几乎中性的分子进化理论认为物种之间在选择有效性方面存在差异。在一个理想化的模型中,人口普查人口规模决定了可靠清除有害变体所需的选择系数的最小值,以及中性多样性的数量。根据经验,“有效种群大小”通常是根据假定的中性遗传多样性的数量来估计的,并且被认为也可以捕获物种选择的有效性。选择有效性的潜在更直接的量度是选择保持优选密码子的程度。然而,过去比较不同物种间密码子偏好的指标被%GC含量和/或氨基酸组成的物种间差异所混淆.这里,我们提出了一种新的物种密码子适应指数(CAIS),基于Kullback-Leibler分歧,这纠正了两种混杂因素。我们演示了CAIS相关性的使用,以及密码子的有效数量,表明更高度适应的脊椎动物物种的蛋白质结构域进化出更高的内在结构紊乱。
进化是种群随时间变化的过程,从生物体遗传序列的突变开始。其中许多突变会损害生物体的生存和繁殖,但只有非常小的数量。一些物种,尤其是那些人口众多的人,可以比其他物种更有效地清除这些轻微有害的突变。这一事实已被“漂移屏障理论”用来解释物种之间的各种深刻差异,包括生物复杂性的差异。在这个理论中,消除轻微有害突变的有效性由“有效”群体规模指定,这取决于不仅仅是人口中的个体数量的因素。有效种群大小通常是根据“中性”突变(根本没有影响)在丢失或接管之前在种群中停留的时间来计算的。估计这个时间需要遗传多样性的代表性数据和突变率的知识。一个主要的限制是这些数据对于大多数物种是不可用的。第二个限制是一个简短的,个人数量的暂时减少对指标的影响过大,相对于其对累积的轻微有害突变数量的影响。Weibel,惠勒等人。开发了一种新的度量标准,可以更直接地确定一个物种清除轻微有害突变的效率。他们的方法基于遗传密码具有“同义”序列的事实。这些序列编码相同的氨基酸构建块,这些序列中的一个比其他序列稍稍优选。Weibel的度量标准,惠勒等人。定量已有效清除了较不优选的同义序列的基因组比例。当同义序列的使用与突变过程预测的使用进一步偏离时,它判断一个群体具有更高的有效群体规模。研究人员预计,自然选择将有利于具有强大三维结构的“有序”蛋白质,即,具有较高有效种群规模的物种将倾向于具有更有序的蛋白质版本。相反,他们发现相反的情况:有效种群数量较高的物种倾向于拥有更多无序版本的相同蛋白质。这改变了我们对自然选择如何作用于蛋白质的看法。为什么物种如此不同仍然是生物学中的一个基本问题。Weibel,惠勒等人。为将来将漂移屏障理论应用于物种差异的各种方式提供了有用的工具。
The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an \'effective population size\' is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species\' effectiveness of selection. A potentially more direct measure of the effectiveness of selection is the degree to which selection maintains preferred codons. However, 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), based on Kullback-Leibler divergence, that corrects for both confounders. We demonstrate the use of CAIS correlations, as well as the Effective Number of Codons, to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder.
Evolution is the process through which populations change over time, starting with mutations in the genetic sequence of an organism. Many of these mutations harm the survival and reproduction of an organism, but only by a very small amount. Some species, especially those with large populations, can purge these slightly harmful mutations more effectively than other species. This fact has been used by the ‘drift barrier theory’ to explain various profound differences amongst species, including differences in biological complexity. In this theory, the effectiveness of eliminating slightly harmful mutations is specified by an ‘effective\' population size, which depends on factors beyond just the number of individuals in the population. Effective population size is normally calculated from the amount of time a ‘neutral’ mutation (one with no effect at all) stays in the population before becoming lost or taking over. Estimating this time requires both representative data for genetic diversity and knowledge of the mutation rate. A major limitation is that these data are unavailable for most species. A second limitation is that a brief, temporary reduction in the number of individuals has an oversized impact on the metric, relative to its impact on the number of slighly harmful mutations accumulated. Weibel, Wheeler et al. developed a new metric to more directly determine how effectively a species purges slightly harmful mutations. Their approach is based on the fact that the genetic code has ‘synonymous’ sequences. These sequences code for the same amino acid building block, with one of these sequences being only slightly preferred over others. The metric by Weibel, Wheeler et al. quantifies the proportion of the genome from which less preferred synonymous sequences have been effectively purged. It judges a population to have a higher effective population size when the usage of synonymous sequences departs further from the usage predicted from mutational processes. The researchers expected that natural selection would favour ‘ordered’ proteins with robust three-dimensional structures, i.e., that species with a higher effective population size would tend to have more ordered versions of a protein. Instead, they found the opposite: species with a higher effective population size tend to have more disordered versions of the same protein. This changes our view of how natural selection acts on proteins. Why species are so different remains a fundamental question in biology. Weibel, Wheeler et al. provide a useful tool for future applications of drift barrier theory to a broad range of ways that species differ.