Each of us can make a difference if we step up and try our best / Becoming Planet Citizens

File:Tree of Life nmicrobiol201648-f1 via Nature.jpg

From Green Policy
(Difference between revisions)
Jump to: navigation, search
Line 13: Line 13:
 
''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 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. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts.''
 
''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 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. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts.''
  
Whole genome reconstruction was first accomplished in 1995, 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 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 genomes14. New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes. These genome-based approaches provide information about metabolic potential and a variety of phylogenetically informative sequences that can be used to classify organisms16. Here, we have constructed a tree of life by making use of genomes from public databases and 1,011 newly reconstructed genomes.
+
Whole genome reconstruction was first accomplished in 1995, 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 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. New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes. These genome-based approaches provide information about metabolic potential and a variety of phylogenetically informative sequences that can be used to classify organisms16. Here, we have constructed a tree of life by making use of genomes from public databases and 1,011 newly reconstructed genomes.
  
  

Revision as of 23:14, 10 February 2019

http://www.nature.com/articles/nmicrobiol201648

http://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html


April 2016

http://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html

The tree of life is one of the most important organizing principles in biology. 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 relationships 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 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.

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 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. Furthermore, unusual sequences, including those with unexpected insertions, may be discarded as artefacts.

Whole genome reconstruction was first accomplished in 1995, 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 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. New bioinformatics methods yield complete and near-complete genome sequences, without a reliance on cultivation or reference genomes. These genome-based approaches provide information about metabolic potential and a variety of phylogenetically informative sequences that can be used to classify organisms16. Here, we have constructed a tree of life by making use of genomes from public databases and 1,011 newly reconstructed genomes.

File history

Click on a date/time to view the file as it appeared at that time.

Date/TimeThumbnailDimensionsUserComment
current00:06, 12 April 2016Thumbnail for version as of 00:06, 12 April 2016695 × 833 (98 KB)Siterunner (Talk | contribs)http://www.nature.com/articles/nmicrobiol201648 April 2016 http://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the e...

Personal tools
Namespaces

Variants
Actions
Log in / Create Account
GreenPolicy360
About Our Network
Daily Green Stories
GreenPolicy360 Updates
Navigation
Green Graphics
GreenPolicy Social Media
Going Green
Earthviews
New Visions of Security
Strategic Demands
Countries & Maps
Digital360
GrnPolicy Reviews
Eco-Education
Online Legis Info (U.S.)
Wiki Ballotpedia (U.S.)
Wiki Politics (U.S.)
Wikimedia Platform
Green News/Dailies
Green News Services (En)
Green Zines (En)
Green Lists @Wikipedia
Climate Action Headlines
Climate Litigation Databases
Climate Agreement / INDCs
Climate Misinformation
Wikipedia on Climate
GrnNews Reddit Daily
Fact-Checking News Sites
GreenPolicy360 & Science
Identify Nature's Creatures
Climate Change - NASA
Ecolivia
Tools