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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Journal ArticleDOI
Mimivirus and the emerging concept of "giant" virus.
Jean-Michel Claverie,Hiroyuki Ogata,Stéphane Audic,Chantal Abergel,Karsten Suhre,Pierre-Edouard Fournier +5 more
TL;DR: It is proposed to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses.
Journal ArticleDOI
Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium.
Qi Ye,Yul Roh,Susan L. Carroll,Benjamin G. Blair,Jizhong Zhou,Chuanlun Zhang,Matthew W. Fields,Matthew W. Fields +7 more
TL;DR: The results demonstrated that the isolate QYMF might represent a novel metal-reducing alkaliphilic species and suggest that bioremediation of metal-contaminated alkaline environments may be feasible and have implications for alkaline anaerobic respiration.
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Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal
D. B. Keeney,Edward J. Heist +1 more
TL;DR: The findings indicate that a major population subdivision exists across the Atlantic Ocean, but not the Pacific Ocean, and that the historical dispersal of this widespread, coastal species may have been interrupted by the rise of the Isthmus of Panama.
Journal ArticleDOI
Tetraponera ants have gut symbionts related to nitrogen–fixing root–nodule bacteria
TL;DR: It is argued that pouch bacteria have been repeatedly ‘domesticated’ by the ants as nitrogen–recycling endosymbionts, the first finding of symbionts related to root–nodule bacteria in animals.
Journal ArticleDOI
Cascading host-associated genetic differentiation in parasitoids of phytophagous insects.
TL;DR: The results suggest that cascading HAD could play an important role in the diversification of parasitoids attacking phytophagous insects, and the existence of cryptic host-associated lineages also suggests that the diversity of Parasitoids may be vastly underestimated.
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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