The effectiveness of selection varies among species. It is often estimated by means of an 'effective population size' based on neutral polymorphism, but this is confounded in complex ways with demography. The strength of codon bias more directly pertains to how well adaptation at many sites can be maintained in the face of deleterious mutations, but past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here we propose a new Codon Adaptation Index of Species (CAIS) that corrects for both confounders. Unlike previous metrics, CAIS yields the expected relationship with adult vertebrate body mass. As an example of the use of CAIS, we ask whether protein domains evolve lower intrinsic structural disorder (ISD) when present in more exquisitely adapted species, as expected given that ISD is higher in eukaryotic proteomes than prokaryotic proteomes. Using phylogenetically corrected linear models, we find, contrary to expectations, that the ISD of a given protein domain evolves to be higher when in well-adapted species. This effect is stronger in young protein domains but is also present in ancient domains.

中文翻译：

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选择更有效的脊椎动物物种的蛋白质结构域具有更大的内在结构障碍

选择的有效性因物种而异。通常通过基于中性多态性的“有效种群规模”进行估算，但这与人口统计学的复杂方式相混淆。密码子偏倚的强度与面对有害突变时在许多位点上的适应能力如何保持更直接相关，但是过去比较物种间密码子偏倚的度量标准因％GC含量和/或氨基酸的种间差异而混淆组成。在这里，我们提出了一个新的物种密码子适应指数（CAIS），可以对两个混杂因素进行校正。与以前的指标不同，CAIS可以得出与成年脊椎动物体重的预期关系。作为使用CAIS的一个例子，我们问当蛋白质结构域存在于适应性更强的物种中时，它们是否会进化出较低的固有结构紊乱（ISD），正如预期的那样，在真核蛋白质组中ISD高于原核蛋白质组。使用系统发育校正的线性模型，我们发现，与预期相反，当在适应性良好的物种中，给定蛋白质结构域的ISD逐渐升高。在年轻的蛋白质结构域中这种作用更强，但在古代的结构域中也存在。