Journal ArticleDOI
MEGA2 : Molecular evolutionary genetics analysis software
TLDR
MEGA2 vastly extends the capabilities of MEGA version 1 by facilitating analyses of large datasets, enabling creation and analyses of groups of sequences, and expanding the repertoire of statistical methods for molecular evolutionary studies.Abstract:
Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: http://www.megasoftware.net.read more
Citations
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Bradyrhizobium betae sp. nov., isolated from roots of Beta vulgaris affected by tumour-like deformations.
Raúl Rivas,Anne Willems,José Luis Palomo,Pablo García-Benavides,Pedro F. Mateos,Eustoquio Martínez-Molina,Monique Gillis,Encarna Velázquez +7 more
TL;DR: DNA-DNA hybridization confirmed that several endophytic slow-growing bacterial strains isolated represent a novel species of the genus Bradyrhizobium, for which the nameBradyrhuzobium betae sp.
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DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected Salmonella enterica Serotypes
Sharinne Sukhnanand,Samuel D. Alcaine,Lorin D. Warnick,Wan-Lin Su,Jessica Hof,Mary Pat J. Craver,Patrick L. McDonough,Kathryn J. Boor,Martin Wiedmann +8 more
TL;DR: Three-gene sequence typing supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages and shows that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages.
Journal ArticleDOI
Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for trichoviruses, capilloviruses, and foveaviruses.
Xavier Foissac,Laurence Svanella-Dumas,Pascal Gentit,Marie-Josée Dulucq,Armelle Marais,Thierry Candresse +5 more
TL;DR: A polyvalent nested reverse transcription-polymerase chain reaction (RT-PCR) test using degenerate primers containing inosine (polyvalent degenerate oligonucleotides [PDO]) was developed for filamentous fruit tree viruses belonging to the genera Trichovirus, Capillovirus and Foveavirus, demonstrating the polyvalence of the test.
Journal ArticleDOI
Genetic Structure of Hmong-Mien Speaking Populations in East Asia as Revealed by mtDNA Lineages
Bo Wen,Hui Li,Song Gao,Xianyun Mao,Gao Yang,Feng Li,Feng Zhang,Yungang He,Yongli Dong,Youjun Zhang,Wenju Huang,Jianzhong Jin,Chunjie Xiao,Daru Lu,Ranajit Chakraborty,Bing Su,Ranjan Deka,Li Jin +17 more
TL;DR: The results indicate that the Hmong populations had experienced more contact with the northern East Asians, a finding consistent with historical evidence.
Journal ArticleDOI
Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China.
Yi-Guang Chen,Xiao-Long Cui,Rüdiger Pukall,Hui-ming Li,Ya-ling Yang,Li-Hua Xu,Mengliang Wen,Qian Peng,Cheng-Lin Jiang +8 more
TL;DR: Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that strain YIM Y15(T) was a member of the genus Salinicoccus, and together with the phenotypic differences, these results supported the proposal of a novel species of this genus.
References
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Book
Molecular Evolution and Phylogenetics
Masatoshi Nei,Sudhir Kumar +1 more
TL;DR: This chapter discusses the molecular basis of evolution, the evolution of organisms based on the fossil record, and the implications of these events for phylogenetic inference.
Journal ArticleDOI
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
TL;DR: In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included.
Book
Molecular Evolution: A Phylogenetic Approach
TL;DR: The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of molecular phylogenetics as mentioned in this paper.
Journal ArticleDOI
Phylogenetic test of the molecular clock and linearized trees.
TL;DR: To estimate approximate divergence times of species or species groups with molecular data, a method of constructing a linearized tree under the assumption of a molecular clock is developed and used to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
Journal ArticleDOI
Molecular Evolution — A Phylogenetic Approach.
TL;DR: The authors set themselves the tasks of showing how evolutionary information is written into gene sequences and describing the methods by which such information can be recovered and succeed, providing a wealth of examples and setting many of them in a historical perspective.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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