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  Extensive copy-number variation of young genes across stickleback populations

Chain, F. J. J., Feulner, P. G. D., Panchal, M., Eizaguirre, C., Samonte, I. E., Kalbe, M., et al. (2014). Extensive copy-number variation of young genes across stickleback populations. PLoS Genetics, 10(12): e1004830. doi:10.1371/journal.pgen.1004830.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0024-5863-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0024-5878-9
Genre: Journal Article

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 Creators:
Chain, Frédéric J. J.1, Author              
Feulner, Philine G. D.1, Author              
Panchal, Mahesh1, Author              
Eizaguirre, Christophe, Author
Samonte, Irene E.1, Author              
Kalbe, Martin2, Author              
Lenz, Tobias L.1, Author              
Stoll, Monika, Author
Bornberg-Bauer, Erich, Author
Milinski, Manfred1, Author              
Reusch, Thorsten B. H.3, Author              
Affiliations:
1Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445634              
2Research Group Parasitology, Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445643              
3External, ou_persistent22              

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 Abstract: Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an ecogenomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineagespecific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.

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Language(s): eng - English
 Dates: 2014-06-202014-10-162014-12-04
 Publication Status: Published online
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 Identifiers: DOI: 10.1371/journal.pgen.1004830
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Title: PLoS Genetics
  Other : PLoS Genet.
Source Genre: Journal
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Publ. Info: San Francisco, CA : Public Library of Science
Pages: - Volume / Issue: 10 (12) Sequence Number: e1004830 Start / End Page: - Identifier: ISSN: 1553-7390
CoNE: /journals/resource/1000000000017180