Extensive Copy-Number Variation of Young Genes across Stickleback Populations. Extensive Copy-Number Variation of Young Genes across Stickleback Populations

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.

重复基因以拷贝数变异（copy-number variations, CNVs）的形式在种群层面产生，并会持续保持拷贝数多态性，直至被固定或丢失。这类基因组结构多态性的成功建立，可通过促进遗传多样性、基因组复杂性与演化创新，在生物演化过程中发挥关键作用。为解析重复基因的早期演化阶段及其潜在的适应性优势，本研究结合比较基因组学与种群基因组学分析方法，对生态基因组学模式物种三刺鱼的多个自然种群中拷贝数变异的分布与影响展开评估。本研究获取了栖息于3种不同生境的66个个体的全基因组序列，分析发现拷贝数变异通常以低频率存在，且往往仅在被调查的11个种群中的某一个种群内被检测到。但有一部分拷贝数变异呈现出种群间的拷贝数分化特征，其种群内频率升高的模式与局部适应性的预期相符。通过比对硬骨鱼基因组以鉴定三刺鱼的谱系特异性基因与基因复制事件，本研究揭示了个体间广泛存在的基因组成差异：其中超过30%的年轻重复基因为拷贝数变异。这些携带拷贝数变异的基因在分子层面演化迅速，且显著富集于与环境互作相关的功能类别，直观展现了种群分化过程中基因处于早期动态拷贝数多态性阶段的特征。