Clone wars in niche space: exploring the evolutionary and genetic basis for bacterial species.

细菌进行克隆繁殖，缺乏真核生物性别的同质化影响。然而，细菌的遗传变异并不是随机分布的。细菌通常以与有性物种相同的方式形成具有重叠生态位的连贯的分支(图1)。因此，尽管关键的适应性状(次生代谢物、毒力因子等)通常与附属基因组相关，但必需代谢基因的遗传变异会产生生态上一致的分支。这就引出了一些问题，包括：是什么驱动了这些不同的基因簇的形成？为什么核心基因或基本基因(与生态位没有明显关系)的遗传变异可以预测生态关联？在这个项目中，我们将评估相互竞争的假说(A)遗传分化遵循选择性扫描后等位基因的中性积累，或(B)核心基因组变异是由适应决定的，这要么是因为不同的生境中倾向于不同的等位基因变体，要么是因为核心和辅助基因组内的上位性相互作用有利于特定的等位基因或基因组合。换句话说，开发新生态位的关键适应可能决定核心基因组中哪些突变更受青睐。研究将集中在蜡状芽孢杆菌组，它包含对人类和动物健康具有重要意义的细菌(蜡状芽孢杆菌、炭疽杆菌)，以及在害虫管理中具有重大经济重要性的细菌(苏云金芽孢杆菌)。该类群中的分支特征良好，生态独特，具有独特的热生物学特征。重要的是，不同的分支具有相似的同步性和非常相似的核心基因组。该项目将涉及生物信息学、田间生态学、表型表征、实验进化和基因组学方法的应用，以及CRIPSR Cas9基因组编辑，以研究不同的生态位如何塑造核心和辅助遗传变异。我们将直接比较中性模型和自适应模型的相对重要性。除了进一步研究这一群体的生态和种群基因组特征外，我们还将利用实验进化直接测试适应性假说。我们将从两个生态特征最好的分支：分支2，中容昆虫致病分支和分支3，适应寒冷的根际分支中复制分离株对，并在低温(12℃)或温暖(32℃)的条件下模拟它们自己的生态位和非典型的生态位(植物根源介质或昆虫宿主)进化这些分离物。在我们的适应性假说下，新生境中的菌株预计会获得必要基因的突变，这些突变可能在它们的新生境中提供优势，并且可能对应于与新生态位相关的菌株核心基因组中的支系特有等位基因。

Bacteria reproduce clonally and lack the homogenizing influence of eukaryotic sex. Nevertheless bacterial genetic variation is not haphazardly distributed. Bacteria commonly form coherent clades with overlapping ecological niches in the same manner as sexual species (Figure 1). Therefore, although key adaptive traits (secondary metabolites, virulence factors etc) are often associated with the accessory genome, genetic variation in essential metabolic genes produces ecologically coherent clades. This leads to questions including: what drives the formation of these distinct genetic clusters? Why does genetic variation in core or essential genes (which are not obviously related to niche) predict ecological association? In this project we will evaluate competing hypotheses (a) that genetic divergence follows neutral accumulation of alleles after selective sweeps and or (b) core genomic variation is shaped by adaptation, either because different allelic variants are favoured in different habitats or because epistatic interactions within the core and accessory genome favour particular allele or gene combinations. In other words, key adaptations to exploit new niches may determine which mutations are favoured in the core genome.Research will focus on the Bacillus cereus group, which contains bacteria with significant importance for human and animal health (B. cereus, B. anthracis) and bacteria with significant economic importance in pest management (Bacillus thuringiensis). Clades in this group are well characterized, ecologically distinct and can have characteristic thermal biology. Importantly, distinct clades have similar synteny and very similar core genomes. This project will involve bioinformatics, field ecology, phenotype characterization, the application of experimental evolution and genomics approaches, as well as CRIPSR Cas9 genome editing to investigate how distinct niches shape core and accessory genetic variation. We will directly compare the relative importance of the neutral and adaptive models. In addition to furthering the ecological and population genomic characterization of this group we will use experimental evolution to test adaptive hypotheses directly. We will take replicate isolate pairs from two of the best ecologically characterized clades: clade 2 the mesotolerant insect pathogenic clade and clade 3 the cold-adapted rhizosphere clade and evolve these isolates in conditions simulating their own niche and an atypical niche (plant root derived media or insect hosts) at cold (12 deg C) or warm (32 deg C) temperatures. Under our adaptive hypothesis, strains in novel habitats are predicted to acquire mutations in essential genes that may provide advantages in their new habitats, and that may be correspond to clade-specific alleles in the core genome of the isolates associated with the new niche.