Positive vs relaxed mtDNA selection

This file describes the files associated with our manuscript on relaxed vs. positive selection in animal mtDNA <br> Each of the seven case studies we examined has its own folder/directory with a set of input, output, and results files. <br> Here's a little about the study: <br> Disentangling different types of selection is a common goal in molecular evolution. Elevated <em>d</em>N/<em>d</em>S ratios (the ratio of nonsynonymous to synonymous substitution rates) in focal lineages are often interpreted as signs of positive selection. Paradoxically, relaxed purifying selection can also result in elevated <em>d</em>N/<em>d</em>S ratios, but tests to distinguish these two causes are seldomly implemented. Here, we reevaluated seven case studies describing elevated <em>d</em>N/<em>d</em>S ratios in animal mtDNA and their accompanying hypotheses regarding selection. They included flightless vs. flighted lineages in birds, bats, and insects, and physiological adaptations in snakes, two groups of electric fishes, and primates. We found that elevated <em>d</em>N/<em>d</em>S ratios were often not caused by the predicted mechanism, and we sometimes found strong support for the opposite mechanism. We discuss reasons why energetic hypotheses may be confounded by other selective forces acting on mtDNA and caution against overinterpreting molecular “spandrels”, including elevated <em>d</em>N/<em>d</em>S ratios.

本文件用于说明与我们关于动物线粒体DNA（mtDNA）中正选择与松弛选择研究的手稿相关的全部配套文件。
本次纳入分析的7项案例研究均配有独立的文件夹/目录，内含输入文件、输出文件与结果文件集合。
本研究概况如下：
厘清不同类型的选择作用是分子进化领域的常见研究目标。研究类群中升高的dN/dS值（即非同义替换率与同义替换率的比值）常被视作正选择作用的标志性特征。但矛盾的是，松弛纯化选择同样可导致dN/dS值升高，然而用于区分这两种成因的检测方法却鲜有应用。
本研究重新评估了7项针对动物线粒体DNA中dN/dS值升高现象及其附带选择假说的案例研究。这些案例涵盖鸟类、蝙蝠与昆虫的无飞行能力类群与具飞行能力类群，以及蛇类、两类电鱼与灵长类的生理适应性演化。
研究结果显示，dN/dS值升高的现象往往并非由预设的选择机制所导致，部分案例甚至为相反的作用机制提供了强有力的支持证据。
本文还探讨了能量代谢相关假说可能受到线粒体DNA上其他选择作用干扰的原因，并提醒学界不应过度解读分子“拱肩”（spandrels）这一概念，包括dN/dS值升高这类现象。