An integrated approach to understanding spontaneous mutation and natural selection in the Chlamydomonas genome

自然选择的进化是由个体之间的遗传变异推动的，而遗传变异最终源于新的突变。因此，新的自发突变的出现速度，无论它们是有益的还是有害的，以及它们影响的大小，都对进化的模式和速度产生深远的影响。例如，如果新的有益突变的出现率很低，适应将经常受到这些突变供应的限制，而如果有益突变的出现率很高，适应将受到其他过程的限制，例如自然选择改变基因频率的速度。不幸的是，估计突变参数被证明是困难的，而且，尽管新突变对进化很重要，但很少有可靠的估计。我们将结合两种方法，目的是提供一个更全面的突变过程在我们的模型系统，单细胞藻衣藻莱茵蒂。检验突变来源的部分困难在于，自然选择在自然种群中起作用，去除有害突变，增加有益突变的频率。因此，我们在种群内和物种之间观察到的遗传差异是那些首先出现的突变的过滤和有偏见的子集。我们的第一种方法是在自然选择的影响最小化的条件下，维持莱茵哈蒂梭的复制系几百代。这将使我们能够检查所有新突变的影响，而不仅仅是那些通过选择过滤的突变。然后，我们将使用最先进的基因组测序技术来检查这些细胞系的一个子集的完整基因组序列，这将使我们能够直接测量DNA水平上突变变化的数量和种类。综合这些信息，我们就能对自然选择中可用的燃料有一个详细的了解。我们的第二种方法还将利用全基因组测序的力量，获得从自然种群中取样的莱茵哈蒂疟原虫基因组变异的详细图像。通过比较基因组不同部分变异的数量和分布，我们将能够量化自然条件下的选择如何作用于最初产生我们观察到的变异的突变。通过比较基因组不同区域之间的遗传差异，我们还将能够解剖基因组的功能组织，并确定哪些区域受到限制，因此保持相对不变，哪些区域有更多的自由变化。我们还计划获得C. reinhardtii最近的亲戚，C. incerta的基因组序列。通过比较莱茵瓢虫和赤瓢虫的基因组序列，我们将能够推断出这两个物种之间基因组的主要适应性变化。这些问题的答案将为进化生物学的许多领域提供重要的见解，从帮助我们理解为什么大多数真核生物物种有性繁殖，到让我们预测种群对环境变化的未来反应是否可能基于现有的或新的遗传变异。

Evolution by natural selection is fueled by genetic variation among individuals that ultimately originates from new mutations. Thus, the rate of appearance of new spontaneous mutations, whether they are beneficial or harmful and the magnitudes of their effects have profound consequences for the mode and speed of evolution. For example, if the rate of appearance of new beneficial mutations is very low, adaptation will frequently be limited by the supply of these mutations, whereas if the rate of beneficial mutations is high, adaptation will be limited by other processes, such as the speed with which natural selection can alter gene frequencies. Unfortunately, estimating mutational parameters has proved difficult, and, in spite of the importance of new mutations for evolution, there are few reliable estimates. We shall combine two approaches that aim to provide a fuller picture of the mutational process in our model system, the single-celled alga Chlamydomonas reinhardtii. Part of the difficulty in examining the supply of mutations is that natural selection operates in natural populations and removes deleterious mutations and increases the frequency of beneficial ones. Thus, the genetic differences that we observe within populations and between species are filtered and biased subsets of those mutations that arose in the first place. Our first approach will be to maintain replicate lines of C. reinhardtii for several hundred generations in conditions in which the effects of natural selection are minimised. This will allow us to examine the effects of the full spectrum of new mutations, not just those that pass through the filter of selection. We will then use state-of-the-art genome sequencing technologies to examine the complete genome sequences of a subset of these lines, which will allow us to measure directly the number and kinds of mutational changes at the DNA level. Taken together this information will provide us with a detailed picture of the fuel available to natural selection. Our second approach will also harness the power of whole genome sequencing to obtain a detailed picture of variation in the genome of C. reinhardtii sampled from a natural population. By comparing the amount and distribution of variation in different parts of the genome, we will be able to quantify how selection in natural conditions has acted on the mutations that originally generated the variation we observe. By comparing the genetic differences between different regions of the genome we will also be able to dissect the functional organisation of the genome, and determine which regions are constrained and so have remained relatively unchanged and which areas have more freedom to vary. We also plan to obtain the genome sequence of the closest relative of C. reinhardtii, C. incerta. By comparing the sequences of the C. reinhardtii and C. incerta genomes we shall be able to infer the principal adaptive changes in the genome between the two species. Answers to these questions will provide important insights in many areas of evolutionary biology, from helping us to understand why most eukaryotic species reproduce sexually to allowing us to predict whether the future responses of populations to environmental change is likely to be based on existing or new genetic variation.