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实验设计、种群动态与微生物实验进化中的多样性。

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution.

机构信息

Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium

Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium.

出版信息

Microbiol Mol Biol Rev. 2018 Jul 25;82(3). doi: 10.1128/MMBR.00008-18. Print 2018 Sep.

Abstract

In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.

摘要

在实验进化中,实验室控制的条件选择了物种的适应,这可以实时监测。尽管目前此类实验非常流行,但长期以来,人们一直认为自然界最普遍的生物力量只能在超出研究人员寿命的时间尺度上观察到,因此只能通过比较手段来研究自然选择进化。最终,微生物快速进化变化的倾向证明我们错了,它们在有限的时间内表现出强烈的进化适应,如今在实验室进化实验中得到了大规模的利用。在这里,我们制定了一个微生物实验进化指南,解释了实验设计,并讨论了进化动态和结果,以及如何将其用于评估生态进化理论、改善具有工业重要性的特征以及解开复杂表型。具体来说,我们全面概述了实验进化中使用的设置。此外,我们还讨论了进化实验过程中的种群动态和遗传或表型多样性,并扩展了遗传相关因素,例如上位性和(有性)生殖的后果。进化的动态和结果受选择环境的时空性质的影响最大,其中不断变化的环境可能导致具有普遍适应性的生物,而结构化的环境可以通过克隆干扰和负频率依赖性选择等因素促进多样性。我们以未来的视角结束了本文,重点介绍了快速发展的技术进步所提供的可能性。这项工作旨在为实验进化领域的新手提供一个入门,为新兴的实验主义者提供一个指南,并为经验丰富的专家提供一个参考。

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