title: Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes.
abstract: BACKGROUND
  Understanding the genetic basis of adaptive evolution is one of the major goals in evolutionary biology. Recently, it has been revealed that gene copy number variations (GCNVs) constitute significant proportions of genomic diversities within natural populations. However, it has been unclear whether GCNVs are under positive selection and contribute to adaptive evolution. Parallel evolution refers to adaptive evolution of the same trait in related but independent lineages, and three-spined stickleback (Gasterosteus aculeatus) is a well-known model organism. Through identification of genetic variations under parallel selection, i.e., variations shared among related but independent lineages, evidence of positive selection is obtained. In this study, we investigated whole-genome resequencing data from the marine and freshwater groups of three-spined sticklebacks from diverse areas along the Pacific and Atlantic Ocean coastlines, and searched for GCNVs under parallel selection.
  
  
  RESULTS
  We identified 24 GCNVs that showed significant differences in the numbers of mapped reads between the two groups, and this number was significantly larger than that expected by chance. The derived group, i.e., freshwater group, was typically characterized by larger gene-copy numbers, which implied that gene duplications or multiplications helped with adaptation to the freshwater environment. Some of the identified GCNVs were those of multigenic family genes, which is consistent with the theory that fatal effects due to copy-number changes of multigenic family genes tend to be less than those of single-copy genes.
  
  
  CONCLUSIONS
  The identification of GCNVs that were likely under parallel selection suggests that contribution of GCNVs should be considered in studies on adaptive evolution.
authors.affiliation: Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba 277-8564, Japan. shirase@aori.u-tokyo.ac.jp.
authors.forename: Shotaro
authors.initials: S
authors.lastname: Hirase
authors.forename: Haruka
authors.initials: H
authors.lastname: Ozaki
authors.forename: Wataru
authors.initials: W
authors.lastname: Iwasaki
mesh_terms: D000818:Animals; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics; D005618:Fresh Water; D017353:Gene Deletion; D018628:Gene Dosage; D020440:Gene Duplication; D015870:Gene Expression; D058977:Molecular Sequence Annotation; D010641:Phenotype; D012623:Seawater; D012641:Selection, Genetic; D023701:Smegmamorpha / Q000235:genetics*
chemical_list: D029941:Fish Proteins