Analysis of Population-Genetic Properties of Copy Number Variations

  • Lingyang Xu
  • Liu Yang
  • Derek M. Bickhart
  • JunYa Li
  • George E. Liu
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)


While single nucleotide polymorphisms (SNPs) are typically the variant of choice for population genetics, copy number variations (CNVs) which comprise insertions, deletions and duplications of genomic sequences, is also an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. Moreover, population-specific CNVs are candidate regions under selection and are potentially responsible for diverse phenotypes.

Key words

Copy number variation Genetic diversity Population genetics Positive selection 



This work was supported in part by Agricultural Science and Technology Innovation Program of China (ASTIP-IAS-TS-16). L.Y.X was supported by the Elite Youth Program in Chinese Academy of Agricultural Sciences.


  1. 1.
    Scherer SW, Lee C, Birney E et al (2007) Challenges and standards in integrating surveys of structural variation. Nat Genet 39(7 Suppl):S7–S15CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Mills RE, Walter K, Stewart C et al (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59–65CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Brown KH, Dobrinski KP, Lee AS et al (2012) Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. Proc Natl Acad Sci U S A 109(2):529–534CrossRefPubMedGoogle Scholar
  4. 4.
    Zhang F, Gu W, Hurles ME et al (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10:451–481CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Sudmant PH, Kitzman JO, Antonacci F et al (2010) Diversity of human copy number variation and multicopy genes. Science 330(6004):641–646CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Conrad DF, Hurles ME (2007) The population genetics of structural variation. Nat Genet 39(7 Suppl):S30–S36CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Sjodin P, Jakobsson M (2012) Population genetic nature of copy number variation. Methods Mol Biol 838:209–223CrossRefPubMedGoogle Scholar
  8. 8.
    Narang A, Jha P, Kumar D et al (2014) Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation. Genome Biol Evol 6(12):3171–3181CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Jakobsson M, Scholz SW, Scheet P et al (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451(7181):998–1003CrossRefPubMedGoogle Scholar
  10. 10.
    McCarroll SA, Kuruvilla FG, Korn JM et al (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40(10):1166–1174CrossRefPubMedGoogle Scholar
  11. 11.
    Berglund J, Nevalainen EM, Molin AM et al (2012) Novel origins of copy number variation in the dog genome. Genome Biol 13(8):R73CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Redon R, Ishikawa S, Fitch KR et al (2006) Global variation in copy number in the human genome. Nature 444(7118):444–454CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Kato M, Kawaguchi T, Ishikawa S et al (2010) Population-genetic nature of copy number variations in the human genome. Hum Mol Genet 19(5):761–773CrossRefPubMedGoogle Scholar
  14. 14.
    Campbell CD, Sampas N, Tsalenko A et al (2011) Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet 88(3):317–332CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Iskow RC, Gokcumen O, Lee C (2012) Exploring the role of copy number variants in human adaptation. Trends Genet 28(6):245–257CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Perry GH, Dominy NJ, Claw KG et al (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39(10):1256–1260CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Xue Y, Sun D, Daly A et al (2008) Adaptive evolution of UGT2B17 copy-number variation. Am J Hum Genet 83(3):337–346CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Xu L, Hou Y, Bickhart DM, Zhou Y et al (2016) Population-genetic properties of differentiated copy number variations in cattle. Sci Rep 6:23161CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Bovine HapMap C, Gibbs RA, Taylor JF et al (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324(5926):528–532CrossRefGoogle Scholar
  20. 20.
    Liu GE, Hou YL, Zhu B et al (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res 20(5):693–703CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Bickhart DM, Xu L, Hutchison JL et al (2016) Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Res 23(3):253–262CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Lingyang Xu
    • 1
  • Liu Yang
    • 1
  • Derek M. Bickhart
    • 2
  • JunYa Li
    • 1
  • George E. Liu
    • 3
  1. 1.Institute of Animal ScienceBeijingChina
  2. 2.Research Microbiologist/BioinformaticianUSDA ARS DFRCMadisonUSA
  3. 3.Animal Genomics and Improvement LaboratoryUSDA ARSBeltsvilleUSA

Personalised recommendations