title: Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans.
abstract: BACKGROUND
  Gene copy-number variation (CNVs), which provides the raw material for the evolution of novel genes, is widespread in natural populations. We investigated whether CNVs constitute a common mechanism of genetic change during adaptation in experimental Caenorhabditis elegans populations. Outcrossing C. elegans populations with low fitness were evolved for >200 generations. The frequencies of CNVs in these populations were analyzed by oligonucleotide array comparative genome hybridization, quantitative PCR, PCR, DNA sequencing across breakpoints, and single-worm PCR.
  
  
  RESULTS
  Multiple duplications and deletions rose to intermediate or high frequencies in independent populations. Several lines of evidence suggest that these changes were adaptive: (i) copy-number changes reached high frequency or were fixed in a short time, (ii) many independent populations harbored CNVs spanning the same genes, and (iii) larger average size of CNVs in adapting populations relative to spontaneous CNVs. The latter is expected if larger CNVs are more likely to encompass genes under selection for a change in gene dosage. Several convergent CNVs originated in populations descended from different low fitness ancestors as well as high fitness controls.
  
  
  CONCLUSIONS
  We show that gene copy-number changes are a common class of adaptive genetic change. Due to the high rates of origin of spontaneous duplications and deletions, copy-number changes containing the same genes arose readily in independent populations. Duplications that reached high frequencies in these adapting populations were significantly larger in span. Many convergent CNVs may be general adaptations to laboratory conditions. These results demonstrate the great potential borne by CNVs for evolutionary adaptation.
authors.affiliation: Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Farslow
authors.affiliation: Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
authors.forename: Kendra J
authors.initials: KJ
authors.lastname: Lipinski
authors.affiliation: Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.
authors.forename: Lucille B
authors.initials: LB
authors.lastname: Packard
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Edgley
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Jon
authors.initials: J
authors.lastname: Taylor
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Stephane
authors.initials: S
authors.lastname: Flibotte
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Donald G
authors.initials: DG
authors.lastname: Moerman
authors.affiliation: Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.|Present address: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA.
authors.forename: Vaishali
authors.initials: V
authors.lastname: Katju
authors.affiliation: Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA. ubergthorsson@cvm.tamu.edu.|Present address: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA. ubergthorsson@cvm.tamu.edu.
authors.forename: Ulfar
authors.initials: U
authors.lastname: Bergthorsson
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D003433:Crosses, Genetic; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D017353:Gene Deletion; D018628:Gene Dosage; D020440:Gene Duplication; D056084:Genetic Fitness; D014644:Genetic Variation; D005828:Genetics, Population; D009154:Mutation; D012091:Repetitive Sequences, Nucleic Acid