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Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans

Nature Ecology & Evolution volume 5, pages 794–807 (2021)Cite this article

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Abstract

Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing decreases the effective population size, effective recombination rate and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times, and all three species, including the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example of how species can avoid the evolutionary dead end associated with selfing.

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Fig. 1: Genetically divergent wild C. elegans strains isolated from the Pacific region.
Fig. 2: Characterization of hyper-divergent regions at the isotype level.
Fig. 3: Punctuated hyper-divergent genomic regions are widespread across the C. elegans species.
Fig. 4: Balancing selection has maintained hyper-divergent haplotypes enriched in environmental response genes.
Fig. 5: Hyper-divergent haplotypes contain ancient genetic diversity.

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Data availability

The raw short-read sequencing reads for the strains used in this project are available from the NCBI Sequence Read Archive (project PRJNA549503). The raw PacBio long-read data, along with the de novo assemblies and gene predictions, are available from the NCBI Sequence Read Archive (project PRJNA692613). Strain information and short-read genomic variation data are available from the CeNDR (www.elegansvariation.org)68.

Code availability

All datasets and code for generating the figures and tables are available from GitHub (https://github.com/AndersenLab/Ce-328pop-div).

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Acknowledgements

We thank members of the Andersen laboratory for providing comments on this manuscript. We especially thank M. Ailion, J. David, R. Luallen, N. Pujol and citizen scientists for contributing wild C. elegans strains to CeNDR. We also thank the Duke University School of Medicine for use of the Sequencing and Genomic Technologies Shared Resource, which provided Pacific Biosciences long-read sequencing. This work was funded by an NSF CAREER award (1751035) and a Human Frontier Science Program Award (RGP0001/2019) (to E.C.A.). This work was also funded by National Institutes of Health (NIH) grant ES029930 (to E.C.A., M.V.R. and L.R.B.). S.Z. received funding from The Cellular and Molecular Basis of Disease training programme (T32GM008061) and the Rappaport Award for Research Excellence through the IBiS graduate programme. A.K.W. is supported by the National Science Foundation Graduate Research Fellowship. Long-read sequencing of three isolates was funded by the NIH (R01 GM117408 to L.R.B.) and a T32 training grant for the University Program in Genetics and Genomics (GM007754). M.V.R. is supported by NIH grant GM121828. M.G.S. was supported by an NWO Domain Applied and Engineering Sciences Veni grant (17282).

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Author notes

  1. Daehan Lee

    Present address: Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

  2. Stefan Zdraljevic

    Present address: Department of Human Genetics, University of California, Los Angeles, CA, USA

  3. Stefan Zdraljevic

    Present address: Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA

  4. Ye Wang

    Present address: Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, People’s Republic of China

  5. These authors contributed equally: Daehan Lee, Stefan Zdraljevic, Lewis Stevens.

Authors and Affiliations

  1. Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA

    Daehan Lee, Stefan Zdraljevic, Lewis Stevens, Ye Wang, Robyn E. Tanny, Timothy A. Crombie, Daniel E. Cook & Erik C. Andersen

  2. Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA

    Stefan Zdraljevic

  3. Department of Biology, Duke University, Durham, NC, USA

    Amy K. Webster, Rojin Chirakar & L. Ryan Baugh

  4. University Program in Genetics and Genomics, Duke University, Durham, NC, USA

    Amy K. Webster

  5. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA

    L. Ryan Baugh

  6. Laboratory of Nematology, Wageningen University and Research, Wageningen, the Netherlands

    Mark G. Sterken

  7. Université Côte d’Azur, CNRS, Inserm, IBV, France, Nice, France

    Christian Braendle

  8. Institut de Biologie de l’Ecole Normale Supérieure, Centre National de la Recherche Scientifique, INSERM, École Normale Supérieure, Paris Sciences et Lettres, Paris, France

    Marie-Anne Félix

  9. Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA

    Matthew V. Rockman

Authors
  1. Daehan Lee
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  2. Stefan Zdraljevic
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  4. Ye Wang
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  15. Erik C. Andersen
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Contributions

D.L., S.Z. and E.C.A. conceived of and designed the study. D.L., S.Z., L.S. and E.C.A. analysed the data and wrote the manuscript. Y.W., R.E.T. and D.E.C. performed whole-genome sequencing and isotype characterization for 609 wild C. elegans strains. R.E.T. performed long-read sequencing for 11 C. elegans wild isolates. R.C., A.K.W. and L.R.B. performed long-read sequencing for three C. elegans wild isolates. M.G.S., C.B., M.V.R. and M.-A.F. contributed wild isolates to the C. elegans strain collection. M.G.S., C.B., M.V.R., M.-A.F. and T.A.C. edited the manuscript.

Corresponding author

Correspondence to Erik C. Andersen.

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The authors declare no competing interests.

