Rooting the tree of life by transition analyses

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Microbial Evolution

Background:

• The root of the tree of life and the characteristics of the earliest cells remain debated in phylogeny.
• Contradictory results from protein paralogue trees and conflicting interpretations of palaeontological and phylogenetic data complicate root placement.
• Previous analyses using transition analysis suggested the root was not within neomura (eukaryotes plus archaebacteria), but its precise location remained controversial.

Purpose of the Study:

• To resolve the location of the universal root of life using comparative and developmental arguments.
• To systematically polarize major evolutionary transitions within eubacteria to infer the deepest phylogenetic branching.
• To reconstruct a fully resolved prokaryotic tree and characterize the Last Universal Common Ancestor (LUCA).

Main Methods:

• Analysis of 13 major evolutionary transitions within eubacteria to polarize character evolution.
• Utilizing palaeontological and phylogenetic evidence, including proteasome evolution, cell wall, and flagellar evolution.
• Examining conserved molecular features such as RNA polymerase and outer membrane protein evolution (Omp85).

Main Results:

• The universal root is inferred to be within eubacteria, specifically outside the clade of neomura and Actinomycetales (proteates).
• A basal stem of the prokaryote tree is identified as Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), characterized by gliding motility and absence of flagella.
• Posibacteria (Actinobacteria and Endobacteria) are shown to be derived from Eurybacteria and ancestral to neomura, with root placement outside this group.
• Evolution of the negibacterial outer membrane suggests the root lies within Eobacteria (Hadobacteria and Chlorobacteria).

Conclusions:

• Chlorobacteria are likely the oldest bacteria, and Archaebacteria the youngest, necessitating a reevaluation of bacterial evolutionary timelines.
• The Last Universal Common Ancestor (LUCA) was a non-flagellate negibacterium with a double membrane, acyl-ester lipids, peptidoglycan walls, and advanced molecular machinery.
• LUCA is proposed to be a photosynthetic green non-sulphur bacterium, contrasting with the heterotrophic, single-membraned posibacterium model.