Dating the bacterial tree of life based on ancient symbiosis

Obtaining a timescale for bacterial evolution is crucial to understanding
early life evolution but is difficult owing to the scarcity of bacterial
fossils and the 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 generally robust to alternative root ages, root positions,
tree topologies, fossil ages, ancestral lifestyle reconstruction, and gene
sets, among other factors. The obtained time tree serves as a foundation
for testing hypotheses regarding bacterial diversification and its
correlation with geobiological events across different timescales.