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Peer review information Nature Ecology & Evolution thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Chromosome-scale selective sweeps across wild C. elegans isotypes.

a, The genome-wide distribution of the most frequent haplotype (red) among 324 wild isotypes with known geographic origin is shown. Grey genomic regions represent other haplotypes, and white represents unclassified haplotypes. Each row is one of the 324 isotypes, grouped by the geographic origin. The genomic position in Mb is plotted on the x-axis, and each tick mark represents 5 Mb of the chromosome. b, Beeswarm plots of the proportion of the most frequent haplotype for each chromosome from (a) for 324 isotypes with known geographic origins are shown. Wild isotypes are grouped by geographic origin. Each point corresponds to one of the 324 isotypes, and geographic origins are shown on the y-axis.

Extended Data Fig. 2 Patterns of molecular diversity across the C. elegans genome.

The chromosomal patterns a, Watterson’s theta (θ) and b, nucleotide diversity (pi) for non-overlapping 1 kb windows are shown. Each dot corresponds to the calculated value for a particular window. The genomic position in Mb is plotted on the x-axis. Diversity statistic values are shown on the y-axis. Smoothed lines (blue) are LOESS fits. c, Tukey box plots of genetic diversity statistics from (a) are shown with outlier data points plotted. Genetic diversity statistics for each sliding window are grouped by the chromosomal region defined previously36. Genetic diversity statistic values are shown on the y-axis. The horizontal line in the middle of the box is the median, and the box denotes the 25th to 75th quantiles of the data. The vertical line represents the 1.5x interquartile range.

Extended Data Fig. 3 Optimization of parameters for the characterization of hyper-divergent regions.

a,b, The total detected hyper-divergent regions in Mb (x-axis) and the percent overlap of long-read and short-read hyper-divergent classification (y-axis) are shown (Methods). Each point corresponds to one of the combination of threshold parameters for the variant count and coverage fraction of 1 kb bin to be classified as hyper-divergent. Each point is coloured by the variant count threshold (a) or the coverage fraction threshold (b). c, The relationship between the total size of hyper-divergent regions detected by the optimized short-read or long-read based approach is shown. Each point corresponds to one of the 15 long-read sequenced isotypes. Total sizes of hyper-divergent regions detected by the short-read based approach are shown on the x-axis, and total sizes of hyper-divergent regions detected by the long-read based approach are shown on the y-axis. d, The overlap between hyper-divergent regions defined by the optimized short-read based approach and long-read based approach is shown. Each point corresponds to one of the 15 long-read sequenced isotypes. Total sizes of hyper-divergent regions detected by either short-read or long-read based approach are shown on the x-axis, and the percentages of hyper-divergent regions detected by both approaches are shown on the y-axis.

Extended Data Fig. 4 Summary statistics for hyper-divergent regions across six chromosomes.

a, Bar plots for the comparisons of variant (SNV/indel) density (top) and coverage fraction (bottom) between hyper-divergent regions (red) and the rest of the regions (blue) in each chromosomal region are shown. Note that no hyper-divergent region was found on the tips of chromosome I. b, Fold differences between hyper-divergent regions and the rest of the regions from (a) are shown.

Extended Data Fig. 5 Genomic signatures of balancing selection in non-divergent regions and hyper-divergent regions.

Tukey box plots of Tajima’s D (a) and standardized beta (b) are shown. Genomic bins (1 kb) (a) or variants (b) are grouped and coloured by their classification: (1) non-divergent bins (yellow), (2) hyper-divergent bins with high variant density (≥ 16 SNVs/indels, red), (3) hyper-divergent bins with low read depth (< 35%, blue). Hyper-divergent bins are grouped by their species-wide frequencies: rare (<1%), intermediate (≥ 1% and < 5%), or common (≥ 5%). The horizontal line in the middle of the box is the median, and the box denotes the 25th to 75th quantiles of the data. The vertical line represents the 1.5x interquartile range.

Extended Data Fig. 6 Gene ontology (GO) enrichment for hyper-divergent regions.

Gene ontology (GO) enrichment for the biological process category (a) and the molecular function category (b) for non-divergent chromosomal arms (square) and hyper-divergent regions (circle) are shown. Significantly enriched GO terms in control regions or hyper-divergent regions or both are shown on the y-axis. Bonferroni-corrected significance values for GO enrichment are shown on the x-axis. Sizes of squares and circles correspond to the fold enrichment of the annotation, and colours of square and circle correspond to the gene counts of the annotation. The blue line shows the Bonferroni-corrected significance threshold (corrected p-value = 0.05). Note, we did not detect any GO-term enrichment of genes in non-divergent chromosomal arms for the biological process category.

Extended Data Fig. 7 Species-wide SNP-based relatedness of divergent regions is in agreement with long-read sequencing results.

The inferred for the C. elegans species-wide relatedness for the hyper-divergent regions that span (a) II:3,667,179-3,701,405, (b) I:2,318,291-2,381,851, and (c) V:20,193,463-20,267,244 are shown. The x-axis represents the dissimilarity of the fraction of identity-by-state in the region. For a-c, the isotype names are coloured to match the haplotypes defined by long-read sequence data in Fig. 5 and Extended Data Figs. 8, 9, respectively. The branch colours correspond to the species-wide genetic groups identified by PCA in Fig. 1c.

