The effect of recombination on incipient speciation in bacteria

了解是什么力量塑造了我们星球上观察到的巨大多样性，这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的最明显的地方是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生物地球化学和生态系统功能中发挥基本作用，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，它们在功能上是如何和为什么不同的，并知道它们之间是否可以潜在地转移功能。描述细菌类型分化的一个流行模型是“稳定生态型模型”。在这个模型中，连续有益的突变使一个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”将通过不同的适应逐渐分化。然而，细菌并不是纯粹的克隆；它们也可以进行“准克隆”，在不同的个体之间转移短的DNA片段。这种‘细菌性’通常非常重要，能够在许多物种中创造比点突变更多的遗传变异。细菌进行伴性繁殖的一个重要方式是转化：从环境中吸收游离DNA，然后将DNA重组到基因组中。重组对稳定的生态型模型具有重要意义，原因有两个。首先，生态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单个最适合(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，重组可以加快适应性分化(即形成新的生态型)。然而，反过来，当一种生态型吸收来自不同生态型的DNA以产生不能很好地适应任何一种生态位的杂交基因型时，重组也可以减缓适应性分化。这项提议将首次通过实验检验假设：1)新兴生态型内的转化是否促进适应2)两种不同新兴生态型之间的转化是否会阻碍适应分化与我提议的国际项目合作伙伴Pal Jarle Johnsen博士(挪威特罗姆索大学)和Gabriel Perron博士(加拿大渥太华大学)合作，将利用实时进化实验来在两个不同的资源(生态位)中进化频繁转化的贝氏不动杆菌。用于转化的DNA的可用性将被操纵为：1)增加适应相同环境的细菌的DNA多样性；2)为细菌提供适应另一环境的细菌的DNA。随后的竞争实验将能够分别揭示适应性发散是被促进还是被阻碍。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为生态和遗传上不同的类型，这对微生物学至关重要。进化表型的实时受控进化将使我们能够第一次测试关键进化变量重组对细菌物种形成第一步的影响。

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.