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

细菌以克隆方式繁殖，缺乏真核生物性别的影响。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分支（图1）。因此，虽然关键的适应性性状（次级代谢产物，毒力因子等）往往与辅助基因组，在必需的代谢基因的遗传变异产生生态连贯的分支。这导致了一些问题，包括：是什么驱动了这些不同的基因簇的形成？为什么核心或必需基因（与生态位没有明显关系）的遗传变异能预测生态关联？在这个项目中，我们将评估相互竞争的假设（a），遗传分化遵循中性积累的等位基因后，选择性扫描和/或（B）核心基因组变异是由适应形成的，无论是因为不同的等位基因变异有利于在不同的栖息地或因为上位性的核心和辅助基因组内的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是有利的。研究将集中在蜡状芽孢杆菌群，其中包含对人类和动物健康具有重要意义的细菌（B）。蜡状芽孢杆菌（B. cereus）、B.炭疽菌）和在害虫管理中具有重要经济意义的细菌（苏云金芽孢杆菌）。在这个组的分支是很好的特点，生态独特，可以有特色的热生物学。重要的是，不同的进化枝具有相似的同线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附属遗传变异。我们将直接比较中性模型和自适应模型的相对重要性。除了进一步的生态和人口的基因组特征，这一组，我们将使用实验进化直接测试适应性假说。我们将从两个最好的生态特征的分支复制隔离对：分支2中耐昆虫病原性分支和分支3冷适应根际分支，并在模拟自己的生态位和非典型生态位（植物根源介质或昆虫宿主）在冷（12摄氏度）或暖（32摄氏度）温度条件下进化这些菌株。根据我们的适应性假设，在新的栖息地的菌株被预测获得突变的必要基因，可能会提供优势，在他们的新的栖息地，这可能是对应于分支特异性等位基因的核心基因组中的分离物与新的生态位。

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.