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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Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts.
TL;DR: Together with previous studies that implicated several PARPs in immunity, as well as those that demonstrated a role for virally encoded macrodomains in host immune evasion, the evolutionary analyses suggest that addition, recognition and removal of ADP-ribosylation is a critical, underappreciated currency in host-virus conflicts.
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Reassortant Highly Pathogenic Influenza A H5N2 Virus Containing Gene Segments Related to Eurasian H5N8 in British Columbia, Canada, 2014
John Pasick,Yohannes Berhane,Tomy Joseph,Victoria Bowes,Tamiko Hisanaga,Katherine Handel,Soren Alexandersen +6 more
TL;DR: The fact that the British Columbia outbreaks also occurred at a time associated with increased migratory waterfowl activity along with reports by the USA of a wholly Eurasian H5N8 virus detected in wild birds in Washington State, strongly suggest that migratoryWaterfowl were responsible for bringing Eurasia H 5N8 to North America where it subsequently reassorted with indigenous viruses.
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Fungal Planet description sheets: 716-784.
Pedro W. Crous,Michael J. Wingfield,Treena I. Burgess,G.E.St.J. Hardy,Josepa Gené,Josep Guarro,Iuri Goulart Baseia,Dania García,Luís Fernando Pascholati Gusmão,Cristina Maria de Souza-Motta,R. Thangavel,Slavomír Adamčík,A. Barili,C. W. Barnes,Jadson D. P. Bezerra,Juan-Julián Bordallo,José F. Cano-Lira,R.J.V. de Oliveira,Enrico Ercole,Vit Hubka,I. Iturrieta-González,Alena Kubátová,María P. Martín,Pierre-Arthur Moreau,Asunción Morte,M.E. Ordoñez,A. Rodríguez,Alberto M. Stchigel,Alfredo Vizzini,Jafar Abdollahzadeh,V.P. Abreu,Katarína Adamčíková,G.M.R. Albuquerque,A. V. Alexandrova,E. Alvarez Duarte,C. Armstrong-Cho,S. Banniza,Renan do Nascimento Barbosa,Jean-Michel Bellanger,José Jailson Lima Bezerra,T.S. Cabral,M. Cabon,E. Caicedo,T. Cantillo,Angus J. Carnegie,L.T. Carmo,Rafael F. Castañeda-Ruiz,Charles R. Clement,Adéla Čmoková,L.B. Conceição,Rhudson Henrique Santos Ferreira da Cruz,Ulrike Damm,B.D.B. da Silva,G. A. da Silva,R. M. da Silva,A. L. C. M. de A. Santiago,L.F. De Oliveira,C.A.F. De Souza,Franck Déniel,Bálint Dima,G. Dong,Jacqueline Edwards,Ciro R. Félix,Jacques Fournier,Tatiana Baptista Gibertoni,Kentaro Hosaka,Teresa Iturriaga,M. Jadan,Jean-Luc Jany,Z. Jurjevic,Miroslav Kolarik,I. Kusan,Melissa Fontes Landell,T.R. Leite Cordeiro,Diogo Xavier Lima,Michael Loizides,S. Luo,A. R. Machado,Hugo Madrid,Oliane Maria Correia Magalhães,Paulo Marinho,Neven Matočec,Armin Mešić,Andrew N. Miller,O.V. Morozova,R.P. Neves,K. Nonaka,Alena Nováková,Nicholas H. Oberlies,José Ribamar C. Oliveira-Filho,Thays Gabrielle Lins de Oliveira,Viktor Papp,Olinto Liparini Pereira,Giancarlo Perrone,Stephen W. Peterson,T.H.G. Pham,Huzefa A. Raja,Daniel B. Raudabaugh,J. Rehulka,E. Rodríguez-Andrade,M. Saba,A. Schauflerova,Roger G. Shivas,G. Simonini,João Paulo Zen Siqueira,Julieth O. Sousa,V. Stajsic,T. Svetasheva,T. Svetasheva,Yu Pei Tan,Zdenko Tkalčec,S. Ullah,Patricia Valente,Nicomedes Valenzuela-Lopez,Masoud Abrinbana,D.A. Viana Marques,P. T. W. Wong,V. Xavier de Lima,Johannes Z. Groenewald +118 more
TL;DR: Novel species of fungi described in this study include those from various countries as follows: Australia, Chaetopsina eucalyPTi on Eucalyptus leaf litter, Colletotrichum cobbittiense from Cordyline stricta × C. australis hybrid.
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Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat.
Muhammad Suleman,Sumera Yasmin,Maria Rasul,Mahreen Yahya,Babar Manzoor Atta,Muhammad Sajjad Mirza +5 more
TL;DR: The results indicated that gluconic acid producing Pseudomonas sp.
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Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Charlotte D. Vavourakis,Rohit Ghai,Francisco Rodriguez-Valera,Dimitry Y. Sorokin,Susannah G. Tringe,Philip Hugenholtz,Gerard Muyzer +6 more
TL;DR: The first “metagenomic snapshots” of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L are presented.
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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