The universal tree of life: an update.

Patrick Forterre

doi:10.3389/fmicb.2015.00717

Abstract

Biologists used to draw schematic “universal” trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese’s universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution.

Highlights

The editors of research topic on “archaeal cell envelopes and surface structures” gave me the challenging task of drawing an updated version of the universal tree of life
The same reaction can be performed in mitochondria by the two universal proteins alone, one (Qri7) that came from Bacteria via the endosymbiotic route and the other (Kae1) corresponding to the eukaryotic version (Wan et al, 2013; Thiaville et al, 2014). These results suggest that last universal common ancestor (LUCA) was able to perform this universally conserved reaction with the ancestors of the two universal proteins and that accessory proteins were added independently in the bacterial and in the archaeal/eukaryal lineages
Martin and colleagues recently reported a lack of correspondence between individual protein trees and the concatenation tree in several datasets of archaeal and bacterial proteins (Thiergart et al, 2014)

Summary

Introduction

The editors of research topic on “archaeal cell envelopes and surface structures” gave me the challenging task of drawing an updated version of the universal tree of life. The reconstruction of ribosomal RNA and protein sequences in LUCA shed serious doubt on its hyperthermophilic nature, and suggests instead that it was either a mesophilic or a moderate thermophilic organism (Galtier et al, 1999; Boussau et al, 2008a) This result is in agreement with the facts that specific thermoadaptation features of lipids in Archaea and Bacteria are not homologous and that reverse gyrase, a protein required for life at very high temperature, was probably not present in the common ancestor of Archaea and Bacteria (Forterre, 1996; Brochier-Armanet and Forterre, 2007; Glansdorff et al, 2008). Are not present in Archaea (Lecompte et al, 2002; Figure 1)

A Tree or a Ring?

Findings

Conclusion