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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Reconstructing the diversification of subtilisins in the pathogenic fungus Metarhizium anisopliae.
TL;DR: While overall divergence of subtilisins followed neutral expectations, amino acids involved in catalysis were under strong selective constraint, homology modeling predicted differences between the Pr1's in their secondary substrate specificities, adsorption properties to cuticle and alkaline stability, indicative of functional differences.
Journal ArticleDOI
Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes.
Wusirika Ramakrishna,Jorge Dubcovsky,Yong-Jin Park,Carlos S. Busso,John Emberton,Phillip SanMiguel,Jeffrey L. Bennetzen +6 more
TL;DR: Orthologous regions in barley, rice, sorghum, and wheat were studied by bacterial artificial chromosome sequence analysis, and general microcolinearity was observed for the four shared genes, but nonsynonymous substitution rates show significant variations between genes 4a and 4b.
Journal ArticleDOI
Delineating a Ca2+ binding pocket within the venus flytrap module of the human calcium-sensing receptor.
Caroline Silve,Christophe Petrel,Christine Leroy,Henri Bruel,Eric Mallet,Didier Rognan,Martial Ruat +6 more
TL;DR: A homology model of the human CaSR VFTM is developed and critical amino acids delineating a Ca2+ binding pocket predicted to be adjacent to, but distinct from, a cavity reminiscent of the binding site described for amino acids in mGluRs, GABA-B receptor, and GPRC6a are identified.
Journal ArticleDOI
Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
TL;DR: Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny and are tested in a wider context than before.
Journal ArticleDOI
Oseltamivir- and amantadine-resistant influenza viruses A (H1N1).
Peter K.C. Cheng,Tommy W.C. Leung,Eric C.M. Ho,Peter C.K. Leung,Anita Y.Y. Ng,Mary Y.Y. Lai,Wilina Lim +6 more
TL;DR: This work detected amantadine and oseltamivir resistance among A/Hong Kong/2652/2006-like viruses (H1N1), caused by genetic reassortment or spontaneous mutation.
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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