Population genomics of Daphnia: mapping the 'arms-race genome'

我们的目标是衡量冲突对基因组进化方式的影响。例如，两个基因组之间的差异有多少是宿主和寄生虫之间军备竞赛的结果？是数量很少，还是这种冲突在分子水平上主导了进化？已经有一些证据表明免疫系统基因确实显示出较高的进化率，但目前尚不清楚这种影响有多普遍，或者与其他原因相比有多大。我们将通过比较参与宿主-寄生虫相互作用的基因（潜在的“军备竞赛”基因）的进化与其他基因的进化来回答这个问题。我们将使用一种生态和进化模式物种——水蚤（Daphnia magna）的基因组来做到这一点。只有同时研究多个基因，即整个基因组，才能解决这些问题。直到最近，这种方法都是站不住脚的：当一个“基因组计划”完成了单个个体的基因组测序时，它就完成了。现在，新的技术进步使得对数十（甚至数百）个人的完整基因组序列进行检查成为可能，而且价格已经下降到这样的“种群基因组”研究完全落在单个项目的范围内。水蚤是在英国和世界各地的池塘中发现的小型淡水甲壳类动物。水蚤在生态学方面得到了很好的研究，所以我们对水蚤的多样性以及它们与环境相互作用时这种多样性是如何产生的有了很多了解。例如，水蚤被用来评估环境中毒素的生态影响；它们在生理上适应广泛的pH值、食物、氧气和温度变化；它们表现出特殊的行为或形态来应对捕食者。从基因的角度来看，水蚤也很有趣，例如，它们在有性繁殖和无性繁殖之间交替，它们的基因比人类多近50%——可能是因为它们已经进化到能够对如此广泛的环境条件做出反应。对于我们的研究来说，最重要的是，水蚤病原体在实验室和野外得到了广泛的研究，因此我们可以确定它们的哪些基因对病原体有反应，以及这些基因对哪些病原体有反应。我们将对来自欧洲各地池塘的50只大水蚤的基因组进行测序，测序后，我们将使用基于种群遗传学理论的统计方法来询问冲突在决定全基因组适应进化率方面有多重要。我们的数据将通过网络免费提供给所有人，包括学者和公众。这将为解释实验室生物（如果蝇）的种群基因组研究提供重要资源。它也将为今后以水蚤为研究系统的生态学、保护学、流行病学和生态毒理学的遗传研究提供一个跳板。

We aim to measure the impact of conflict on the way genomes evolve. For example, what fraction of the differences between two genomes are a consequence of the arms-race between hosts and parasites? Is it a tiny amount, or do such conflicts dominate evolution at the molecular level? There is already some evidence that immune-system genes do show high rates of evolution, but it is not clear how general the effect is, or how big it is compared to other causes. We will answer this question by comparing the evolution of genes involved in host-parasite interaction (potential 'arms-race' genes), to the evolution of other genes. We will do this using the genome of an ecological and evolutionary model species - the water flea (Daphnia magna). It is only possible to address such questions by studying many genes simultaneously - i.e. whole genomes. Until recently, such an approach was untenable: a 'genome project' was complete when it had sequenced the genome of a single individual. Now, new advances in technology make it possible to examine full genome sequences for tens (or even hundreds) of individuals, and the price has fallen to the point at which such 'population genomic' studies fall well within the range of a single project. Daphnia are small freshwater crustaceans found in ponds throughout the UK and the world. Daphnia are well studied in terms of their ecology, so we know a great deal about the diversity of Daphnia and how this diversity arises when they interact with their environment. For example, Daphnia are used to assess the ecological impact of toxins in the environment; they adapt physiologically to a wide range of pH, food, oxygen, and temperature variation; and they exhibit specialised behaviour or morphology in response to predators. Daphnia are also interesting from a genetic perspective, for example they alternate between sexual and asexual reproduction, and they have nearly 50% more genes than humans - possibly because they have evolved to respond to such a wide range of environmental conditions. Most importantly for our study, Daphnia pathogens are widely studied in the lab and the field, so that we can identify which of their genes respond to pathogens, and to which pathogens those genes respond.We will sequence the genomes of 50 Daphnia magna from ponds all across Europe, and after sequencing, we will use statistical methods based on population-genetic theory to ask how important conflict is in determining the genome-wide rate of adaptive evolution. Our data will be made freely available to everyone, both academics and the public, over the web. This will provide a vital resource for interpreting population-genomic studies in laboratory organisms, such as the fruit fly (Drosophila). It will also provide a spring-board for future genetic studies of ecology, conservation, epidemiology and ecotoxicology that use Daphnia as a study system.