Dating the bacterial tree of life with ancient symbiosis

Abstract

Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils and absence of maximum age constraints of the available 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 mitochondria-originated genes where the mitochondrial lineage representing eukaryotes is embedded within Proteobacteria, such that the date constraints of eukaryotes established by their abundant fossils are 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 robust to alternative root ages, root positions, tree topologies, fossil ages, ancestral lifestyle reconstruction, gene sets, among other factors. The timetree obtained enables the validation of various hypotheses, such as the survival of life during the late heavy bombardment, the absence of a connection between ancient stromatolites and cyanobacteria, and the presence of aerobic enzymes before the oldest geochemical records of molecular oxygen. Significance StatementBacteria, with their vast diversity and ancient history, play a crucial role in shaping Earths biogeochemistry. However, the scarcity of fossils complicates the determination of their evolution timescale and its link to Earths history. To address this issue, we have devised and implemented novel methods that utilize ancient symbiosis and eukaryotic fossils to calibrate bacterial evolution by molecular clock. We obtain a comprehensive genus-level evolutionary timeline of bacteria that sheds light on their profound influence on the development and diversity of life on our planet, as well as its environmental dynamics. This research greatly contributes to our understanding of microbial evolution and its implications for Earths past and present.