title: Extensive copy-number variation of young genes across stickleback populations.
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 eco-genomic 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 lineage-specific 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.
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Frédéric J J
authors.initials: FJ
authors.lastname: Chain
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany; Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, Münster, Germany.
authors.forename: Philine G D
authors.initials: PG
authors.lastname: Feulner
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Mahesh
authors.initials: M
authors.lastname: Panchal
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
authors.forename: Christophe
authors.initials: C
authors.lastname: Eizaguirre
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Irene E
authors.initials: IE
authors.lastname: Samonte
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kalbe
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Tobias L
authors.initials: TL
authors.lastname: Lenz
authors.affiliation: Genetic Epidemiology, Westfälische Wilhelms University, Münster, Germany.
authors.forename: Monika
authors.initials: M
authors.lastname: Stoll
authors.affiliation: Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfälische Wilhelms University, Münster, Germany.
authors.forename: Erich
authors.initials: E
authors.lastname: Bornberg-Bauer
authors.affiliation: Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Milinski
authors.affiliation: Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
authors.forename: Thorsten B H
authors.initials: TB
authors.lastname: Reusch
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000818:Animals; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D005260:Female; D017353:Gene Deletion; D018628:Gene Dosage; D020440:Gene Duplication; D020131:Genes, Duplicate / Q000235:genetics*; D014644:Genetic Variation; D008297:Male; D056186:Metagenomics; D010802:Phylogeny; D023701:Smegmamorpha / Q000235:genetics*