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.
Highlights
Structural polymorphisms such as copy-number variations (CNVs) epitomize the dynamic nature of genomes
After a locus is duplicated in a genome, individuals from a population instantaneously differ in the number of copies of this locus producing a copy-number variation (CNV)
Using whole genome sequences from several populations of three-spined sticklebacks that inhabit different environments, we find that a third of young duplicated genes are CNVs
Summary
Structural polymorphisms such as copy-number variations (CNVs) epitomize the dynamic nature of genomes. Most deletions and duplications are thought to be under purifying selection and eventually eliminated from genomes [11,12], high gene duplication rates provide ample opportunities for functional diversification and adaptation given the right ecological circumstances [13,14,15,16]. The duplication event occurs in one individual genome within the population, producing a locus that varies in quantity (copy-number) amongst individuals. Under neutrality, this early copy-number polymorphic stage of a new duplicate gene can persist for millions of years before fixation or loss in a population [17]. As a small subset of CNVs may eventually give rise to new genes [18,19,20], their
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