![]() Lineages lacking an isolated representative are highlighted with non-italicized names and red dots. Major lineages are assigned arbitrary colours and named, with well-characterized lineage names, in italics. The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic supergroups. 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). 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. ![]() New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes 7, 15. ![]() 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. Contributing to this expansion in genome numbers are single cell genomics 13 and metagenomics studies. 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). 12), with a near-exponential increase in the number of draft genomes reported each subsequent year. Whole genome reconstruction was first accomplished in 1995 (ref. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses. 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. The depiction is both a global overview and a snapshot of the diversity within each major lineage. 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. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts 7, 8. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships 3– 5 or on the known, well-classified diversity of life with an emphasis on eukaryotes 6. 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. The tree of life is one of the most important organizing principles in biology 1.
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