Synonymous mutations do not change the amino acid but do change the synonymous codon usage. In genomes of different organisms, the gene conversion process is biased toward GC, which is irrespective of mutation bias. In the coding region, this trend is especially obvious and it is possibly caused by the preference on G/C-ending codons over the A/T-ending ones. If the G/C-ending codons are advantageous, then the synonymous mutations that change A/T to G/C would be “optimal” compared to the opposite ones. In theory, one should observe signals of positive selection on these optimal synonymous mutations. The recently released single-nucleotide polymorphism (SNP) data from the 1001 genome project of Arabidopsis thaliana provided researchers with an unprecedented opportunity to verify this assumption. I fully take advantage of the SNP data from 1,135 A thaliana lines and came to the conclusion that synonymous mutations in natural populations are not strictly neutral: the synonymous mutations that increase GC content (from A/T to G/C) tend to have higher derived allele frequencies (DAFs) and, therefore, are likely to be positively selected. My current study broadens our knowledge of the selection patterns of synonymous mutations and should be appealing to evolutionary biologists.

One sentence summary: In 1135 genomes of Arabidopsis thaliana, the synonymous mutations that increase the GC content tend to have higher derived allele frequencies (DAFs) and are likely to be positively selected.

同义突变不会改变氨基酸，但会改变同义密码子用法。在不同生物的基因组中，基因转换过程偏向于GC，而与突变偏见无关。在编码区域中，这种趋势尤其明显，这可能是由于G / C末端密码子比A / T末端密码子的偏好。如果G / C末端密码子是有利的，那么与相反的相比，将A / T改变为G / C的同义突变将是“最优的”。从理论上讲，应该观察到对这些最佳同义突变的正选择信号。最近发布的拟南芥1001基因组计划的单核苷酸多态性（SNP）数据为研究人员提供了前所未有的机会来验证这一假设。我充分利用了来自1,135个拟南芥品系的SNP数据，得出的结论是，自然种群中的同义突变不是严格中性的：增加GC含量（从A / T到G / C）的同义突变倾向于更高衍生等位基因频率（DAFs），因此很可能会被积极选择。我目前的研究拓宽了我们对同义突变选择模式的认识，应该吸引进化生物学家。

一句话总结：在拟南芥的1135个基因组中，增加GC含量的同义突变往往具有较高的衍生等位基因频率（DAF），并可能被积极选择。