Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA, 22904-4328, USA.
Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
BMC Evol Biol. 2014 Dec 24;14:268. doi: 10.1186/s12862-014-0268-y.
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.
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.
These results suggest that mechanisms leading to 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.
尽管质体基因组在大多数被子植物中高度保守，但多个谱系的结构重排和核苷酸替换率都有所增加。这些谱系在相似的质体基因子集表现出过多的非同义替换（即升高的 dN/dS 比值），表明类似的机制可能导致这些基因的松弛和/或正选择。然而，对于这些机制是否继续在种内水平上塑造序列多样性，我们知之甚少。
我们研究了风铃草属植物质体基因组的种间分歧和种内多态性模式，并在质体基因中发现了 dN/dS 和 pN/pS 之间（即 dN/dS 的种内等效物）的显著相关性。包括 ycf1、ycf2、clpP 和核糖体蛋白基因在内的一些基因表现出较高的 dN/dS 比值。麦当劳-克里坦测试检测到这些基因几乎没有正选择的证据，这可能是由于存在大量的种内分歧。
这些结果表明，导致质体基因组中核苷酸替换率增加的机制仍在种内水平上起作用。加速的质体基因组进化可能增加种内细胞质-核遗传不相容的可能性，并因此有助于物种形成过程的早期阶段。
