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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Biodegradation of ether pollutants by Pseudonocardia sp. strain ENV478
Simon Vainberg,Kevin McClay,Hisako Masuda,Duane Root,Charles W. Condee,Gerben J. Zylstra,Robert J. Steffan +6 more
TL;DR: The results suggest that the inability of strain ENV478 and possibly other THF-degrading bacteria to grow on 1, 4-dioxane is related to their inability to efficiently metabolize the 1,4-doxane degradation product 2HEAA but that strain ENv478 may nonetheless be useful as a biocatalyst for remediating 1,3-dioxidant-contaminated aquifers.
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The molecular evolution of the interleukin-1 family of cytokines; IL-18 in teleost fish
TL;DR: Elucidation of the human, the mouse and the Fugu rubripes (pufferfish) genome enables a more comprehensive overview of this cytokine family and its receptors in several vertebrate classes and supports the concept of an ancestral role of this family, possibly in the brain.
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Enhanced discrimination of African swine fever virus isolates through nucleotide sequencing of the p54, p72, and pB602L (CVR) genes
Carmina Gallardo,Dufton M. Mwaengo,Joseph M. Macharia,Marisa Arias,Evans A. Taracha,Alejandro Soler,Edward Okoth,Elena Martín,Jackline Kasiti,Richard P. Bishop +9 more
TL;DR: In this paper, p54-gene from 67 European, American, and West and East African Swine Fever virus (ASFV) isolates revealed that West African and European ASFV isolates classified within the predominant Genotype I according to partial sequencing of p72 were discriminated into four major sub-types on the basis of their p54 sequences.
Journal ArticleDOI
Evolution of the vertebrate ABC gene family: analysis of gene birth and death.
Tarmo Annilo,Zhang-qun Chen,Sergey Shulenin,Julie Costantino,Lauren Thomas,Hong Lou,Stefan Stefanov,Michael Dean +7 more
TL;DR: This work identified ABC proteins from the sea squirt, zebrafish, and chicken and, using phylogenetic analysis, identified those genes with a one-to-one orthologous relationship to human ABC proteins.
Journal ArticleDOI
Evidence for balancing selection from nucleotide sequence analyses of human G6PD.
Brian C. Verrelli,John H. McDonald,George Argyropoulos,Giovanni Destro-Bisol,Alain Froment,Anthi Drousiotou,Gérard Lefranc,Ahmed Noureddine Helal,Jacques Loiselet,Sarah A. Tishkoff +9 more
TL;DR: It is demonstrated that nucleotide sequence analyses can reveal signatures of both historical and recent selection in the genome and may elucidate the impact that infectious disease has had during human evolution.
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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