A new view of the tree of life

Abstract

The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…The phylogenetic relationships of the UBA genomes were determined across bacterial and archaeal trees inferred from three concatenated protein sets: (1) a syntenic block of 16 ribosomal proteins (rp1) recently used to infer genome-based phylogenies 10,30 (Supplementary Table 4), (2) 23 ribosomal proteins (rp2) previously tested for lateral gene transfer 4 (Supplementary Table 5), and (3) 120 bacterial (bac120) and 122 archaeal (ar122) proteins we have identified as being suitable for phylogenetic inference (Supplementary Tables 6 and 7). The trees span ~19,000 bacterial and ~1,000 archaeal genomes after specieslevel dereplication of the UBA genomes and 67,479 genomes in RefSeq/GenBank release 76 (Supplementary Table 8).…”

“…In addition, they comprise the first genomic representatives of 17 bacterial and 3 archaeal phyla (see section 'UBA genomes are the first representatives of several phyla'). To provide an objective taxonomic analysis of the UBA data set, we used the phylogenetic criterion of mean branch length to extant taxa 30 as existing taxonomic classifications are not phylogenetically uniform 1 . The results were highly consistent across all trees and, as expected, named groups at each taxonomic rank vary substantially in their mean branch length to extant taxa ( Fig.…”

“…These include elucidation of several phyla previously lacking genomic representatives [27][28][29] , including the Patescibacteria superphylum 4 , which has subsequently been referred to as the 'Candidate Phyla Radiation' (CPR) as it may consist of upwards of 35 candidate phyla 10,30 . Notable evolutionary and metabolic insights include the discovery of eukaryotic-like cytoskeleton genes in the archaeon Lokiarchaeota 31,32 and the identification of putative methane-metabolizing genes in the Bathyarchaeota and Verstraetearchaeota phyla 33,34 .…”

New CRISPR–Cas systems from uncultivated microbes

“…This system includes Cas1, Cas2, Cas4 and an uncharacterized ~980 aa protein that we refer to as CasX. The high conservation (68% protein sequence identity, Supplementary Data 1) of this protein in two organisms belonging to different phyla, Deltaproteobacteria and Planctomycetes, suggests a recent cross-phyla transfer 29 . The CRISPR arrays associated with each CasX had highly similar repeats (86% identity) of 37 nt, spacers of 33-34 nt, and a putative tracrRNA between the Cas operon and the CRISPR array (Fig.…”

“…We identified another new class 2 Cas protein encoded in the genomes of certain candidate phyla radiation (CPR) bacteria 6,29 (Fig. 1, Extended Data Table 1).…”