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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Are Human P[14] Rotavirus Strains the Result of Interspecies Transmissions from Sheep or Other Ungulates That Belong to the Mammalian Order Artiodactyla?
Jelle Matthijnssens,Christiaan A. Potgieter,Max Ciarlet,Viviana Parreño,Vito Martella,Krisztián Bányai,Lorena Garaicoechea,Enzo A. Palombo,Luis Novo,Mark Zeller,Serenella Arista,Giuseppe Gerna,Mustafizur Rahman,Mustafizur Rahman,Marc Van Ranst +14 more
TL;DR: The genotype and phylogenetic analyses strongly suggest a common origin for the human P[14] strains and those of the even-toed ungulates belonging to the mammalian order Artiodactyla, with sheep probably playing a key role in the interspecies transmission responsible for the introduction of P[ 14] rotavirus strains into the human population.
Journal ArticleDOI
Nitrogen storage and seasonal nitrogen cycling in Populus: bridging molecular physiology and ecophysiology
TL;DR: This review explores cellular and molecular events implicated in seasonal N cycling in Populus, as well as environmental cues that modulate both the phenology of seasonalN cycling, and the efficiency and proficiency of autumn N resorption.
Journal Article
Comparative Genomics and Evolution of Genes Encoding Bacterial (p)ppGpp Synthetases/Hydrolases (the Rel, RelA and SpoT Proteins)
TL;DR: The distribution pattern of the paralogous RelA and SpoT proteins supports a new model of linear bacterial evolution, which postulates that the gamma subdivision of proteobacteria represents the most recently evolved bacterial lineage.
Journal ArticleDOI
Integrated stress response of vertebrates is regulated by four eIF2α kinases.
TL;DR: The data suggests that the four known eIF2α kinases are sufficient for ISR and that there are no additional eIF 2 α kinases in vertebrates.
Journal ArticleDOI
A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family
TL;DR: The Arabidopsis genome was searched to identify predicted proteins containing armadillo (ARM) repeats, a motif known to mediate protein-protein interactions in a number of different animal proteins, and these proteins represented the largest class ofArabidopsis ARM repeat proteins, which were found to be functional E3 ubiquitin ligases.
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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