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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Desulfonatronum Thiodismutans sp. nov., a Novel Alkaliphilic, Sulfate-reducing Bacterium Capable of Lithoautotrophic Growth
Elena V. Pikuta,Richard B. Hoover,Asim K. Bej,Damien Marsic,William B. Whitman,David Cleland,Paul Krader +6 more
TL;DR: The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon and is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline.
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Use of Highly Variable Intergenic Spacer Sequences for Multispacer Typing of Rickettsia conorii Strains
TL;DR: This study supports the usefulness of MST for strain genotyping and suggests this tool may be useful for tracing a strain and identifying its source during outbreaks, including those resulting from bioterrorism.
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Characterisation of bovine strains of Pasteurella multocida and comparison with isolates of avian, ovine and porcine origin.
TL;DR: Comparison of the OMP profiles of bovine isolates with those of avian, ovine and porcine strains showed that a high proportion of the respiratory tract infections in each of these species are caused by different strains of P. multocida.
Journal ArticleDOI
NHE3 in an ancestral vertebrate: primary sequence, distribution, localization, and function in gills
Keith P. Choe,Akira Kato,Shigehisa Hirose,Consuelo Plata,Aleksandra Sindic,Michael F. Romero,James B. Claiborne,David H. Evans +7 more
TL;DR: This study provides the first N HE3 cloned from an elasmobranch and is the first to demonstrate an increase in gill NHE3 expression during acclimation to low salinities, suggesting that NHE 3 can absorb Na+ from ion-poor environments.
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Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea, China
TL;DR: The diversity and abundance of indigenous oil-degrading bacteria and functional genes in crude oil-contaminated seawater of the Dalian coast provide evidence that there exists an active aerobic microbial community indigenous to the coastal area of the Yellow sea that is capable of degrading petroleum hydrocarbons.
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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