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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Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing
John R. Stephen,John R. Stephen,George A. Kowalchuk,Mary Ann Bruns,Mary Ann Bruns,Allison E. McCaig,Carol J. Phillips,T. Martin Embley,James I. Prosser +8 more
TL;DR: The present study demonstrates the value of DGGE and probing for rapid analysis of natural soil communities of β-subgroup proteobacterial ammonia oxidizers, indicates significant pH-associated differences in Nitrosospira populations, and suggests that NitrosOSPira cluster 2 may be of significance for ammonia-oxidizing activity in acid soils.
Journal ArticleDOI
Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America
TL;DR: Within the large group of African sinorhizobia, similar symbiotic gene types were found in different chromosomal backgrounds, suggesting that transfer of symbiotic genes has occurred across species boundaries, and the factors that appear to have influenced the evolution of rhizobial symbiosis genes vary in importance at different taxonomic levels.
Journal ArticleDOI
Frondibacter mangrovi sp. nov., a member of the family Flavobacteriaceae isolated from seawater by in situ cultivation, and emended description of Frondibacter aureus.
TL;DR: A Gram-stain-negative, rod-shaped, non-motile, strictly aerobic, chemoheterotrophic, light-yellow-pigmented bacterium, designated strain 02OK1/10-76T, was isolated from a mangrove estuary in Japan by use of an in situ cultivation technique.
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Photosynthetic bradyrhizobia are natural endophytes of the African wild rice Oryza breviligulata.
Clémence Chaintreuil,Eric Giraud,Yves Prin,Jean Lorquin,Amadou Moustapha Bâ,Monique Gillis,Philippe de Lajudie,Bernard Dreyfus +7 more
TL;DR: The discovery that photosynthetic Bradyrhizobium strains, which are usually known to induce nitrogen-fixing nodules on stems of the legume Aeschynomene, are also natural true endophytes of the primitive rice O. breviligulatacould significantly enhance cultivated rice production is found.
Journal ArticleDOI
Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA
TL;DR: A bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging to the so-called crown of eukaryote evolution suggests that animals, true fungi, and choanoflagellates share a common origin and that the animals no longer appear as a monophyletic grouping in most distance trees.
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.