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Open Access Highly Accessed Research article

Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes

Shotaro Hirase1*, Haruka Ozaki2 and Wataru Iwasaki123*

Author Affiliations

1 Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba 277-8564, Japan

2 Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-8568, Japan

3 Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan

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BMC Genomics 2014, 15:735  doi:10.1186/1471-2164-15-735

Published: 29 August 2014



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.


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.


The identification of GCNVs that were likely under parallel selection suggests that contribution of GCNVs should be considered in studies on adaptive evolution.

Gene copy number variations; Parallel evolution; Positive selection; Three-spined stickleback