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Dating the bacterial tree of life based on ancient symbiosis
Systematic Biology ( IF 6.1 ) Pub Date : 2025-01-23 , DOI: 10.1093/sysbio/syae071
Sishuo Wang, Haiwei Luo

Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with genes found in the mitochondrial lineages phylogenetically embedded within Proteobacteria. The expanded mitochondria-bacterial tree allows the node age constraints of eukaryotes established by their abundant fossils to be propagated to ancient co-evolving bacterial symbionts and across the bacterial tree of life. Importantly, we formulate a new probabilistic framework that considers uncertainty in inference of the ancestral lifestyle of modern symbionts to apply 19 relative time constraints (RTC) each informed by host-symbiont association to constrain bacterial symbionts no older than their eukaryotic host. Moreover, we develop an approach to incorporating substitution mixture models that better accommodate substitutional saturation and compositional heterogeneity for dating deep phylogenies. Our analysis estimates that the last bacterial common ancestor (LBCA) occurred approximately 4.0-3.5 billion years ago (Ga), followed by rapid divergence of major bacterial clades. It is generally robust to alternative root ages, root positions, tree topologies, fossil ages, ancestral lifestyle reconstruction, gene sets, among other factors. The obtained timetree serves as a foundation for testing hypotheses regarding bacterial diversification and its correlation with geobiological events across different timescales.

中文翻译:


根据古老的共生关系对细菌生命树进行测年



获得细菌进化的时间尺度对于了解早期生命进化至关重要,但由于细菌化石的稀缺,因此很困难。在这里,我们引入了多个新的时间约束来校准基于古代共生关系的细菌进化。这个想法是使用由线粒体谱系中发现的基因构建的细菌树来实现的,这些基因系统发育嵌入了变形菌门中。扩展的线粒体细菌树允许由其丰富化石建立的真核生物的节点年龄限制传播到古老的共同进化的细菌共生体和整个细菌生命树。重要的是,我们制定了一个新的概率框架,该框架考虑了现代共生体祖先生活方式推断的不确定性,以应用 19 个相对时间约束 (RTC),每个相对时间约束 (RTC) 都由宿主-共生体关联提供信息,以限制不比其真核宿主老的细菌共生体。此外,我们开发了一种整合替代混合模型的方法,该模型更好地适应替代饱和度和组成异质性,以测定深度系统发育的年代。我们的分析估计,最后一个细菌共同祖先 (LBCA) 发生在大约 4.0-35 亿年前 (Ga),随后主要细菌分支迅速分化。它通常对替代根年龄、根位置、树木拓扑、化石年龄、祖先生活方式重建、基因集等因素具有鲁棒性。获得的时间树可作为检验有关细菌多样化及其在不同时间尺度上与地球生物事件相关性的假设的基础。
更新日期:2025-01-23
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