the gene. c, Phylogeny constructed for srx-43 and related genes in C. elegans, C. briggsae and C. remanei demonstrates that the srx-43 alleles in N2 and MY14 are closely related alleles of a single gene. Genes are colour-coded by species (green, C. elegans; blue, C. briggsae; orange, C. remanei). Protein sequences and gene names are as previously described38.

Extended Data Figure 7 Substantial recombination between roam-1 and surrounding regions.

Top, phylogenies constructed with 152 diverse wild-type isolates revealing differences for the region surrounding srx-43 and the regions immediately to the left and right of the 30-kb haplotype. Bottom, graph showing the number of variants and Tajima’s D score calculated for 5-kb bins across a 250-kb region. The bin containing srx-43 has 250 polymorphisms and a Tajima’s D of 1.01, which is high both at the genomic level (<3.4% of bins had a higher value) and for the chromosomal location of srx-43 (<3.6% of bins had a higher value).

Extended Data Figure 8 Recombination between srx-43 and glc-1 in natural isolates.

a, The glc-1 gene has previously been shown to be subject to balancing selection33 and is chromosomally near srx-43. The blue line shows the number of SNPs per kb for N2 and MY14 averaged over 5-kb intervals for the region spanning srx-43 and glc-1. The large region of low heterozygosity between srx-43 and glc-1 indicates that balancing selection on glc-1 is unlikely to account for the high heterozygosity near srx-43. b, Dendrogram for the glc-1 region for the strains shown in Fig. 4a. The clades for roam-1MY14 and glc-1 are not identical.

Extended Data Figure 9 Standard curve for digital PCR experiments.

Best-fit line of digital PCR results for known ratios of N2 to roam-1MY14 DNA created by mixing different ratios of genomic DNA extracted from independent N2 or roam-1MY14 populations.

Extended Data Table 1 dN/dS for srx-43 and other genes in the roam-1 region

Supplementary information

Supplementary Data

This file contains Supplementary Table 1, genotypes and pheromone responses of 94 RILs and the two parental strains. (XLSX 270 kb)

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Greene, J., Brown, M., Dobosiewicz, M. et al. Balancing selection shapes density-dependent foraging behaviour. Nature 539, 254–258 (2016). https://doi.org/10.1038/nature19848

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