Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland.
Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
Viruses. 2019 Mar 5;11(3):220. doi: 10.3390/v11030220.
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host⁻virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.
病毒的当代基因组多样性是过去生态和进化过程不断动态相互作用的结果。因此，病毒的基因组序列可以成为了解这些过程的有价值信息来源。在这篇综述中，我们首先描述了塑造病毒基因组变异的相关过程，重点介绍了宿主-病毒共同进化的作用及其产生生态进化反馈循环的潜力。我们进一步简要概述了可用于从基因组数据中提取有关这些过程信息的现有方法。短的世代时间和小的基因组使病毒成为研究复杂共同进化和生态进化相互作用对遗传进化的联合影响的理想模型系统。这种复杂性，加上病毒中多种多样的寿命和繁殖策略，需要对现有推断方法进行扩展，例如整合多个信息源。这种整合可以拓宽遗传推断方法的适用性，从而进一步提高我们对病毒在生物群落中所起作用的理解。
