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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Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth
Ming Li,Guangyan Xiong,Rui Li,Jiajun Cui,Ding Tang,Baocai Zhang,Markus Pauly,Zhukuan Cheng,Yihua Zhou +8 more
TL;DR: In this paper, a narrow leaf and dwarf1 (nd1) rice mutant that shows significant reduction in plant growth due to retarded cell division was characterized. But the results were limited to two specific tissues, culms and root tips, which were used to investigate the specific wall defects.
Journal ArticleDOI
Rhizosphere bacterial communities associated with disease suppressiveness stages of take‐all decline in wheat monoculture
Hervé Sanguin,Hervé Sanguin,Alain Sarniguet,Kévin Gazengel,Yvan Moënne-Loccoz,Yvan Moënne-Loccoz,Geneviève L. Grundmann,Geneviève L. Grundmann +7 more
TL;DR: In conclusion, take-all decline correlated with multiple changes in rhizobacterial community composition, far beyond the sole case of pseudomonads, as well as with a broader range of taxa.
Journal ArticleDOI
Hyperinvasive Neonatal Group B Streptococcus Has Arisen from a Bovine Ancestor
Naiel Bisharat,Derrick W. Crook,James A. Leigh,Rosalind M. Harding,Phil N. Ward,Tracey J. Coffey,Martin C. J. Maiden,Tim E. A. Peto,Nicola Jones +8 more
TL;DR: Split decomposition analysis revealed that the human isolate ST-17 complex, the major hyperinvasive neonatal clone, has recently arisen from a bovine lineage.
Journal ArticleDOI
Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana.
TL;DR: The genetic variation at two types of chloroplast DNA markers, polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) and microsatellites, was assessed in 26 natural hazel populations distributed across the range of C. avellana and seems to indicate a history of past hybridization among the European Corylus species and cultivars.
Journal ArticleDOI
Spread of Hepatitis C Virus among European Injection Drug Users Infected with HIV: A Phylogenetic Analysis
Liselotte van Asten,Inge Verhaest,Saida Lamzira,Ildefonso Hernández-Aguado,Robert Zangerle,Faroudy Boufassa,Giovanni Rezza,Barbara Broers,J. Roy Robertson,Raymond P. Brettle,Jim McMenamin,Maria Prins,Alexandra Cochrane,Peter Simmonds,Roel A. Coutinho +14 more
TL;DR: HCV exchange between European IDU populations has occurred on a large scale, and, overall, country-specific clustering for HCV was less than that shown for HIV.
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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