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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Reconstructing Native American population history
David Reich,David Reich,Nick Patterson,Desmond Campbell,Desmond Campbell,Arti Tandon,Arti Tandon,Stéphane Mazières,Stéphane Mazières,Nicolas Ray,María Victoria Parra,María Victoria Parra,Winston Rojas,Winston Rojas,Constanza Duque,Constanza Duque,Natalia Mesa,Natalia Mesa,Luis F. García,Omar Triana,Silvia Blair,Amanda Maestre,Juan Carlos Dib,Claudio M. Bravi,Claudio M. Bravi,Graciela Bailliet,Daniel Corach,Tábita Hünemeier,Tábita Hünemeier,Maria Cátira Bortolini,Francisco M. Salzano,Maria Luiza Petzl-Erler,Victor Acuña-Alonzo,Carlos A. Aguilar-Salinas,Samuel Canizales-Quinteros,Teresa Tusié-Luna,Laura Riba,Maricela Rodríguez-Cruz,Mardia López-Alarcón,Ramón Mauricio Coral-Vázquez,Thelma Canto-Cetina,Irma Silva-Zolezzi,Juan Carlos Fernández-López,Alejandra V. Contreras,Gerardo Jimenez-Sanchez,María José Gómez-Vázquez,Julio Molina,Angel Carracedo,Antonio Salas,Carla Gallo,Giovanni Poletti,David B. Witonsky,Gorka Alkorta-Aranburu,Rem I. Sukernik,Ludmila P. Osipova,Sardana A. Fedorova,René Vasquez,Mercedes Villena,Claudia Moreau,Ramiro Barrantes,David L. Pauls,Laurent Excoffier,Laurent Excoffier,Gabriel Bedoya,Francisco Rothhammer,Jean-Michel Dugoujon,Georges Larrouy,William Klitz,Damian Labuda,Judith R. Kidd,Kenneth K. Kidd,Anna Di Rienzo,Nelson B. Freimer,Alkes L. Price,Alkes L. Price,Andres Ruiz-Linares +75 more
TL;DR: It is shown that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America.
Journal ArticleDOI
A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks
Andrew S. Greenberg,D Avila,Marianne K. Hughes,Austin L. Hughes,E C McKinney,Martin F. Flajnik +5 more
TL;DR: The isolation of a new member of the immunoglobulin superfamily from the nurse shark, Ginglymostoma cirratum, is reported, which contains one variable and five constant domains and is found as a dimer in serum.
Journal ArticleDOI
Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.
TL;DR: Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus Sphingomonas can be divided into four clusters.
Journal ArticleDOI
Structural and Evolutionary Relationships among Protein Tyrosine Phosphatase Domains
Jannik N. Andersen,Ole Hartvig Mortensen,Günther H.J. Peters,Paul G. Drake,Lars Fogh Iversen,Ole Hvilsted Olsen,Peter Gildsig Jansen,Henrik Sune Andersen,Nicholas K. Tonks,Niels Møller +9 more
TL;DR: A comparative analysis of the structural relationships among vertebrate PTP domains is presented and a comprehensive resource for sequence analysis of phosphotyrosine-specific PTPs is provided.
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Kalign – an accurate and fast multiple sequence alignment algorithm
TL;DR: Kalign, a method employing the Wu-Manber string-matching algorithm, is developed to improve both the accuracy and speed of multiple sequence alignment and is especially well suited for the increasingly important task of aligning large numbers of sequences.
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.