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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Anaerobic microbial dehalogenation.
Hauke Smidt,Willem M. de Vos +1 more
TL;DR: This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating--or completely mineralizing--halogenated hydrocarbons by fermentative, oxidative, or reductive pathways.
Journal ArticleDOI
Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.
Abdourahmane Sy,Eric Giraud,Philippe Jourand,Nelly Garcia,Anne Willems,Philippe de Lajudie,Yves Prin,Marc Neyra,Monique Gillis,Catherine Boivin-Masson,Bernard Dreyfus +10 more
TL;DR: The discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus is reported, which is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer.
Journal ArticleDOI
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
TL;DR: This work has constructed robust phylogenies for fungi based on whole genome analysis that provide strong support for the classification of phyla, sub-phyla, classes and orders.
Journal ArticleDOI
TreeFam: a curated database of phylogenetic trees of animal gene families
Heng Li,Avril Coghlan,Jue Ruan,Lachlan J. M. Coin,Jean-Karim Hériché,Lara Osmotherly,Ruiqiang Li,Tao Liu,Zhang Zhang,Lars Bolund,Gane Ka-Shu Wong,Wei-Mou Zheng,Paramvir S. Dehal,Jun Wang,Richard Durbin +14 more
TL;DR: Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families, which represent over 128 000 genes from nine fully sequenced animal genomes and over 45’000 other animal proteins from UniProt.
Journal ArticleDOI
Comparative genomics provides evidence for an ancient genome duplication event in fish.
TL;DR: It is estimated that the unlinked duplicated zebrafish genes are between 300 and 450 Myr, which means that genome duplication could have provided the genetic raw material for teleost radiation and the loss of different duplicates in different populations may have promoted speciation in ancient teleost populations.
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.