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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Journal ArticleDOI
Genetic and Neutralization Properties of Subtype C Human Immunodeficiency Virus Type 1 Molecular env Clones from Acute and Early Heterosexually Acquired Infections in Southern Africa
Ming Li,Jesus F. Salazar-Gonzalez,Cynthia A. Derdeyn,Lynn Morris,Carolyn Williamson,James E. Robinson,Julie M. Decker,Yingying Li,Maria G. Salazar,Victoria R. Polonis,Koleka Mlisana,Salim S. Abdool Karim,Kunxue Hong,Kelli Greene,Miroslawa Bilska,Jintao Zhou,Susan Allen,Elwyn N. Chomba,Joseph Mulenga,Cheswa Vwalika,Feng Gao,Ming Zhang,Bette T. Korber,Eric Hunter,Beatrice H. Hahn,David C. Montefiori +25 more
TL;DR: Key genetic and antigenic properties of subtype C HIV-1 that might impact the design and testing of candidate vaccines are illustrated.
Journal ArticleDOI
Visualizing spatial population structure with estimated effective migration surfaces.
TL;DR: This work uses a population genetic model to relate effective migration rates to expected genetic dissimilarities, and illustrates its potential and limitations using simulations and data from elephant, human and Arabidopsis thaliana populations.
Journal ArticleDOI
Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota
TL;DR: The Peninsular Desert can no longer be considered a subset of the Sonoran Desert-it is a separate regional desert with its own unique evolutionary history, ecological arena, and conservation value.
Journal ArticleDOI
Molecular phylogeny of Acremonium and its taxonomic implications.
TL;DR: Maximum parsimony and neighborjoin- ing analyses were performed using partial sequences of the nuclear small subunit ribosomal DNA (18S rDNA) to eliminate some of the heterogeneity within Acremonium while also emphasizing the unique biological, morpholog- ical, and ecological characteristics of the grass.
Journal ArticleDOI
Structure of the 16 S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis
TL;DR: The thermophilic cyanobacterial strain, PCC7518, originally identified as ‘Mastigocladus laminosus HTF’ does not show branchings or heterocysts, and is likely to belong to the cluster of heterocystous species and has most probably lost the ability to produceheterocysts by mutation.
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.