title: Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity.
abstract: 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.
authors.affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, New Jersey, USA.
authors.forename: Erik C
authors.initials: EC
authors.lastname: Andersen
authors.forename: Justin P
authors.initials: JP
authors.lastname: Gerke
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Shapiro
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Crissman
authors.forename: Rajarshi
authors.initials: R
authors.lastname: Ghosh
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Bloom
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Félix
authors.forename: Leonid
authors.initials: L
authors.lastname: Kruglyak
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics*; D016000:Cluster Analysis; D003710:Demography; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic