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. Author Summary 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). Over time, the joint effects of selection and other evolutionary forces will act to either eliminate the extra genetic copy or retain it. Depending on this evolutionary interplay, young duplications, including newly duplicated genes, can persist for millions of years as CNVs. CNVs may especially be prevalent between populations that have colonized and adapted to disparate environments in which selective pressures differ. 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. These young CNV genes are enriched with environmental response functions and evolving rapidly at the molecular level, making them promising candidates for a role in the rapid ecological adaptation to novel environments.
【초록키워드】 Evolution, adaptive, Variation, Genome, Genetic, Local, Population, Comparative genomics, genetic diversity, molecular, population genomics, distribution, CNV, interactions, function, Frequency, Innovation, low frequencies, Duplicate genes, copy-number variation, natural populations, three-spined stickleback, three-spined sticklebacks, copy-number variations, duplicate gene, Candidates, locus, individual, complexity, population level, Stage, candidate, selective pressures, CNV genes, CNVs, duplications, eco-genomic model, lineage-specific genes, teleost genomes, duplication, whole genome sequence, over, Effect, Genes, selective pressure, populations, prevalent, highlight, joint, identify, evaluate, elevated, functional, occur, analysis, producing, category, subset, fixed, disparate, ecological, CNV gene, lineage-specific gene, structural polymorphism, teleost genome, 【제목키워드】 Population, copy-number variation, Extensive,