Département de Biologie, Université Laval, Québec, QC, Canada.
Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
Mol Biol Evol. 2017 Sep 1;34(9):2173-2186. doi: 10.1093/molbev/msx153.
Identifying the molecular changes that lead to ecological specialization during speciation is one of the major goals of molecular evolution. One question that remains to be thoroughly investigated is whether ecological specialization derives strictly from adaptive changes and their associated trade-offs, or from conditionally neutral mutations that accumulate under relaxed selection. We used whole-genome sequencing, genome annotation and computational analyses to identify genes that have rapidly diverged between two incipient species of Saccharomyces paradoxus that occupy different climatic regions along a south-west to north-east gradient. As candidate loci for ecological specialization, we identified genes that show signatures of adaptation and accelerated rates of amino acid substitutions, causing asymmetric evolution between lineages. This set of genes includes a glycyl-tRNA-synthetase, GRS2, which is known to be transcriptionally induced under heat stress in the model and sister species S. cerevisiae. Molecular modelling, expression analysis and fitness assays suggest that the accelerated evolution of this gene in the Northern lineage may be caused by relaxed selection. GRS2 arose during the whole-genome duplication (WGD) that occurred 100 million years ago in the yeast lineage. While its ohnolog GRS1 has been preserved in all post-WGD species, GRS2 has frequently been lost and is evolving rapidly, suggesting that the fate of this ohnolog is still to be resolved. Our results suggest that the asymmetric evolution of GRS2 between the two incipient S. paradoxus species contributes to their restricted climatic distributions and thus that ecological specialization derives at least partly from relaxed selection rather than a molecular trade-off resulting from adaptive evolution.
确定导致物种形成过程中生态特化的分子变化是分子进化的主要目标之一。一个仍需深入研究的问题是，生态特化是严格来自适应性变化及其相关的权衡，还是来自条件中性突变，这些突变在选择放松的情况下积累。我们使用全基因组测序、基因组注释和计算分析，鉴定了在两个处于不同生态位的酿酒酵母近缘种之间快速分化的基因，这些近缘种占据了西南到东北梯度上不同的气候区。作为生态特化的候选基因座，我们鉴定了具有适应性和加速氨基酸替换率特征的基因，导致谱系间的不对称进化。这组基因包括一个甘氨酰-tRNA 合成酶，GRS2，它在模型和姐妹种酿酒酵母中已知在热应激下转录诱导。分子建模、表达分析和适应性试验表明，该基因在北方谱系中的加速进化可能是由于选择放松。GRS2 是在酵母谱系 1 亿年前发生的全基因组复制（WGD）中产生的。虽然它的同源基因 GRS1 被保存在所有 WGD 后的物种中，但 GRS2 经常丢失且进化迅速，这表明该同源基因的命运仍有待解决。我们的结果表明，GRS2 在两个初生的酿酒酵母近缘种之间的不对称进化有助于它们的有限气候分布，因此，生态特化至少部分来自选择放松，而不是来自适应性进化的分子权衡。
