Estimating selection on amino-acid sequence polymorphisms in Drosophila

突变是DNA复制中非常罕见的错误的结果，它导致指定生物体特性的遗传信息发生变化。生物学中的一个主要问题是突变在多大程度上影响生物体的适应性（即其生存和成功繁殖的能力）。特别是，如果我们想知道由于有害突变的积累，已经减少到非常少量个体的物种是否有灭绝的危险，那么了解突变的适应度效应是非常重要的。由于突变频率的偶然波动过程（遗传漂变），这种情况在小种群中发生得尤其迅速，这可能会压倒自然选择消除有害突变的能力。这种情况发生的速度既取决于种群中存在的突变数量，也取决于它们对适应性的影响。突变的许多影响是通过它们对蛋白质分子结构的影响来介导的，而蛋白质分子结构是由相应基因的DNA序列决定的。因此，我们至少可以通过观察从整个基因组中随机取样的一组基因中改变蛋白质序列的突变对适应度的影响，来评估突变对群体中个体适应度的一些影响。然后，我们可以将基因组作为一个整体进行放大，以便估计突变对整个种群适应性的可能影响，以及由此导致的种群规模减少的风险。大多数突变的适应度影响可能很小，无法直接测量，因此我们必须使用间接方法，基于种群中基因行为的理论模型。一个种群或物种相对于一个DNA分子上的给定位点的状态，可以根据该位点上可能存在的四个可选核苷酸“字母”的相对频率来精确地指定：a、T、G或c。这些可以通过确定从一个种群中取样的个体的DNA序列来测量。通过比较一个物种内影响蛋白质序列的突变与由没有这种影响的突变引起的变异的DNA序列变化，以及通过比较相关物种成员之间的DNA序列，可以分析与突变、选择和漂变影响的数学和计算机模型有关的结果。这使我们能够估计改变蛋白质序列的有害突变的适应度效应。为此，我建议使用两种相近的果蝇，即米兰达果蝇（Drosophila miranda）和伪蝇（d.p pseudobscura）。它们生活在北美西部的山林中，栖息地不受人类活动的干扰，不像进化研究中使用的许多种类的果蝇。近年来，人们对pseudobscura的基因组进行了测序，这反映了其作为遗传和进化研究的经典生物的地位。我将收集这些物种中大约60个基因的DNA序列变异性数据，并将这些序列与更远的亲戚D. affinis进行比较。对于这一目的来说，没有受到最近种群规模扰动的物种，如D. miranda的情况，特别有用。利用两个物种的变异数据，其中一个物种（D. miranda）比另一个物种（D. pseudoobscura）罕见得多，从理论研究中得知，这对于估计有害突变的适应度效应特别有用。利用这些数据还可以回答一个非常有趣的问题，即亲缘物种之间蛋白质序列的差异有多少是由自然选择引起的，积累了提高适应性的突变，以及其他几个对生物学家研究进化很重要的问题。

Mutations are the result of very rare errors in the replication of DNA, which lead to a change in the genetic information specifying the properties of organisms. A major question in biology is the extent to which mutations affect the fitness of an organism (i.e. its ability to survive and reproduce successfully). In particular, knowledge of the fitness effects of mutations is of great importance if we want to know whether species that have been reduced to very small numbers of individuals risk extinction because of the accumulation of harmful mutations. This happens especially rapidly in small populations, by the process of chance fluctuations of frequencies of mutations (genetic drift), which can overwhelm the ability of natural selection to eliminate harmful mutations. The rate at which this happens depends both on the numbers of mutations present in the population and on their effects on fitness. Many of the effects of mutations are mediated through their effects on the structure of protein molecules, determined by the DNA sequences of the corresponding genes. We can therefore assess at least some of the effects of mutations on the fitnesses of individuals in a population by looking at the fitness effects of mutations that change protein sequences, in a set of genes sampled at random from the whole genome. We can then scale up to the genome as a whole, in order to estimate the likely impact of mutations on the fitness of the population as whole, and the consequent risks of reducing population size. Most mutations probably have such small fitness effects that they cannot be measured directly, so we have to use indirect methods, based on theoretical models of the behaviour of genes in populations. The state of a population or species with respect to a given site on a DNA molecule can be exactly specified in terms of the relative frequencies of the four alternative nucleotide 'letters' that can exist at the site: A, T, G or C. These can be measured by determining the DNA sequences of individuals sampled from a population. By comparing DNA sequence variation within a species for mutations affecting protein sequences with variation caused by mutations with no such effects, and by comparing DNA sequences between members of related species, it is possible to analyse the results in relation to what is expected from mathematical and computer models of the effects of mutation, selection and drift. This allows us to estimate the fitness effects of harmful mutations that change protein sequences. I propose to use two closely species of fruitfly, Drosophila miranda and D. pseudoobscura, for this purpose. They live in the mountain forests of western North America, in habitats that are undisturbed by human activity, unlike many species of Drosophila used in evolutionary studies. The genome of D. pseudoobscura has recently being sequenced, reflecting its status as a classic organism for genetic and evolutionary studies. I will collect data on DNA sequence variability within these species for a set of about 60 genes, and compare these sequences with a more distant relative, D. affinis. Species which have not been subject to recent disturbances of population size, as seems to be the case for D. miranda, are especially useful for this purpose. The use of data on variability in two species, one of which (D. miranda) is much rarer than the other (D. pseudoobscura), is known from theoretical studies to be especially useful for the purpose of estimating the fitness effects of harmful mutations. It is also possible to use these data to answer the very interesting question of what fraction of the differences in protein sequences among related species have been caused by natural selection accumulating mutations which improve fitness, as well as several other questions of importance to biologists studying evolution.