The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TLDR
The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.Abstract:
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.read more
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Book ChapterDOI
Molecular Evolution and Taxonomy of the Cyanobacteria
TL;DR: In the cyanobacteria, the use of molecular methods to study the genotypic relationships is underway, and initial results are promising and may be used to evaluate and revise existing classifications.
Journal ArticleDOI
Rumen Bacterial Community Transition During Adaptation to High-grain Diet
Kiyoshi Tajima,Shozo Arai,Koretsugu Ogata,Takafumi Nagamine,Hiroki Matsui,Mutsumi Nakamura,Rustam Aminov,Yoshimi Benno +7 more
TL;DR: Transitional changes of the ruminal bacterial community structure in cows during the switch from roughage to high-grain diet were monitored by PCR amplification and sequencing of 16S rDNA clone libraries.
Journal ArticleDOI
cDNA cloning and tissue-specific expression of a novel basic helix-loop-helix/PAS factor (Arnt2) with close sequence similarity to the aryl hydrocarbon receptor nuclear translocator (Arnt).
Ken ichiro Hirose,Masanobu Morita,Masatsugu Ema,Junsei Mimura,Hiroshi Hamada,Hideta Fujii,Saijo Yukio,Osamu Gotoh,Kazuhiro Sogawa,Yoshiaki Fujii-Kuriyama +9 more
TL;DR: In this article, the authors isolated mouse cDNA clones (Arnt2) that are highly similar to but distinct from the aryl hydrocarbon receptor (AhR) nuclear translocator (ArNT), and the composite cDNA covered a 2,443-bp sequence consisting of a putative 2,136-bp open reading frame encoding a polypeptide of 712 amino acids.
Journal ArticleDOI
Identification of a Vinyl Reductase Gene for Chlorophyll Synthesis in Arabidopsis thaliana and Implications for the Evolution of Prochlorococcus Species
TL;DR: In this paper, the identification of the gene for 3,8-divinyl protochlorophyllide a 8-vinyl reductase (DVR), which is indispensable for monovinyl chlorophyll synthesis, has been identified.
Journal ArticleDOI
Phylogenetic Analysis of Rumen Bacteria by Comparative Sequence Analysis of Cloned 16S rRNA Genesß
TL;DR: The majority of rDNA sequences analysed in this study represent novel rumen bacteria which have not yet been isolated, and these sequences clustered with members of the genus Clostridia.
References
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Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Book
Principles of numerical taxonomy
Robert R. Sokal,P.H.A. Sneath +1 more
TL;DR: The authors continued the story of psychology with added research and enhanced content from the most dynamic areas of the field, such as cognition, gender and diversity studies, neuroscience and more, while at the same time using the most effective teaching approaches and learning tools.