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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START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
TL;DR: Structural conservation of the mammalian phosphatidylcholine transfer protein (PCTP) START domain in plants is shown, consistent with a common role in lipid transport and metabolism.
Journal ArticleDOI
Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula
TL;DR: This work examined the genetic continuity of the acorn barnacle Balanus glandula, an abundant member of rocky intertidal communities of the northeastern Pacific Ocean, and compared these genetic patterns to the nearshore oceanography described by trajectories of surface drifters.
Journal ArticleDOI
Analysis of Equid Herpesvirus 1 Strain Variation Reveals a Point Mutation of the DNA Polymerase Strongly Associated with Neuropathogenic versus Nonneuropathogenic Disease Outbreaks
J. Nugent,Ian Birch-Machin,Ken C. Smith,J. A. Mumford,Z. Swann,J. R. Newton,Rory Bowden,G. P. Allen,Nicholas Davis-Poynter +8 more
TL;DR: Variation of a single amino acid of the DNA polymerase is strongly associated with neurological versus nonneurological disease outbreaks and occurs at a highly conserved position for herpesvirus DNA polymerases, suggesting an important functional role.
Journal ArticleDOI
The multilocus sequence typing network: mlst.net
TL;DR: This work provides the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method for identifying clonal complexes within a species and displaying the overall structure of the population.
Journal ArticleDOI
Genome-Wide Analysis of the Cyclin Family in Arabidopsis and Comparative Phylogenetic Analysis of Plant Cyclin-Like Proteins
Guanfang Wang,Hongzhi Kong,Yujin Sun,Xiaohong Zhang,Wei Zhang,Naomi Altman,Claude W. dePamphilis,Hong Ma +7 more
TL;DR: An exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals.
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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