Section of Evolutionary Biology, Ludwig-Maximilian University, Munich, Germany.
Genome Biol Evol. 2011;3:528-38. doi: 10.1093/gbe/evr057. Epub 2011 Jun 16.
The impact of the effective population size (Ne) on the efficacy of selection has been the focus of many theoretical and empirical studies over the recent years. Yet, the effect of Ne on evolution under epistatic fitness interactions is not well understood. In this study, we compare selective constraints at independently evolving (unpaired) and coevolving (paired) sites in orthologous transfer RNAs (tRNA molecules for vertebrate and drosophilid species pairs of different Ne. We show that patterns of nucleotide variation for the two classes of sites are explained well by Kimura's one- and two-locus models of sequence evolution under mutational pressure. We find that constraints in orthologous tRNAs increase with increasing Ne of the investigated species pair. Thereby, the effect of Ne on the efficacy of selection is stronger at unpaired sites than at paired sites. Furthermore, we identify a "core" set of tRNAs with high structural similarity to tRNAs from all major kingdoms of life and a "peripheral" set with lower similarity. We observe that tRNAs in the former set are subject to higher constraints and less prone to the effect of Ne, whereas constraints in tRNAs of the latter set show a large influence of Ne. Finally, we are able to demonstrate that constraints are relaxed in X-linked drosophilid tRNAs compared with autosomal tRNAs and suggest that Ne is responsible for this difference. The observed effects of Ne are consistent with the hypothesis that evolution of most tRNAs is governed by slightly to moderately deleterious mutations (i.e., |Nes|≤5).
近年来，有效种群大小（Ne）对选择效果的影响一直是许多理论和实证研究的焦点。然而，Ne 对上位适合度相互作用下进化的影响还不是很清楚。在这项研究中，我们比较了在独立进化（未配对）和共同进化（配对）的位置上的选择限制，在同源转移 RNA（tRNA）分子中，对脊椎动物和果蝇物种对的不同 Ne 进行了研究。我们表明，这两类位点的核苷酸变异模式很好地解释了 Kimura 在突变压力下的单和双座位序列进化的模型。我们发现，在同源 tRNA 中，随着所研究物种对 Ne 的增加，约束性增加。因此，Ne 对选择效果的影响在未配对位点比在配对位点更强。此外，我们确定了一组具有高度结构相似性的 tRNA，与生命所有主要王国的 tRNA 相似，以及一组具有较低相似性的 tRNA。我们观察到，前者的 tRNA 受到更高的限制，不太容易受到 Ne 的影响，而后者的 tRNA 受到的限制则受到 Ne 的很大影响。最后，我们能够证明 X 连锁的果蝇 tRNA 比常染色体 tRNA 的限制更宽松，并表明 Ne 是造成这种差异的原因。所观察到的 Ne 的影响与大多数 tRNA 的进化受轻微至中度有害突变（即|Nes|≤5）的假设一致。
