MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
TLDR
An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.Abstract:
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.read more
Citations
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Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis.
Pushpendra Singh,Andrej Benjak,Verena J. Schuenemann,Alexander Herbig,Charlotte Avanzi,Philippe Busso,Kay Nieselt,Johannes Krause,Johannes Krause,Lucio Vera-Cabrera,Stewart T. Cole +10 more
TL;DR: Comparisons of the genomes of Mycobacterium lepromatosis and M. leprae show that the two species are very closely related and derived from a common ancestor that underwent genome downsizing and gene decay.
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Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation.
Bat-Erdene Jugder,Haluk Ertan,Susanne Bohl,Matthew Lee,Christopher P. Marquis,Mike Manefield +5 more
TL;DR: The paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases, and the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.
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Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung
Julio Diaz Caballero,Shawn T. Clark,Shawn T. Clark,Bryan Coburn,Yu Zhang,Pauline W. Wang,Sylva L. Donaldson,D. Elizabeth Tullis,Yvonne C. W. Yau,Valerie Waters,David M. Hwang,David M. Hwang,David S. Guttman +12 more
TL;DR: A short-term population genomic analysis of 233 P. aeruginosa isolates collected from 12 sputum specimens obtained over a 1-year period from a single patient identifies the expansion of two clonal lineages and reveals important intraspecies dynamics that explain a clinically important phenomenon not evident at a lower-resolution analysis of community structure.
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Hepatitis C reinfection after sustained virological response.
Håvard Midgard,Håvard Midgard,Benedikte Bjøro,Arild Mæland,Zbigniew Konopski,Hege Kileng,Jan Kristian Damås,Jørn Paulsen,Lars Heggelund,Per Sandvei,Jetmund O. Ringstad,Lars Normann Karlsen,Kathrine Stene-Johansen,John H.-O. Pettersson,Dagny Haug Dorenberg,Olav Dalgard,Olav Dalgard +16 more
TL;DR: Over time, persistent HCV reinfection was common among individuals who had relapsed to IDU after treatment and should be systematically addressed and prevented when providing HCV care for PWID.
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A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.
Sudip Patel,Radhey S. Gupta +1 more
TL;DR: In this paper, a phylogenetic tree of Bacillaceae species was reconstructed based on multiple datasets of proteins, including 1172 core Bacillus proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-rpoC proteins, and UvrD-PolA proteins.
References
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MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
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