Data from: Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

Background: Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in similar subsets of plastid genes, suggesting that similar mechanisms may be leading to relaxed and/or positive selection on these genes. However, little is known regarding whether these mechanisms continue to shape sequence diversity at the intraspecific level. Results: We examined patterns of interspecific divergence and intraspecific polymorphism in the plastid genome of Campanulastrum americanum, and across plastid genes found a significant correlation between dN/dS and pN/pS (i.e., the within-species equivalent of dN/dS). A number of genes including ycf1, ycf2, clpP, and ribosomal protein genes exhibited high dN/dS ratios. McDonald-Kreitman tests detected little evidence for positive selection acting on these genes, likely due to the presence of substantial intraspecific divergence. Large-scale structural variation was also observed between populations. Conclusions: These results suggest that mechanisms leading to structural rearrangements and increased nucleotide substitution rates in the plastid genome are continuing to act at the intraspecific level. Accelerated plastid genome evolution may increase the likelihood of intraspecific cytonuclear genetic incompatibilities, and thereby contribute to the early stages of the speciation process. Background: Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in similar subsets of plastid genes, suggesting that similar mechanisms may be leading to relaxed and/or positive selection on these genes. However, little is known regarding whether these mechanisms continue to shape sequence diversity at the intraspecific level. Results: We examined patterns of interspecific divergence and intraspecific polymorphism in the plastid genome of Campanulastrum americanum, and across plastid genes found a significant correlation between dN/dS and pN/pS (i.e., the within-species equivalent of dN/dS). A number of genes including ycf1, ycf2, clpP, and ribosomal protein genes exhibited high dN/dS ratios. McDonald-Kreitman tests detected little evidence for positive selection acting on these genes, likely due to the presence of substantial intraspecific divergence. Large-scale structural variation was also observed between populations. Conclusions: These results suggest that mechanisms leading to structural rearrangements and increased nucleotide substitution rates in the plastid genome are continuing to act at the intraspecific level. Accelerated plastid genome evolution may increase the likelihood of intraspecific cytonuclear genetic incompatibilities, and thereby contribute to the early stages of the speciation process.

### 研究背景
尽管绝大多数被子植物（angiosperms）的质体基因组（plastid genome）高度保守，但多个演化支系的结构重排速率与核苷酸替换速率均显著升高。这些支系在质体基因的相似子集内呈现出非同义替换过量的特征，即非同义替换速率与同义替换速率之比（dN/dS）升高，暗示存在相似的分子机制推动这些基因受到松弛选择乃至正向选择。然而目前对于这些机制是否同样作用于种内水平的序列多样性塑造，尚缺乏足够的认知。

### 研究结果
本研究针对美洲风铃草（Campanulastrum americanum）的质体基因组展开分析，探究其种间分化与种内多态性模式；在质体基因层面，我们发现dN/dS与种内等效的dN/dS比值（即pN/pS，种内非同义多态性与同义多态性之比）之间存在显著相关性。包括ycf1、ycf2、clpP以及核糖体蛋白基因在内的多个基因的dN/dS比值较高。麦当劳-克里特曼检验（McDonald-Kreitman test）未检测到这些基因受到正向选择的显著证据，这大概率源于种群间存在显著的种内分化。此外，我们还在不同种群之间观测到了大规模的基因组结构变异。

### 研究结论
上述结果表明，驱动质体基因组结构重排与核苷酸替换速率提升的分子机制，同样在种内水平持续发挥作用。加速演化的质体基因组可能提升种内胞质-核遗传不相容性（cytonuclear genetic incompatibility）的发生概率，进而推动物种形成过程的早期阶段。

### 研究背景
尽管绝大多数被子植物（angiosperms）的质体基因组（plastid genome）高度保守，但多个演化支系的结构重排速率与核苷酸替换速率均显著升高。这些支系在质体基因的相似子集内呈现出非同义替换过量的特征，即非同义替换速率与同义替换速率之比（dN/dS）升高，暗示存在相似的分子机制推动这些基因受到松弛选择乃至正向选择。然而目前对于这些机制是否同样作用于种内水平的序列多样性塑造，尚缺乏足够的认知。

### 研究结果
本研究针对美洲风铃草（Campanulastrum americanum）的质体基因组展开分析，探究其种间分化与种内多态性模式；在质体基因层面，我们发现dN/dS与种内等效的dN/dS比值（即pN/pS，种内非同义多态性与同义多态性之比）之间存在显著相关性。包括ycf1、ycf2、clpP以及核糖体蛋白基因在内的多个基因的dN/dS比值较高。麦当劳-克里特曼检验（McDonald-Kreitman test）未检测到这些基因受到正向选择的显著证据，这大概率源于种群间存在显著的种内分化。此外，我们还在不同种群之间观测到了大规模的基因组结构变异。

### 研究结论
上述结果表明，驱动质体基因组结构重排与核苷酸替换速率提升的分子机制，同样在种内水平持续发挥作用。加速演化的质体基因组可能提升种内胞质-核遗传不相容性（cytonuclear genetic incompatibility）的发生概率，进而推动物种形成过程的早期阶段。