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A rooted phylogeny resolves early bacterial evolution.

Gareth A Coleman1, Adrián A Davín2, Tara A Mahendrarajah3

  • 1School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.

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|May 7, 2021
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Summary
This summary is machine-generated.

This study models bacterial gene family evolution to root the bacterial tree, revealing the last bacterial common ancestor (LBCA) was likely a free-living, double-membraned organism. Vertical gene transfer remains dominant despite significant horizontal gene transfer (HGT).

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Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Establishing a rooted bacterial tree is crucial for understanding early bacterial evolution.
  • The precise location of the root and the extent of horizontal gene transfer (HGT) remain debated.
  • The characteristics of the last bacterial common ancestor (LBCA) are poorly understood.

Purpose of the Study:

  • To model the evolution of 11,272 gene families to determine the root of the bacterial tree.
  • To quantify the extent of horizontal gene transfer (HGT) in bacterial evolution.
  • To infer the characteristics of the last bacterial common ancestor (LBCA).

Main Methods:

  • Phylogenetic analysis of 11,272 bacterial gene families.
  • Modeling of gene family evolution to infer evolutionary history.
  • Comparative genomics to reconstruct ancestral traits.

Main Results:

  • The bacterial tree is rooted between the Terrabacteria and Gracilicutes clades.
  • The LBCA is characterized as a free-living, flagellated, rod-shaped, double-membraned organism.
  • The Candidate Phyla Radiation is not basal but branches within Terrabacteria, sister to Chloroflexota.
  • While 92% of gene families show evidence of HGT, 66% of gene transmissions are vertical.

Conclusions:

  • A rooted bacterial tree, with the proposed root position, provides a valid framework for interpreting bacterial evolution.
  • The LBCA possessed complex traits, including a double membrane and flagella.
  • Vertical gene transfer plays a more significant role than previously suggested by some studies, despite widespread HGT.