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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Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system
Laura A. Sauder,Mads Albertsen,Katja Engel,Jasmin Schwarz,Per Halkjær Nielsen,Michael Wagner,Josh D. Neufeld +6 more
TL;DR: The cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare is reported, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada), which encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown and encodes several key genes for dealing with oxidative stress.
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The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines
Yuchen Han,Mirjam Perner +1 more
TL;DR: Sulfurimonas’ versatile energy metabolisms are summarized and their physiological properties to their global distribution are linked.
Journal ArticleDOI
Non-self- and self-recognition models in plant self-incompatibility
TL;DR: In non-self-recognition SI systems, the transition from self-compatibility (SC) to SI may be more common than previously thought and reversible transition between SI and SC in plants may have contributed to their adaptation to diverse and fluctuating environments.
Journal ArticleDOI
First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.
Kaisa Koskinen,Manuela R. Pausan,A. Perras,A. Perras,Michael Beck,Corinna Bang,Maximilian Mora,Anke Schilhabel,Ruth A. Schmitz,Christine Moissl-Eichinger +9 more
TL;DR: Conservative protocols based on specifically archaea-targeting, PCR-based methods were established to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin, and were able to detect unexpectedly high diversity of archaea associated with different body parts.
Journal ArticleDOI
Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics
Masaru K. Nobu,Jeremy A. Dodsworth,Jeremy A. Dodsworth,Senthil K. Murugapiran,Christian Rinke,Christian Rinke,Esther A. Gies,Gordon Webster,Patrick Schwientek,Peter Kille,R. John Parkes,Henrik Sass,Bo Barker Jørgensen,Andrew J. Weightman,Wen Tso Liu,Steven J. Hallam,George Tsiamis,Tanja Woyke,Brian P. Hedlund +18 more
TL;DR: C cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum, and confirmed the monophyly of the ‘Atribacteria’ inclusive of OP9 and JS1.
References
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Journal ArticleDOI
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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