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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Structural characterisation of a cyprinid (Cyprinus carpio L.) CRH, CRH-BP and CRH-R1, and the role of these proteins in the acute stress response
Mark O. Huising,Juriaan R. Metz,C. van Schooten,Anja J. Taverne-Thiele,Trudi Hermsen,B.M.L. Verburg-van Kemenade,Gert Flik +6 more
TL;DR: These factors are actively involved in the regulation of acute stress responses in the teleost fish, and via real-time quantitative PCR that expression of hypothalamic CRH and CRH-BP following a 24 h restraint significantly increases, whereas PDCRH-R1 expression decreases, reflecting desensitisation of the PD for hypothalamicCRH output.
Journal ArticleDOI
Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples.
TL;DR: A range of group‐specific PCR primers for studying the prey diversity found in predator stomach contents and scats are developed and their application to studying prey diversity and identity in predator diet is described.
Journal ArticleDOI
Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates
TL;DR: DNA sequences of the nuclear-encoded recombination activating genes from all three major lungfish groups, the Australian Neoceratodis forsteri, the South American Lepidosiren paradoxa and the African lungfish Protopterus dolloi, and the Indonesian coelacanth Latimeria menadoensis are determined.
Journal ArticleDOI
Multilocus Sequence Typing of Intercontinental Bovine Staphylococcus aureus Isolates
Edward M. Smith,Laura E. Green,Graham F. Medley,H. E. Bird,Lawrence K. Fox,Ynte H. Schukken,J. V. Kruze,Andrew J. Bradley,Ruth N. Zadoks,Christopher G. Dowson +9 more
TL;DR: It is demonstrated that MLST is suitable for the differentiation of bovine S. aureus isolates from various sites (milk, teat skin, milking machine unit liners, hands, and bedding) and countries, and that a single clonal group has achieved a widespread distribution and is responsible for the majority of infections.
Journal ArticleDOI
Novel lyssaviruses isolated from bats in Russia.
Alexandr D. Botvinkin,Elena M. Poleschuk,Ivan V. Kuzmin,Tatyana I. Borisova,Suren V. Gazaryan,Pamela A. Yager,Charles E. Rupprecht +6 more
TL;DR: Preliminary antigenic and genetic characterization found that both rabies-related viruses discovered in Russia should be considered as new putative lyssavirus genotypes.
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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