Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

The nematode Caenorhabditis elegans is central to research in molecular, cell and developmental biology, but nearly all of this research has been conducted on a single strain of C. elegans. Little is known about the population genomic and evolutionary history of this species. We characterized C. elegans genetic variation using high-throughput selective sequencing of a worldwide collection of 200 wild strains and identified 41,188 SNPs. Notably, C. elegans genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases. Population genetic modeling showed that this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years. These sweeps, which we hypothesize to be a result of human activity, have drastically reshaped the global C. elegans population in the recent past.

• Publication year

  2011

• Venue

  Nature Genetics

• Publication date

  2011-12-05

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1038/ng.1050PMID 22286215PMCID 3365839
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• [Caenorhabditis elegans].

  2020cited by this paper
• Selection at Linked Sites Shapes Heritable Phenotypic Variation in C. elegans

  2010cited by this paper
• The natural history of Caenorhabditis elegans.

  2010cited by this paper
• Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors.

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• Recombinational Landscape and Population Genomics of Caenorhabditis elegans

  2009cited by this paper
• Whole population, genome-wide mapping of hidden relatedness.

  2009cited by this paper
• A Polymorphism in npr-1 Is a Behavioral Determinant of Pathogen Susceptibility in C. elegans

  2009cited by this paper
• Frequency Spectrum Neutrality Tests: One for All and All for One

  2009cited by this paper
• Selection at a Single Locus Leads to Widespread Expansion of Toxoplasma gondii Lineages That Are Virulent in Mice

  2009cited by this paper
• Testing for Neutrality in Samples With Sequencing Errors

  2008cited by this paper
• Whole-genome sequencing and variant discovery in C. elegans

  2008cited by this paper
• Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

  2008cited by this paper
• Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate.

  2008cited by this paper
• Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae

  2008cited by this paper
• Efficient Control of Population Structure in Model Organism Association Mapping

  2008cited by this paper
• PLINK: a tool set for whole-genome association and population-based linkage analyses.

  2007cited by this paper
• Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows

  2007cited by this paper
• Temporal Dynamics and Linkage Disequilibrium in Natural Caenorhabditis elegans Populations

  2007cited by this paper
• High Nucleotide Polymorphism and Rapid Decay of Linkage Disequilibrium in Wild Populations of Caenorhabditis remanei

  2006cited by this paper
• One perfect worm.

  2006cited by this paper
• Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae

  2006cited by this paper
• Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis elegans

  2006cited by this paper
• Sampling from natural populations with RNAI reveals high outcrossing and population structure in Caenorhabditis elegans.

  2005cited by this paper
• High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations.

  2005cited by this paper
• Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss

  2004cited by this paper
• Methods for high-density admixture mapping of disease genes.

  2004cited by this paper
• High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome

  2004cited by this paper
• Evolutionary history of Caenorhabditis elegans inferred from microsatellites: evidence for spatial and temporal genetic differentiation and the occurrence of outbreeding.

  2004cited by this paper
• Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species.

  2003cited by this paper
• Selection at linked sites in the partial selfer Caenorhabditis elegans.

  2003cited by this paper
• Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing.

  2003cited by this paper
• Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

  2003cited by this paper
• Levels of DNA polymorphism vary with mating system in the nematode genus caenorhabditis.

  2002cited by this paper
• ARACHNE: a whole-genome shotgun assembler.

  2002cited by this paper
• Detecting recent positive selection in the human genome from haplotype structure

  2002cited by this paper
• High-throughput gene mapping in Caenorhabditis elegans.

  2002cited by this paper
• Two-locus sampling distributions and their application.

  2001cited by this paper
• Inference of population structure using multilocus genotype data.

  2000cited by this paper
• Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans.

  2000cited by this paper
• Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis.

  1999cited by this paper
• C. Elegans II

  1998cited by this paper
• Cloning of an avermectin-sensitive glutamate-gated chloride channel from Caenorhabditis elegans

  1994cited by this paper
• [Genetics of Caenorhabditis elegans].

  1989cited by this paper
• The genetics of Caenorhabditis elegans.

