MOLECULAR EVOLUTIONARY CONSEQUENCES OF ENDOSYMBIOSIS

大多数专性内共生细菌的基因组具有进化速度快、GC含量极低和基因组大小的特点。这些共同的特征表明，细菌的生活方式严重影响分子进化的模式。然而，很少有比较研究涉及驱动内共生体序列和基因组进化的过程。这项拟议的研究的目标是利用系统发育和种群遗传学方法区分形成内共生菌基因组的分子和进化机制。我们建议对比不同种类的伽马-3亚组变形杆菌的进化速率和模式，包括自由生活的肠杆菌和相关的木蚁、采采蝇和蚜虫的细菌内共生体。这项研究的具体目的是(1)通过对几个蛋白质编码基因座的分子进化和群体遗传学分析，量化突变偏见、漂移和选择对细胞内细菌蛋白质进化的影响；(2)通过测试适应密码子的使用和量化这些物种中的突变偏见，探索形成内共生体同义变异的力；(3)通过测试基因组大小是否缩小，修复未鉴定的木工内共生体中的基因丢失，并探索这些小细菌基因组中对缺失的突变偏见，来检测内共生体的基因组减少模式。这项研究的长期目标是了解细菌内共生的分子进化后果。我们将通过检查发生在专性的、细胞内联系的基因组变化来解决这个问题。该项目的结果将使我们了解细胞内细菌的进化模式，包括病原体和互助体，并将揭示在细菌进化中改变突变和选择之间平衡的力量。这项工作还将有助于开发更现实的DNA序列进化模型，包括细胞器基因组和脊椎动物和其他类群的偏向基因区域。

Genomes of most obligately endosymbiotic bacteria are characterized by fast evolutionary rates, extremely low GC contents, and small genome sizes. These shared features suggest that bacterial lifestyle severely affects patterns of molecular evolution. However, few comparative studies have addressed the processes that drive sequence and genome evolution in endosymbionts. The goal of the proposed study is to distinguish molecular and evolutionary mechanisms that shape endosymbiont genomes using phylogenetic and population genetic approaches. We propose to contrast rates and patterns of evolution across species of gamma-3 subdivision Proteobacteria, including free- living species of enterobacteria and related bacterial endosymbionts of carpenter ants, tsetse flies, and aphids. The specific aims of this study are (1) to quantify the impact of mutational biases, drift, and selection on protein evolution of intracellular bacteria, through molecular evolutionary and population genetic analyses of several protein-coding loci, (2) to explore forces that shape synonymous variation in endosymbionts, by testing for adaptive codon usage and quantifying mutational biases in these species, (3) to examine patterns of genome reduction in endosymbionts by testing for reduced genome size and repair gene loss in the uncharacterized endosymbionts of carpenter ants, and exploring mutational biases toward deletions in these small bacterial genomes. The long-range objective of this study is to understand the molecular evolutionary consequences of endosymbiosis in bacteria. We will approach this issue by examining genomic changes that occur in the context of obligate, intracellular associations. Results of this project will inform our understanding of the modes of evolution of intracellular bacteria, including both pathogens and mutualists, and will shed light on forces that shift the balance between mutation and selection in bacterial evolution. This work will also contribute to the development of more realistic evolutionary models for DNA sequences with biased base compositions, including genomes of organelles, and biased gene regions of vertebrates and other taxa.