Molecular Biology and Evolution, Vol 4, 406-425, Copyright © 1987 by Society for Molecular Biology and Evolution
N Saitou and M Nei
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.
ORIGINAL ARTICLE
The neighbor-joining method: a new method for reconstructing phylogenetic trees
Center for Demographic and Population Genetics, University of Texas Health Science Center, Houston 77225.
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K. Duangmal, A. Thamchaipenet, A. Matsumoto, and Y. Takahashi Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1487 - 1491. [Abstract] [Full Text] [PDF]
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J. Li, G.-Z. Zhao, S. Qin, W.-Y. Zhu, L.-H. Xu, and W.-J. Li Streptomyces sedi sp. nov., isolated from surface-sterilized roots of Sedum sp. Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1492 - 1496. [Abstract] [Full Text] [PDF]
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M. Otoguro, T. Tamura, K.-i. Suzuki, and M. Hayakawa Saccharothrix violaceirubra sp. nov., isolated from soil and plant litter Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1504 - 1507. [Abstract] [Full Text] [PDF]
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E. Tortoli, S. Baruzzo, Y. Heijdra, H.-P. Klenk, S. Lauria, A. Mariottini, and J. van Ingen Mycobacterium insubricum sp. nov. Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1518 - 1523. [Abstract] [Full Text] [PDF]
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H. An, L. Zhang, Y. Tang, X. Luo, T. Sun, Y. Li, Y. Wang, J. Dai, and C. Fang Skermanella xinjiangensis sp. nov., isolated from the desert of Xinjiang, China Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1531 - 1534. [Abstract] [Full Text] [PDF]
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K. Watanabe, H. Makino, M. Sasamoto, Y. Kudo, J. Fujimoto, and S. Demberel Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1535 - 1540. [Abstract] [Full Text] [PDF]
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S. W. Park, S. M. Kim, S. T. Park, and Y. M. Kim Tsukamurella carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1541 - 1544. [Abstract] [Full Text] [PDF]
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P. Kampfer, N. Lodders, I. Warfolomeow, and H.-J. Busse Tessaracoccus lubricantis sp. nov., isolated from a metalworking fluid Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1545 - 1549. [Abstract] [Full Text] [PDF]
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G. Peter, J. Tornai-Lehoczki, and D. Dlauchy Trichomonascus apis sp. nov., a heterothallic yeast species from honeycomb Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1550 - 1554. [Abstract] [Full Text] [PDF]
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 S. Blomqvist, C. Savolainen-Kopra, A. Paananen, T. Hovi, and M. Roivainen Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses J. Gen. Virol., June 1, 2009; 90(6): 1371 - 1381. [Abstract] [Full Text] [PDF]
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T. Utsumi, M. I. Lusida, Y. Yano, V. E. Nugrahaputra, M. Amin, Juniastuti, Soetjipto, Y. Hayashi, and H. Hotta Complete Genome Sequence and Phylogenetic Relatedness of Hepatitis B Virus Isolates in Papua, Indonesia J. Clin. Microbiol., June 1, 2009; 47(6): 1842 - 1847. [Abstract] [Full Text] [PDF]
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 J. P. Palavicini, M. A. O'connell, and J. J.C. Rosenthal An extra double-stranded RNA binding domain confers high activity to a squid RNA editing enzyme RNA, June 1, 2009; 15(6): 1208 - 1218. [Abstract] [Full Text] [PDF]
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Y. Han, J. M. Burnette III, and S. R. Wessler TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences Nucleic Acids Res., June 1, 2009; 37(11): e78 - e78. [Abstract] [Full Text] [PDF]
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P. K. Wust, M. A. Horn, G. Henderson, P. H. Janssen, B. H. A. Rehm, and H. L. Drake Gut-Associated Denitrification and In Vivo Emission of Nitrous Oxide by the Earthworm Families Megascolecidae and Lumbricidae in New Zealand Appl. Envir. Microbiol., June 1, 2009; 75(11): 3430 - 3436. [Abstract] [Full Text] [PDF]
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H. Shinmoto, K. Taniguchi, T. Ikawa, K. Kawai, and S.-i. Oshima Phenotypic Diversity of Infectious Red Sea Bream Iridovirus Isolates from Cultured Fish in Japan Appl. Envir. Microbiol., June 1, 2009; 75(11): 3535 - 3541. [Abstract] [Full Text] [PDF]
