A new view of the tree of life
Laura A. Hug, Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, Alex W. Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A. Relman, Kari M. Finstad, Ronald Amundson, Brian C. Thomas & Jillian F. Banfield
Nature Microbiology Article number: 16048 (2016)
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Environmental microbiologyPhylogenetics
Received: 25 January 2016 Accepted: 10 March 2016
Published online: 11 April 2016
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 branches 2, 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 relationships 3,4,5 or on the known, well-classified diversity of life with an emphasis on eukaryotes 6. 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 contexts 7,8. 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.
Early approaches to describe the tree of life distinguished organisms based on their physical characteristics and metabolic features. Molecular methods dramatically broadened the diversity that could be included in the tree because they circumvented the need for direct observation and experimentation by relying on sequenced genes as markers for lineages. Gene surveys, typically using the small subunit ribosomal RNA (SSU rRNA) gene, provided a remarkable and novel view of the biological world 1,9,10, but questions about the structure and extent of diversity remain. Organisms from novel lineages have eluded surveys, because many are invisible to these methods due to sequence divergence relative to the primers commonly used for gene amplification 7,11. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts 7.
Whole genome reconstruction was first accomplished in 1995 (ref. 12), with a near-exponential increase in the number of draft genomes reported each subsequent year. There are 30,437 genomes from all three domains of life—Bacteria, Archaea and Eukarya—which are currently available in the Joint Genome Institute's Integrated Microbial Genomes database (accessed 24 September 2015). Contributing to this expansion in genome numbers are single cell genomics 13 and metagenomics studies. Metagenomics is a shotgun sequencing-based method in which DNA isolated directly from the environment is sequenced, and the reconstructed genome fragments are assigned to draft genomes 14. New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes 7,15. These genome- (rather than gene) based approaches provide information about metabolic potential and a variety of phylogenetically informative sequences that can be used to classify organisms 16. Here, we have constructed a tree of life by making use of genomes from public databases and 1,011 newly reconstructed genomes that we recovered from a variety of environments (see Methods).
To render this tree of life, we aligned and concatenated a set of 16 ribosomal protein sequences from each organism. This approach yields a higher-resolution tree than is obtained from a single gene, such as the widely used 16S rRNA gene16. The use of ribosomal proteins avoids artefacts that would arise from phylogenies constructed using genes with unrelated functions and subject to different evolutionary processes. Another important advantage of the chosen ribosomal proteins is that they tend to be syntenic and co-located in a small genomic region in Bacteria and Archaea, reducing binning errors that could substantially perturb the geometry of the tree. Included in this tree is one representative per genus for all genera for which high-quality draft and complete genomes exist (3,083 organisms in total).
Despite the methodological challenges, we have included representatives of all three domains of life. Our primary focus relates to the status of Bacteria and Archaea, as these organisms have been most difficult to profile using macroscopic approaches, and substantial progress has been made recently with acquisition of new genome sequences 7,8,13. The placement of Eukarya relative to Bacteria and Archaea is controversial 1,4,5,17,18. Eukaryotes are believed to be evolutionary chimaeras that arose via endosymbiotic fusion, probably involving bacterial and archaeal cells 19. Here, we do not attempt to confidently resolve the placement of the Eukarya. We position them using sequences of a subset of their nuclear-encoded ribosomal proteins, an approach that classifies them based on the inheritance of their information systems as opposed to lipid or other cellular structures 5.
Figure 1 presents a new view of the tree of life. This is one of a relatively small number of three-domain trees constructed from molecular information so far, and the first comprehensive tree to be published since the development of genome-resolved metagenomics. We highlight all major lineages with genomic representation, most of which are phylum-level branches (see Supplementary Fig. 1 for full bootstrap support values). However, we separately identify the Classes of the Proteobacteria, because the phylum is not monophyletic (for example, the Deltaproteobacteria branch away from the other Proteobacteria, as previously reported2,20).
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