  1974cited by this paper
• BIOINFORMATICS ORIGINAL PAPER

  year unknowncited by this paper
• Bioinformatics Applications Note Genetics and Population Analysis Msms: a Coalescent Simulation Program including Recombination, Demographic Structure and Selection at a Single Locus

  year unknowncited by this paper

• Evidence for natural selection shaping the evolution of collective behavior among global Caenorhabditis elegans populations

  2026cites this paper
• Mutational divergence over years in local populations of the selfing nematode Caenorhabditis elegans

  2026cites this paper
• Allelic variation at tRNA genes in three nematode species indicates mutation load despite strong purifying selection

  2026cites this paper
• Parasite defense covaries with reproductive timing, not with resistance

  2026cites this paper
• Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans

  2025cites this paper
• Polymorphism can extensively reshape the genome-wide crossover landscape in Arabidopsis thaliana

  2025cites this paper
• Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

  2025influential citation
• Wild strains reveal natural variation in C. elegans avoidance behaviors

  2025influential citation
• Nictation behavior in nematodes

  2025cites this paper
• Behavioral adaptations of Caenorhabditis elegans against pathogenic threats

  2025cites this paper
• Transposable elements and heterochromatic regions are enriched for structural variation and sequence divergence in the genome of wild-type Caenorhabditis elegans

  2025cites this paper
• Independent mechanisms of benzimidazole resistance across Caenorhabditis nematodes

  2025cites this paper
• Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans

  2025cites this paper
• Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades.

  2025cites this paper
• Genetic Background and Gene Essentiality

  2025cites this paper
• Caenorhabditis diversity on Pohnpei, Micronesia, provides evidence that the Elegans Supergroup has its roots in the Americas and diversified in the Pacific en route to Asia

  2025cites this paper
• High rate of mutation and efficient removal by selection of structural variants from natural populations of Caenorhabditis elegans

  2025cites this paper
• Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing

  2025cites this paper
• The olfactory receptor SNIF-1 mediates foraging for leucine-rich diets in C. elegans

  2025influential citation
• Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation

  2024cites this paper
• Polygenic selection to a changing optimum under self–fertilisation

  2024cites this paper
• Transposon-mediated genic rearrangements underlie variation in small RNA pathways

  2024cites this paper
• Repeated global adaptation across plant species

  2024cites this paper
• Getting around the roundworms: Identifying knowledge gaps and research priorities for the ascarids.

  2024cites this paper
• Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans

  2024influential citation
• An empirical test of Baker's law: Dispersal favors increased rates of self-fertilization.

  2024cites this paper
• The impact of differential transposition activities of autonomous and non-autonomous hAT transposable elements on genome architecture and gene expression in Caenorhabditis inopinata.

  2024cites this paper
• Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior

  2024cites this paper
• The long and short of hyperdivergent regions.

  2024cites this paper
• Life history in Caenorhabditis elegans: from molecular genetics to evolutionary ecology

  2024cites this paper
• Reproductive system, temperature, and genetic background effects in experimentally evolving populations of Caenorhabditis elegans

  2024cites this paper
• A high-throughput behavioral screening platform for measuring chemotaxis by C. elegans

  2024cites this paper
• The regulatory architecture of gene expression variation in C. elegans revealed by multi-strain allele-specific analysis

  2024cites this paper
• Caenorhabditis elegans immune responses to microsporidia and viruses.

  2024cites this paper
• The rhythmic transcriptional landscape in Caenorhabditis elegans: daily, circadian and novel 16-hour cycling gene expression revealed by RNA-sequencing

  2024cites this paper
• Chromosome fusion and programmed DNA elimination shape karyotypes of nematodes.

  2024cites this paper
• Quantifying the fitness effects of resistance alleles with and without anthelmintic selection pressure using Caenorhabditis elegans

  2024cites this paper
• Repeated global adaptation across plant species

  2024cites this paper
• A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory

  2024cites this paper
• Comparative Genomics of Sex, Chromosomes, and Sex Chromosomes in Caenorhabditis elegans and Other Nematodes.

  2024cites this paper
• Parental age effect on the longevity and healthspan in Drosophila melanogaster and Caenorhabditis elegans

  2023cites this paper
• rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers.

  2023cites this paper
• Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes

  2023cites this paper
• Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice

  2023cites this paper
• Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages of C. elegans

  2023influential citation
• Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans

  2023cites this paper
• Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans

  2023cites this paper
• Evolution of fertilization ability in obligatorily outcrossing populations of Caenorhabditis elegans

  2023cites this paper
• Moderate heat stress-induced sterility is due to motility defects and reduced mating drive in C. elegans Males.

