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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Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile.
TL;DR: Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture.
Journal ArticleDOI
Helicobacter bilis sp. nov., a novel Helicobacter species isolated from bile, livers, and intestines of aged, inbred mice.
James G. Fox,L Yan,Floyd E. Dewhirst,Bruce J. Paster,Brian D. Shames,James C. Murphy,Alison Hayward,J C Belcher,E N Mendes +8 more
TL;DR: Although the organism is associated with multifocal chronic hepatitis, further studies are required to ascertain whether H. bilis is responsible for causing chronic hepatitis and/or hepatocellular tumors in mice.
Journal ArticleDOI
Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria
Anthony D'Onofrio,Jason M. Crawford,Eric J. Stewart,Kathrin Witt,Ekaterina Gavrish,Slava S. Epstein,Jon Clardy,Kim Lewis +7 more
TL;DR: It is shown here that previously uncultured isolates from marine sediment biofilm grow on a Petri dish in the presence of cultured organisms from the same environment.
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Limitations of the evolutionary parsimony method of phylogenetic analysis.
Li Jin,Masatoshi Nei +1 more
TL;DR: The theoretical basis of Lake's evolutionary parsimony method of constructing a phylogenetic tree, which is primarily applied to four DNA sequences, is examined and it is found that when the rates of two transversional changes from a nucleotide are unequal, his invariance property breaks down.
Journal ArticleDOI
Coalescent methods for estimating phylogenetic trees.
TL;DR: Recent models to estimate phylogenetic trees under the multispecies coalescent review shows that species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount.
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.