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Title: A new view of the tree of life

Abstract

The tree of life is one of the most important organizing principles in biology. Gene surveys suggest the existence of an enormous number of branches, 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 or on the known, well-classified diversity of life with an emphasis on eukaryotes. 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. 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 biogeochemicalmore » models and identifies radiations that are probably important for future evolutionary analyses.« less

Authors:
 [1];  [2];  [3]; ORCiD logo [3];  [3];  [3];  [3]; ORCiD logo [3];  [4];  [4];  [5];  [6];  [7];  [3];  [3];  [3];  [3]
  1. Univ. of California, Berkeley, CA (United States); Univ. of Waterloo, ON (Canada)
  2. Univ. of Texas-Austin, Port Aransas, TX (United States). Dept. of Marine Science
  3. Univ. of California, Berkeley, CA (United States)
  4. Japan Atomic Energy Agency (JAEA), Tokai (Japan)
  5. Univ. of Tokyo (Japan)
  6. Univ. of California, Santa Cruz, CA (United States)
  7. Stanford Univ., CA (United States); Veterans Affairs Palo Alto Health Care System, Palo Alto, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1579922
Grant/Contract Number:  
AC02-05CH11231; SC10010566
Resource Type:
Accepted Manuscript
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 1; Journal Issue: 5; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Hug, Laura A., Baker, Brett J., Anantharaman, Karthik, Brown, Christopher T., Probst, Alexander J., Castelle, Cindy J., Butterfield, Cristina N., Hernsdorf, Alex W., Amano, Yuki, Ise, Kotaro, Suzuki, Yohey, Dudek, Natasha, Relman, David A., Finstad, Kari M., Amundson, Ronald, Thomas, Brian C., and Banfield, Jillian F. A new view of the tree of life. United States: N. p., 2016. Web. doi:10.1038/nmicrobiol.2016.48.
Hug, Laura A., Baker, Brett J., Anantharaman, Karthik, Brown, Christopher T., Probst, Alexander J., Castelle, Cindy J., Butterfield, Cristina N., Hernsdorf, Alex W., Amano, Yuki, Ise, Kotaro, Suzuki, Yohey, Dudek, Natasha, Relman, David A., Finstad, Kari M., Amundson, Ronald, Thomas, Brian C., & Banfield, Jillian F. A new view of the tree of life. United States. doi:10.1038/nmicrobiol.2016.48.
Hug, Laura A., Baker, Brett J., Anantharaman, Karthik, Brown, Christopher T., Probst, Alexander J., Castelle, Cindy J., Butterfield, Cristina N., Hernsdorf, Alex W., Amano, Yuki, Ise, Kotaro, Suzuki, Yohey, Dudek, Natasha, Relman, David A., Finstad, Kari M., Amundson, Ronald, Thomas, Brian C., and Banfield, Jillian F. Mon . "A new view of the tree of life". United States. doi:10.1038/nmicrobiol.2016.48. https://www.osti.gov/servlets/purl/1579922.
@article{osti_1579922,
title = {A new view of the tree of life},
author = {Hug, Laura A. and Baker, Brett J. and Anantharaman, Karthik and Brown, Christopher T. and Probst, Alexander J. and Castelle, Cindy J. and Butterfield, Cristina N. and Hernsdorf, Alex W. and Amano, Yuki and Ise, Kotaro and Suzuki, Yohey and Dudek, Natasha and Relman, David A. and Finstad, Kari M. and Amundson, Ronald and Thomas, Brian C. and Banfield, Jillian F.},
abstractNote = {The tree of life is one of the most important organizing principles in biology. Gene surveys suggest the existence of an enormous number of branches, 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 or on the known, well-classified diversity of life with an emphasis on eukaryotes. 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. 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.},
doi = {10.1038/nmicrobiol.2016.48},
journal = {Nature Microbiology},
number = 5,
volume = 1,
place = {United States},
year = {2016},
month = {4}
}

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