  2023cites this paper
• Selection and the direction of 1 phenotypic evolution 2

  2023cites this paper
• Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

  2023influential citation
• eQTL mapping in transgenic alpha-synuclein carrying Caenorhabditis elegans recombinant inbred lines

  2023cites this paper
• rec-1 loss of function is insufficient to homogenize crossover distribution in Caenorhabditis elegans

  2023cites this paper
• An efficient behavioral screening platform classifies natural products and other chemical cues according to their chemosensory valence in C. elegans

  2023cites this paper
• Identification of a spontaneously arising variant affecting thermotaxis behavior in a recombinant inbred Caenorhabditis elegans line

  2023cites this paper
• A QTL on chromosome IV explains a natural variation of QR.pap final position in Caenorhabditis elegans

  2023cites this paper
• Cosegregation of recombinant chromatids maintains genome-wide heterozygosity in an asexual nematode

  2023cites this paper
• Effect of recombination on genetic diversity of Caenorhabditis elegans

  2023cites this paper
• Cas9-induced nonhomologous recombination in C. elegans

  2023cites this paper
• Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms

  2023cites this paper
• No detectable changes in reproductive behaviour of Caenorhabditis elegans males after 97 generations under obligatory outcrossing

  2023cites this paper
• Heritable Cas9-induced nonhomologous recombination in C. elegans

  2023cites this paper
• A novel sperm-derived seminal fluid protein in Caenorhabditis nematodes

  2023influential citation
• Natural variation in the Caenorhabditis elegans egg-laying circuit modulates an intergenerational fitness trade-off

  2023cites this paper
• CaeNDR, the Caenorhabditis Natural Diversity Resource

  2023cites this paper
• The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits

  2022cites this paper
• Natural variation in C. elegans short tandem repeats

  2022influential citation
• Selection and the direction of phenotypic evolution

  2022cites this paper
• Genome size changes by duplication, insertion and divergence in Caenorhabditis worms

  2022cites this paper
• Trade‐offs in defence to pathogen species revealed in expanding nematode populations

  2022cites this paper
• Evolution of Reproductive Efficiency in Caenorhabditis elegans Under Obligatory Outcrossing

  2022cites this paper
• Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data

  2022cites this paper
• Isolating Caenorhabditis elegans from the Natural Habitat.

  2022cites this paper
• Reproductive consequences of transient pathogen exposure across host genotypes and generations

  2022cites this paper
• An atlas of gene expression variation across the Caenorhabditis elegans species

  2022cites this paper
• Temperature Stressed Caenorhabditis elegans Males Prioritize Feeding over Mating Resulting in Sterility

  2022cites this paper
• Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations

  2022cites this paper
• Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism

  2022cites this paper
• Bergerac strains of Caenorhabditis elegans revisited: expansion of Tc1 elements imposes a significant genomic and fitness cost

  2022cites this paper
• Rapid Isolation of Wild Nematodes by Baermann Funnel.

  2022cites this paper
• Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegans

  2022cites this paper
• Variation in mutational (co)variances

  2022cites this paper
• Natural genetic variation as a tool for discovery in Caenorhabditis nematodes

  2022cites this paper
• Genetic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

  2022influential citation
• Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes

  2022cites this paper
• The neuropeptide FLP-17 regulates an oviposition behavior in the nematode Caenorhabditis elegans that increases maternal reproductive fitness in low oxygen environments

  2022cites this paper
• Effects of aqueous and ethanolic extracts of Lepidium meyenii Walp (red and black maca) on Caenorhabditis elegans

  2022cites this paper
• C. elegans toxicant responses vary among genetically diverse individuals

  2022cites this paper
• Natural genetic variation in the pheromone production of C. elegans

  2022cites this paper
• Genetic diversity estimates for the Caenorhabditis Intervention Testing Program screening panel

  2022cites this paper
• A role for worm cutl-24 in background- and parent-of-origin-dependent ER stress resistance

  2021cites this paper
• Evaluation of changes in C. elegans immune response during bacterial infection: A single nematode approach.

  2021cites this paper
• Post-insemination selection dominates pre-insemination selection in driving rapid evolution of male competitive ability

  2021cites this paper
• From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation.

  2021cites this paper
• The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

  2021cites this paper
• Genetic load may increase or decrease with selfing depending upon the recombination environment

  2021cites this paper
• Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut

  2021cites this paper
• Host genetic drift and adaptation in the evolution and maintenance of parasite resistance

  2021cites this paper
• Diversification of small RNA pathways underlies germline RNAi incompetence in wild C . 1 elegans strains 2 3 4

  2021cites this paper
• Cryptic genetic variation in a heat shock protein modifies the outcome of a mutation affecting epidermal stem cell development in C. elegans

  2021cites this paper