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
Citations
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Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.
TL;DR: The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny was evaluated, and the utility of the currently used optimization principles in phylogenetic construction is questioned.
Journal ArticleDOI
Cell Death Mediated by the N-Terminal Domains of a Unique and Highly Conserved Class of NB-LRR Protein
TL;DR: It is reported that, in contrast to CC-NB-LRR proteins, the CCR domains of both NRG1- and ADR1-like proteins are sufficient for the induction of defense responses, and that this activity appears to be SGT1-independent.
Journal ArticleDOI
Definition of supertypes for HLA molecules using clustering of specificity matrices.
Ole Lund,Morten Nielsen,Can Keşmir,Can Keşmir,Anders Petersen,Claus Lundegaard,Peder Worning,Christina Sylvester-Hvid,Kasper Lamberth,Gustav Røder,Sune Justesen,Søren Buus,Søren Brunak +12 more
TL;DR: In this article, the functional relationship between all known HLA molecules with known specificities was studied in a uniform and automated way, and a method for clustering sequence motifs was developed.
Journal ArticleDOI
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum).
Elizabeth Pierce,Gary Xie,Gary Xie,Ravi D. Barabote,Ravi D. Barabote,Elizabeth Saunders,Elizabeth Saunders,Cliff Han,Cliff Han,John C. Detter,John C. Detter,Paul D. Richardson,Paul D. Richardson,Thomas Brettin,Thomas Brettin,Amaresh Das,Lars G. Ljungdahl,Stephen W. Ragsdale +17 more
TL;DR: This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration.
Journal ArticleDOI
Plastidial thioredoxin z interacts with two fructokinase-like proteins in a thiol-dependent manner: evidence for an essential role in chloroplast development in Arabidopsis and Nicotiana benthamiana.
Borjana Arsova,Ursula Hoja,Matthias Wimmelbacher,Eva Greiner,Suayib Üstün,Michael Melzer,Kerstin Petersen,Wolfgang Lein,Frederik Börnke +8 more
TL;DR: It is shown that the FLN2 redox state changes in vivo during light/dark transitions and that this change is mediated by TRX z, which strongly suggest an important role for TRXZ and both FLNs in the regulation of PEP-dependent transcription in chloroplasts.
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.