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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Three proteins, MBNL, MBLL and MBXL, co-localize in vivo with nuclear foci of expanded-repeat transcripts in DM1 and DM2 cells
Majid Fardaei,Mark T. Rogers,Helena M. Thorpe,Kenneth Larkin,Marion G. Hamshere,Peter S. Harper,J. David Brook +6 more
TL;DR: Green fluorescent protein-tagged versions of MBNL, MBLL and MBXL co-localize with nuclear foci in DM1 and DM2 cells, suggesting that all three proteins may play a role in DM pathophysiology.
Journal ArticleDOI
Co-evolution of proteins with their interaction partners.
TL;DR: PGK, an enzyme that forms its active site between its two domains, is used to develop a standard for measuring the co-evolution of interacting proteins, and the correlation coefficient for the trees of the two domains of PGK is calculated, which establishes an upper bound for theCo-Evolution of a protein domain with its binding partner.
Journal ArticleDOI
Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival.
Chris Greening,Ambarish Biswas,Carlo R Carere,Colin J. Jackson,Matthew C. Taylor,Matthew B. Stott,Gregory M. Cook,Gregory M. Cook,Sergio E. Morales +8 more
TL;DR: It is predicted that this hydrogenase diversity supports H2-based respiration, fermentation and carbon fixation processes in both oxic and anoxic environments, in addition to various H1N1-sensing, electron-bifurcation and energy-conversion mechanisms.
Journal ArticleDOI
Molecular and Functional Characterization of a Novel Mouse Transient Receptor Potential Protein Homologue TRP7 Ca2+-PERMEABLE CATION CHANNEL THAT IS CONSTITUTIVELY ACTIVATED AND ENHANCED BY STIMULATION OF G PROTEIN-COUPLED RECEPTOR
Takaharu Okada,Ryuji Inoue,Kazuto Yamazaki,Akito Maeda,Tomohiro Kurosaki,Tohru Yamakuni,Isao Tanaka,Shunichi Shimizu,Kazuhiro Ikenaka,Keiji Imoto,Yasuo Mori +10 more
TL;DR: These findings reveal an interesting correspondence of TRP7 to the background and receptor stimulation-induced cation currents in various native systems and suggest that the TRP6 channel is a new member of diacylglycerol-activated cation channels.
Journal ArticleDOI
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Richard Desper,Olivier Gascuel +1 more
TL;DR: A greedy approach to minimum evolution which produces a starting topology in O(n(2)) time and yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy.
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.