Extended Data Fig. 8 Two hyper-divergent haplotypes at the peel-1 zeel-1 incompatibility locus.

a, The protein-coding gene contents of the two hyper-divergent haplotypes at the peel-1 zeel-1 incompatibility locus on the left arm of chromosome I (I:2,318,291-2,381,851 of the N2 reference genome). The tree was inferred using SNVs and coloured by inferred haplotypes. For each distinct haplotype, we chose a single isotype as a haplotype representative (orange haplotype: N2, blue haplotype: CB4856) and predicted protein-coding genes using both protein-based alignments and ab initio approaches. Protein-coding genes are shown as boxes; those genes that are conserved in all haplotypes are coloured based on their haplotype, and those genes that are not are coloured light grey. Dark grey boxes behind genes indicate coordinates of divergent regions. Genes with locus names in N2 are highlighted. b, Heatmaps showing amino acid identity for alleles of four genes (mcm-4, srbc-64, ugt-31, and sydn-1). The percentage identity was calculated using alignments of protein sequences from all 16 isotypes. Heatmaps are ordered by the SNV tree shown in (a). c, Maximum-likelihood gene trees of four genes (mcm-4, srbc-64, ugt-31, and sydn-1) inferred using amino acid alignments. Trees are plotted on the same scale (scale shown; scale is in substitutions per site). Strain names are coloured by their haplotype.

Extended Data Fig. 9 Hyper-divergent haplotypes at a region on the right arm of chromosome V.

a, The protein-coding gene contents of the seven hyper-divergent haplotypes at a region on the right arm of chromosome V (V:20,193,463-20,267,244 of the N2 reference genome). The tree was inferred using SNVs and coloured by inferred haplotypes. For each distinct haplotype, we chose a single isotype as a haplotype representative (orange haplotype: N2, light blue haplotype: JU2526, red haplotype: EG4725, pink haplotype: ECA36, green haplotype: DL238, dark blue haplotype: QX1794, purple haplotype: NIC526) and predicted protein-coding genes using both protein-based alignments and ab initio approaches. JU2526 shares the reference haplotype at fbxa-113 and fbxb-59 (six hyper-divergent haplotypes at these loci) but is divergent at Y113G7B.15 (seven hyper-divergent haplotypes at this locus). Protein-coding genes are shown as boxes; those genes that are conserved in all haplotypes are coloured based on their haplotypes, and those genes that are not are coloured light grey. Dark grey boxes behind genes indicate coordinates of divergent regions. Genes with locus names in N2 are highlighted. Of the 25 genes that are not conserved in all haplotypes (light grey boxes), ten are alleles of the three reference haplotype (N2) loci coloured in light grey. The remaining 15 do not have a clear one-to-one relationship with a gene in the reference haplotype. Seven of these 15 have homology to F54E12.2 (present in the reference haplotype) and are likely the product of duplication and diversification. Six have homology to either M04C3.1, F19B2.5, or F54E12.2, all of which are genes with SNF2 family N-terminal domains and which exist elsewhere in the N2 reference genome. Of the remaining two genes, one has homology to Y113G7B.15, which is present in the reference haplotype, and the other has homology to W09C3.8, a gene on chromosome I in the reference genome. Functional annotations of all unconserved loci (including BLAST hits and Pfam domains identified by InterProScan) can be found in Supplementary Data 4. b, Heatmaps show amino acid identity for between alleles of five genes (srh-217, fbxb-113, fbxb-59, Y113G7B.15, and mdt-17). The percentage identity was calculated using alignments of proteins sequences from all 16 isotypes. Heatmaps are ordered by the SNV tree shown in (a). c, Maximum-likelihood gene trees of five genes (srh-217, fbxb-113, fbxb-59, Y113G7B.15, and mdt-17) inferred using amino acid alignments. Trees are plotted on the same scale (scale shown; scale is in substitutions per site). Strain names are coloured by their haplotype.

Extended Data Fig. 10 Hyper-divergent regions in C. briggsae.

The genome-wide distribution of hyper-divergent regions across 35 non-reference wild C. briggsae strains is shown. In the top panel, each row is one of the 35 strains, grouped by previously defined clades (tropical or others) ordered by the total amount of genome covered by hyper-divergent regions (black). In the bottom panel, brown bars indicate genomic positions in which more than 10% of strains are classified as hyper-divergent at the locus. The genomic position in Mb is plotted on the x-axis, and each tick represents 5 Mb of the chromosome.

Supplementary information

Supplementary Information

Supplementary Figs. 1–8 and Tables 1–6.

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Supplementary Tables 1–6.

Supplementary Data

Supplementary Data 1–4.

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Lee, D., Zdraljevic, S., Stevens, L. et al. Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans. Nat Ecol Evol 5, 794–807 (2021). https://doi.org/10.1038/s41559-021-01435-x

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