The effect of recombination on incipient speciation in bacteria

重组对细菌初期物种形成的影响

• 批准号: NE/L013177/1
• 负责人: Michiel Vos
• 金额: $ 5.11万
• 依托单位: UNIVERSITY OF EXETER
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FL013177%2F1
• 关键词: effect; recombination; incipient; speciation; bacteria

Understanding what forces shape the tremendous diversity observed on our planet is one of the main goals of evolutionary biology. This requires a detailed understanding of how new species arise, as species form the basic unit of biodiversity. Nowhere is our lack of understanding of species formation more apparent than for the most diverse component of global biodiversity: the bacteria. This is problematic, because bacteria play fundamental roles not only in global biogeochemistry and ecosystem functioning, but also in health and disease and many industrial sectors, from agriculture to biotechnology. It is therefore vital to be able to identify bacteria, to understand how they originate, and how and why they are functionally different, and to know whether functions can potentially be transferred between them. A popular model describing the divergence of bacterial types is the 'Stable Ecotype Model'. In this model, successive beneficial mutations allow a population to adapt to its environment. Two populations inhabiting different ecological niches will accumulate different beneficial mutations and so both 'ecotypes' will gradually diverge through differential adaptation. However, bacteria are known to not be purely clonal; they can also engage in 'parasex', transferring short fragments of DNA between different individuals. This 'bacterial sex' is often very important, being able to create more genetic variation than does point mutation in many species. One important way in which bacteria engage in parasex is transformation: the uptake of free DNA from the environment, followed by recombination of that DNA into the genome. Recombination has important implications for the Stable Ecotype Model for two reasons. First, adaptation within an ecotype is expected to proceed faster because different beneficial mutations arising at the same time in the population can be combined into a single most fit (i.e. well-adapted) genome (rather than the beneficial mutations competing against each other in different individuals). Recombination could thus speed up adaptive divergence (i.e. formation of novel ecotypes). However conversely, recombination could also slow down adaptive divergence when an ecotype takes up DNA originating from a different ecotype to create hybrid genotypes that are not well-adapted to either niche. This proposal will for the first time experimentally test the hypotheses:1) whether transformation within an emerging ecotype promotes adaptation 2) whether transformation between two different emerging ecotypes hinders adaptive divergenceIn collaboration with my proposed international project partners Dr. Pal Jarle Johnsen (University of Tromso, Norway) and Dr. Gabriel Perron ((University of Ottawa, Canada), a real-time evolution experiment will be used to evolve the frequently transforming species Acinetobacter baylyi in two distinct resources (niches). The availability of DNA for transformation will be manipulated to 1) increase the diversity of DNA from bacteria adapting to the same environment and 2) provide bacteria with DNA from bacteria adapting to the other environment. Subsequent competition experiments will be able to reveal whether adaptive divergence is promoted or hindered respectively. Understanding what ecological and evolutionary mechanisms cause a common bacterial ancestor to diversify into ecologically and genetically distinct types is of crucial importance to microbiology. Real-time controlled evolution of evolved phenotypes will enable us for the first time to test the influence of the key evolutionary variable, recombination, on the first steps in bacterial speciation.

了解是什么力量塑造了我们星球上观察到的巨大多样性，是进化生物学的主要目标之一。这需要详细了解新物种是如何产生的，因为物种构成了生物多样性的基本单位。我们对物种形成缺乏了解，最明显的莫过于全球生物多样性中最多样化的组成部分：细菌。这是有问题的，因为细菌不仅在全球地球化学和生态系统功能中发挥着重要作用，而且在健康和疾病以及从农业到生物技术的许多工业部门中也发挥着重要作用。因此，至关重要的是能够识别细菌，了解它们是如何起源的，以及它们在功能上如何以及为什么不同，并知道功能是否可以在它们之间转移。描述细菌类型分歧的流行模型是“稳定生态型模型”。在这个模型中，连续的有益突变使种群能够适应其环境。居住在不同生态位的两个种群将积累不同的有益突变，因此两个“生态型”将通过差异适应逐渐分化。然而，已知细菌不是纯粹的克隆;它们也可以参与“寄生”，在不同个体之间转移DNA的短片段。这种“细菌性别”通常是非常重要的，能够创造更多的遗传变异比点突变在许多物种。细菌进行异交的一个重要方式是转化：从环境中摄取游离DNA，然后将该DNA重组到基因组中。由于两个原因，退化对稳定生态型模型有重要的影响。首先，一个生态类型内的适应预计会进行得更快，因为在种群中同时出现的不同有益突变可以组合成一个最适合（即适应良好）的基因组（而不是不同个体中相互竞争的有益突变）。因此，同化可以加速适应性分化（即新生态型的形成）。然而，相反，重组也可以减缓适应性分歧时，一个生态型采取了DNA来源于不同的生态型，以创造杂交基因型，不适应任何一个生态位。该提案将首次通过实验验证以下假设：1）一种新兴生态类型内的转化是否促进适应2）两种不同新兴生态类型之间的转化是否阻碍适应性差异与我提议的国际项目合作伙伴Dr. Jarle Johnsen（挪威特罗姆瑟大学）和Gabriel Perron博士（加拿大渥太华大学）合作，将使用实时进化实验来进化两种不同资源（生态位）中频繁转化的物种不动杆菌。将操纵用于转化的DNA的可用性以1）增加来自适应相同环境的细菌的DNA的多样性和2）向细菌提供来自适应另一环境的细菌的DNA。随后的竞争实验将能够揭示适应性分歧是促进还是阻碍。了解是什么生态和进化机制导致一个共同的细菌祖先多样化成生态和遗传上不同的类型对微生物学至关重要。进化表型的实时控制进化将使我们能够首次测试关键进化变量重组对细菌物种形成的第一步的影响。

项目成果

Prokaryote genome fluidity is dependent on effective population size.

• DOI: 10.1038/ismej.2017.36
• 发表时间: 2017-07
• 期刊: The ISME journal
• 作者: Andreani NA;Hesse E;Vos M
• 通讯作者: Vos M