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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Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest
TL;DR: The high diversity and huge variation detected across time points, sites and hosts implies that the AM fungal types are ecologically distinct and thus may have the potential to influence recruitment and host composition in tropical forests.
Journal ArticleDOI
Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics
TL;DR: It is proposed that mitochondrial tRNAs may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago and designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.
Journal ArticleDOI
Sampling properties of DNA sequence data in phylogenetic analysis.
TL;DR: It was found that blocks of contiguous sites were less likely to lead to the whole-genome tree than samples composed of sites drawn individually from throughout the genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies.
Journal ArticleDOI
Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen.
TL;DR: Strain 130ZT is a capnophilic, osmotolerant succinogen that utilizes a broad range of sugars and accumulates high concentrations of succinic acid, and is proposed that it be classified as a new species, Actinobacillus succ inogenes.
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Gene Loss and Evolutionary Rates Following Whole-Genome Duplication in Teleost Fishes
Frédéric Brunet,Hugues Roest Crollius,Mathilde Paris,Jean-Marc Aury,Patricia Gibert,Olivier Jaillon,Vincent Laudet,Marc Robinson-Rechavi +7 more
TL;DR: By phylogenetic analysis, the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes are determined, showing that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.
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.