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. M..., , , # Dating the bacterial tree of life based on ancient symbiosis

[https://doi.org/10.5061/dryad.1c59zw42s](https://doi.org/10.5061/dryad.1c59zw42s)

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More detailed introductions for each folder and data set are given in a_more_detailed_readme.zip.
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## Description of the data and file structure

Original data and results for the study \"Dating the bacterial tree of life based on ancient symbiosis\". Organized into the following archives:

Note that **Supplemental data** are available at [https://zenodo.org/records/14348151](https://zenodo.org/records/14348151) (see **Related works** on the right-hand side)

#### **DATING**

*Relevant figures and tables:* Figs. 2-3, Figs. S15-S19.

Included in this folder are the **results of the MCMCtree analysis**.

* bootstrap/: using the focal strategy (some alternatives included)
* bootstrap.root2/: with different root placements
* date-alt/: analyses under various alternative dating schemes to explore the uncertainty associated with divergence t...