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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Identification in situ and phylogeny of uncultured bacterial endosymbionts
TL;DR: The phylogenetic position of H. obtusa in the α group of Proteobacteria was determined by 16S rRNA sequence analysis and the sequences were used to design species- as well as genus-specific rRNA hybridization probes, which enabled us to detect and differentiate individual cells of the endosymbionts in situ.
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Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data
Sinara Artico,Sarah Muniz Nardeli,Osmundo Brilhante,Maria Fatima Grossi-de-Sa,Marcio Alves-Ferreira +4 more
TL;DR: This evaluation recommends the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs to enable more accurate and reliablenormalization of qPCR results for gene expression studies in this important crop.
Journal ArticleDOI
Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications
TL;DR: Although the inactivation of the hominoid Uox gene was caused by independent nonsense or frameshift mutations, the gene has taken a two-step deterioration process, first in the promoter and second in the coding region during primate evolution.
Journal ArticleDOI
Loss-of-function mutations in a human gene related to Chlamydomonas reinhardtii dynein IC78 result in primary ciliary dyskinesia.
Gaëlle Pennarun,Estelle Escudier,Catherine Chapelin,Anne-Marie Bridoux,Valère Cacheux,Gilles Roger,Annick Clement,Michel Goossens,Serge Amselem,Bénédicte Duriez +9 more
TL;DR: Data reveal the critical role of DNAI1 in the development of human axonemal structures and open up new means for identification of additional genes involved in related developmental defects.
Journal ArticleDOI
Genetic relationship of populations in China
Jiayou Chu,Wei Huang,S. Q. Kuang,J. M. Wang,Junjie Xu,Z. T. Chu,Zhaoyong Yang,K. Q. Lin,P. Li,Min Wu,Z. C. Geng,C. C. Tan,R. F. Du,Li Jin,Li Jin +14 more
TL;DR: Genetic evidence does not support an independent origin of Homo sapiens in China, and it is more likely that ancestors of the populations currently residing in East Asia entered from Southeast Asia.
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.