title: A new view of the tree of life.
abstract: The tree of life is one of the most important organizing principles in biology(1). 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(3-5) 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.
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.
authors: Laura A
authors: LA
authors: Hug
authors: Department of Marine Science, University of Texas Austin, Port Aransas, Texas 78373, USA.
authors: Brett J
authors: BJ
authors: Baker
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.
authors: Karthik
authors: K
authors: Anantharaman
authors: Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California 94720, USA.
authors: Christopher T
authors: http://orcid.org/0000-0002-7758-6447
authors: CT
authors: Brown
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.
authors: Alexander J
authors: AJ
authors: Probst
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.
authors: Cindy J
authors: CJ
authors: Castelle
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.
authors: Cristina N
authors: CN
authors: Butterfield
authors: Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California 94720, USA.
authors: Alex W
authors: http://orcid.org/0000-0002-3737-380X
authors: AW
authors: Hernsdorf
authors: Sector of Decommissioning and Radioactive Wastes Management, Japan Atomic Energy Agency, Ibaraki 319-1184, Japan.
authors: Yuki
authors: Y
authors: Amano
authors: Sector of Decommissioning and Radioactive Wastes Management, Japan Atomic Energy Agency, Ibaraki 319-1184, Japan.
authors: Kotaro
authors: K
authors: Ise
authors: Graduate School of Science, The University of Tokyo, Tokyo 113-8654, Japan.
authors: Yohey
authors: Y
authors: Suzuki
authors: Department of Ecology and Evolutionary Biology, UC Santa Cruz, Santa Cruz, California 95064, USA.
authors: Natasha
authors: N
authors: Dudek
authors: Departments of Medicine and of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.
authors: David A
authors: DA
authors: Relman
authors: Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California 94720, USA.
authors: Kari M
authors: KM
authors: Finstad
authors: Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California 94720, USA.
authors: Ronald
authors: R
authors: Amundson
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.
authors: Brian C
authors: BC
authors: Thomas
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, California 94720, USA.|Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California 94720, USA.
authors: Jillian F
authors: JF
authors: Banfield
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics*; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D044822:Biodiversity; D017753:Ecosystem; D056890:Eukaryota / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D010802:Phylogeny