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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Connections between the Atlantic and the Amazonian forest avifaunas represent distinct historical events
TL;DR: In this article, the authors combined phylogenetic data with distributional data using a supermatrix approach in order to depict the historical connection dynamics between these biomes for New World suboscines and provided the first general temporal and spatial model of how the Atlantic and Amazonian forests were connected in the past.
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The 2014 Ebola virus disease outbreak in West Africa
TL;DR: A new outbreak of the Ebola virus disease (EVD) was reported in Guinea on 23 March 2014, which began in December 2013 in Guinee Forestiere (Forested Guinea), the eastern sector of the Republic of Guinea as mentioned in this paper.
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WGS accurately predicts antimicrobial resistance in Escherichia coli
Gregory H. Tyson,Patrick F. McDermott,Cong Li,Yuansha Chen,Daniel A. Tadesse,Sampa Mukherjee,Sonya Bodeis-Jones,Claudine Kabera,Stuart A. Gaines,Guy H. Loneragan,Tom S. Edrington,Mary E. Torrence,Dayna M. Harhay,Shaohua Zhao +13 more
TL;DR: WGS can provide comprehensive resistance genotypes and is capable of accurately predicting resistance phenotypes, making it a valuable tool for surveillance, and the ability to accurately predict resistance suggest that WGS may be used as a screening tool in selecting anti-infective therapy, especially as costs drop and methods improve.
Journal ArticleDOI
Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales.
Matthew J. Neave,Rita Rachmawati,Liping Xun,Craig T. Michell,David G. Bourne,Amy Apprill,Christian R. Voolstra +6 more
TL;DR: This work demonstrates that both corals harbor Endozoicomonas bacteria as their prevalent symbiont, and contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.
Journal ArticleDOI
Fungal Planet description sheets: 469-557
Pedro W. Crous,Pedro W. Crous,Michael J. Wingfield,Treena I. Burgess,G.E.St.J. Hardy,C. E. Crane,Sarah Barrett,José F. Cano-Lira,Johannes J. Le Roux,Raja Thangavel,Josep Guarro,Alberto M. Stchigel,María P. Martín,Donis S. Alfredo,Paul A. Barber,Robert W. Barreto,Iuri Goulart Baseia,Julia Cano-Canals,Ratchadawan Cheewangkoon,Renato Juciano Ferreira,Josepa Gené,Christian Lechat,Gabriel Moreno,Francois Roets,Roger G. Shivas,Julieth O. Sousa,Yu Pei Tan,Nathan P. Wiederhold,Sandra E. Abell,Thiago Accioly,José Luis Albizu,Janaina L. Alves,Zaida Inês Antoniolli,Nick Aplin,João P.M. Araújo,Mahdi Arzanlou,Jadson D. P. Bezerra,Jean-Philippe Bouchara,J. R. Carlavilla,A. Castillo,Vanina Lilián Castroagudín,Paulo Cezar Ceresini,Gordon F. Claridge,Gilberto Coelho,Victor R. M. Coimbra,L. A. Costa,Keith C. da Cunha,Silvana Santos da Silva,Rosalie Daniel,Z. Wilhelm de Beer,Margarita Dueñas,Jacqueline Edwards,P. Enwistle,Patrícia Oliveira Fiuza,Jacques Fournier,Dania García,Tatiana Baptista Gibertoni,Sandrine Giraud,Marcela Guevara-Suarez,Luís Fernando Pascholati Gusmão,Sukanya Haituk,Michel Heykoop,Yuuri Hirooka,Tina A. Hofmann,Jos Houbraken,David P. Hughes,Ivona Kautmanová,Olga Koppel,Ondřej Koukol,Ellen Larsson,K. P. Deepna Latha,Dong-Hyeon Lee,Daniela O. Lisboa,W. S. Lisboa,Ángela López-Villalba,João Leodato Nunes Maciel,Patinjareveettil Manimohan,José Luis Manjón,Seonju Marincowitz,Thomas S. Marney,M. Meijer,Andrew N. Miller,Ibai Olariaga,Laura M. Paiva,Meike Piepenbring,Juan Carlos Poveda-Molero,K. N. Anil Raj,Huzefa A. Raja,Amandine Rougeron,Isabel Salcedo,Rosita Samadi,Tiago Santos,Kelly Scarlett,Keith A. Seifert,Lucas A. Shuttleworth,Gladstone Alves da Silva,Meiriele da Silva,João Paulo Zen Siqueira,Cristina Maria de Souza-Motta,Steven L. Stephenson,Deanna A. Sutton,Nisachon Tamakeaw,M. Teresa Telleria,N. Valenzuela-Lopez,Altus Viljoen,Cobus M. Visagie,Alfredo Vizzini,Felipe Wartchow,Brenda D. Wingfield,Eugene Yurchenko,Juan Carlos Zamora,Johannes Z. Groenewald +111 more
TL;DR: Novel species of fungi described in this study include those from various countries as follows: Apiognomonia lasiopetali on Lasiopetalum sp.
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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