Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota

Abstract

The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome.

Keywords: Archaea; Euryarchaeota; Proteoarchaeota; phylogenomics; root.

Fig. 1.—

Bayesian phylogenetic trees of Archaea rooted on bacterial sequences. (A) Tree based on the concatenation of 32 ribosomal proteins (2,560 sites). (B) Tree based on the concatenation of 38 new conserved protein markers (9,540 sites). The groups Bacteria (Ba), Aigarchaeota (Ai), Crenarchaeota (Cr), Korarchaeota (Ko), Thaumarchaeota (Th), and Euryarchaeota (Eu) are indicated. Numbers at branches are Bayesian PPs followed by ML bootstrap values. The scale bar indicates the number of substitutions per position.

Fig. 2.—

Schematic Bayesian phylogenetic trees of Archaea rooted on bacterial sequences. All trees are shown at the same scale to compare the distance between Archaea and Bacteria. (A) Tree based on 32 ribosomal proteins (2,560 sites). (B) Tree based on 38 new conserved proteins (9,540 sites). (C) Tree based on the complete data set of 70 proteins (10,963 sites). The scale bar indicates the number of substitutions per position.

Fig. 3.—

Bayesian phylogenetic tree of Archaea rooted on bacterial sequences based on the concatenation of 32 ribosomal proteins and 38 new conserved proteins (10,963 sites). The groups Bacteria (Ba), Aigarchaeota (Ai), Crenarchaeota (Cr), Korarchaeota (Ko), Thaumarchaeota (Th), and Euryarchaeota (Eu) are indicated. Numbers at branches are PPs followed by ML bootstrap values. The scale bar indicates the number of substitutions per position.

Fig. 4.—

Unrooted Bayesian phylogenetic tree of Archaea including ultrasmall archaeal taxa (Nanoarchaeota, Parvarchaeota, and Nanohaloarchaeota). The tree is based on the concatenation of 32 ribosomal proteins and 38 new conserved proteins (10,963 sites). The groups Bacteria (Ba), Aigarchaeota (Ai), Crenarchaeota (Cr), Korarchaeota (Ko), Thaumarchaeota (Th), and Euryarchaeota (Eu) are indicated Numbers at branches are PPs. The scale bar indicates the number of substitutions per position.