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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Biomimetic synthesis of silver nanoparticles from Streptomyces atrovirens and their potential anticancer activity against human breast cancer cells
R. Subbaiya,Muthupandian Saravanan,Andavar Raja Priya,Konathala Ravi Shankar,M. Masilamani Selvam,Muhammad Ovais,Ramachandran Balajee,Hamed Barabadi +7 more
TL;DR: The present results showed that biosynthesised AgNPs might be emerging alternative biomaterials for human breast cancer therapy, and the inhibition of MCF-7 breast cancer cell line was found to be dose dependent on treatment with AgNPS.
Journal ArticleDOI
Red squirrels in the British Isles are infected with leprosy bacilli
Charlotte Avanzi,Jorge Del-Pozo,Andrej Benjak,Karen Stevenson,Victor R. Simpson,Philippe Busso,Joyce McLuckie,Chloé Loiseau,Colin Lawton,Janne M. Schoening,Darren J. Shaw,Jérémie Piton,Lucio Vera-Cabrera,Jesús Salvador Velarde-Félix,Fergal McDermott,Stephen V. Gordon,Stewart T. Cole,Anna Meredith +17 more
TL;DR: Red squirrels in Great Britain have increasingly been observed with leprosy-like lesions on the head and limbs, and using genomics, histopathology, and serology, M. lepromatosis was found in squirrels from England, Ireland, and Scotland, and Mycobacterium leprae in Squirrels from Brownsea Island, England.
Journal ArticleDOI
Diversity of fungal feruloyl esterases : updated phylogenetic classification, properties, and industrial applications
Adiphol Dilokpimol,Miia R. Mäkelä,Maria Victoria Aguilar-Pontes,Isabelle Benoit-Gelber,Kristiina Hildén,Ronald P. de Vries,Ronald P. de Vries +6 more
TL;DR: The discovery of new FAEs using genome mining and phylogenetic analysis of current publicly accessible fungal genomes has led to a new subfamily classification of fungal FAEs that takes into account both phylogeny and substrate specificity.
Journal ArticleDOI
Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases
Zhiqiang Wu,Liang Lu,Jiang Du,Li Yang,Xianwen Ren,Bo Liu,Jinyong Jiang,Jian Yang,Jie Dong,Lilian Sun,Yafang Zhu,Yuhui Li,Dandan Zheng,Chi Zhang,Haoxiang Su,Yu-ting Zheng,Hongning Zhou,Guangjian Zhu,Hongying Li,Aleksei A. Chmura,Fan Yang,Peter Daszak,Jianwei Wang,Qiyong Liu,Qi Jin +24 more
TL;DR: The results expand the understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia.
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Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.
Guillaume Méric,Maria Miragaia,Mark de Been,Koji Yahara,Koji Yahara,Ben Pascoe,Leonardos Mageiros,Jane Mikhail,Llinos G. Harris,Thomas S. Wilkinson,Joana Rolo,Sarah Lamble,James E. Bray,Keith A. Jolley,William P. Hanage,Rory Bowden,Martin C. J. Maiden,Dietrich Mack,Hermínia de Lencastre,Hermínia de Lencastre,Edward J. Feil,Jukka Corander,Samuel K. Sheppard +22 more
TL;DR: A comparative analysis of 324 S. aureus and S. epidermidis genomes provided a context for considering the nature of recombinational boundaries between these ecologically similar staphylococcal species and, the selective forces that influence realized recombination between these species.
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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