Document Detail


Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.
MedLine Citation:
PMID:  22399455     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."
Authors:
Pere Puigbò; Yuri I Wolf; Eugene V Koonin
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, N.I.H., Intramural    
Journal Detail:
Title:  Methods in molecular biology (Clifton, N.J.)     Volume:  856     ISSN:  1940-6029     ISO Abbreviation:  Methods Mol. Biol.     Publication Date:  2012  
Date Detail:
Created Date:  2012-03-08     Completed Date:  2012-07-03     Revised Date:  2013-12-08    
Medline Journal Info:
Nlm Unique ID:  9214969     Medline TA:  Methods Mol Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  53-79     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Archaea / genetics*
Bacteria / genetics*
Gene Transfer, Horizontal / genetics
Genomics / methods*
Phylogeny*
Grant Support
ID/Acronym/Agency:
Z99 LM999999/LM/NLM NIH HHS
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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