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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Evaluation of ACC-deaminase-producing rhizobacteria to alleviate water-stress impacts in wheat (Triticum aestivum L.) plants
Dinesh Chandra,Rashmi Srivastava,Vadakattu V. S. R. Gupta,Vadakattu V. S. R. Gupta,Christopher M. M. Franco,Anil Kumar Sharma +5 more
TL;DR: Findings imply that PGPB having ACC deaminase activity together with other PGP traits could potentially be effective inoculants to improve the growth of wheat plants in water-stressed rain-fed environments.
Journal ArticleDOI
Evolutionary Insights into IL17A in Lagomorphs.
TL;DR: This study gives further support to the hypothesis that European rabbit might be a more suitable animal model for studies on human IL17, and observes that this protein is highly conserved between these species, with a similarity of 97–99% in leporids and ~88% between leporid and American pika.
Journal ArticleDOI
Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype
Chad M. Kurylo,Matthew Parks,Manuel F. Juette,Boris Zinshteyn,Roger B. Altman,Jordana K. Thibado,C. Theresa Vincent,C. Theresa Vincent,C. Theresa Vincent,Scott C. Blanchard +9 more
TL;DR: It is shown that nutrient limitation-induced stress in E. coli changes the relative expression of rDNA operons to alter the rRNA composition within the actively translating ribosome pool, establishing that endogenously encoded, naturally occurring rRNA sequence variation can modulate ribosomes function, central aspects of gene expression regulation, and cellular physiology.
Journal ArticleDOI
Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion.
Renxing Liang,Irene A. Davidova,Christopher R. Marks,Blake W. Stamps,Brian H. Harriman,Bradley S. Stevenson,Kathleen E. Duncan,Joseph M. Suflita +7 more
TL;DR: It is suggested that predominant halophiles associated with unconventional shale gas extraction could proliferate and produce sulfide and acetate from the metabolism of polysaccharides used in hydraulic fracturing fluids and return to the surface and transported in pipelines to cause pitting corrosion in downstream infrastructure.
Journal ArticleDOI
Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice
Atsushi Hayashi,Yohei Mikami,Kentaro Miyamoto,Nobuhiko Kamada,Toshiro Sato,Shinta Mizuno,Makoto Naganuma,Toshiaki Teratani,Ryo Aoki,Shinji Fukuda,Wataru Suda,Masahira Hattori,Masayuki Amagai,Manabu Ohyama,Takanori Kanai,Takanori Kanai +15 more
TL;DR: It is found that antibiotic-induced dysbiosis, in particular, overgrowth of Lactobacillus murinus, impaired gut metabolic function and led to the development of alopecia in mice fed a biotin-deficient diet.
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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