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S. H. Thomas, E. Padilla-Crespo, P. M. Jardine, R. A. Sanford, and F. E. Loffler Diversity and Distribution of Anaeromyxobacter Strains in a Uranium-Contaminated Subsurface Environment with a Nonuniform Groundwater Flow Appl. Envir. Microbiol., June 1, 2009; 75(11): 3679 - 3687. [Abstract] [Full Text] [PDF]
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H. Teramoto, M. Inui, and H. Yukawa Regulation of Expression of Genes Involved in Quinate and Shikimate Utilization in Corynebacterium glutamicum Appl. Envir. Microbiol., June 1, 2009; 75(11): 3461 - 3468. [Abstract] [Full Text] [PDF]
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 C.-H. Tzeng, C.-S. Chen, P.-C. Tang, and T.-S. Chiu Microsatellite and mitochondrial haplotype differentiation in blue mackerel (Scomber australasicus) from the western North Pacific ICES J. Mar. Sci., June 1, 2009; 66(5): 816 - 825. [Abstract] [Full Text] [PDF]
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 Y. Kazama, M. T. Fujiwara, A. Koizumi, K. Nishihara, R. Nishiyama, E. Kifune, T. Abe, and S. Kawano A SUPERMAN-like Gene is Exclusively Expressed in Female Flowers of the Dioecious Plant Silene latifolia Plant Cell Physiol., June 1, 2009; 50(6): 1127 - 1141. [Abstract] [Full Text] [PDF]
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R. Bao and M. Friedrich Molecular Evolution of the Drosophila Retinome: Exceptional Gene Gain in the Higher Diptera Mol. Biol. Evol., June 1, 2009; 26(6): 1273 - 1287. [Abstract] [Full Text] [PDF]
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 H. Chen, S. Kshirsagar, I. Jensen, K. Lau, R. Covarrubias, S. F. Schluter, and J. J. Marchalonis Characterization of arrangement and expression of the T cell receptor {gamma} locus in the sandbar shark PNAS, May 26, 2009; 106(21): 8591 - 8596. [Abstract] [Full Text] [PDF]
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X. Hu, G. Van der Auwera, S. Timmery, L. Zhu, and J. Mahillon Distribution, Diversity, and Potential Mobility of Extrachromosomal Elements Related to the Bacillus anthracis pXO1 and pXO2 Virulence Plasmids Appl. Envir. Microbiol., May 15, 2009; 75(10): 3016 - 3028. [Abstract] [Full Text] [PDF]
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L. F. Dong, C. J. Smith, S. Papaspyrou, A. Stott, A. M. Osborn, and D. B. Nedwell Changes in Benthic Denitrification, Nitrate Ammonification, and Anammox Process Rates and Nitrate and Nitrite Reductase Gene Abundances along an Estuarine Nutrient Gradient (the Colne Estuary, United Kingdom) Appl. Envir. Microbiol., May 15, 2009; 75(10): 3171 - 3179. [Abstract] [Full Text] [PDF]
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C. C. P. Hardoim, R. Costa, F. V. Araujo, E. Hajdu, R. Peixoto, U. Lins, A. S. Rosado, and J. D. van Elsas Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters Appl. Envir. Microbiol., May 15, 2009; 75(10): 3331 - 3343. [Abstract] [Full Text] [PDF]
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S. N. Lindner, S. Knebel, H. Wesseling, S. M. Schoberth, and V. F. Wendisch Exopolyphosphatases PPX1 and PPX2 from Corynebacterium glutamicum Appl. Envir. Microbiol., May 15, 2009; 75(10): 3161 - 3170. [Abstract] [Full Text] [PDF]
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F. S. Boretti, A. Perreten, M. L. Meli, V. Cattori, B. Willi, N. Wengi, S. Hornok, H. Honegger, D. Hegglin, R. Woelfel, et al. Molecular Investigations of Rickettsia helvetica Infection in Dogs, Foxes, Humans, and Ixodes Ticks Appl. Envir. Microbiol., May 15, 2009; 75(10): 3230 - 3237. [Abstract] [Full Text] [PDF]
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S. Mieszkin, J.-P. Furet, G. Corthier, and M. Gourmelon Estimation of Pig Fecal Contamination in a River Catchment by Real-Time PCR Using Two Pig-Specific Bacteroidales 16S rRNA Genetic Markers Appl. Envir. Microbiol., May 15, 2009; 75(10): 3045 - 3054. [Abstract] [Full Text] [PDF]
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 N. P. Tavakoli, H. Wang, M. Dupuis, R. Hull, G. D. Ebel, E. J. Gilmore, and P. L. Faust Fatal Case of Deer Tick Virus Encephalitis N. Engl. J. Med., May 14, 2009; 360(20): 2099 - 2107. [Abstract] [Full Text] [PDF]
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