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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High-throughput monitoring of wild bee diversity and abundance via mitogenomics
Min Tang,Chloe J. Hardman,Yinqiu Ji,Guanliang Meng,Shanlin Liu,Meihua Tan,Shenzhou Yang,Ellen D. Moss,Jingxin Wang,Chenxue Yang,Catharine Bruce,Timothy D. Nevard,Simon G. Potts,Xin Zhou,Douglas W. Yu,Douglas W. Yu +15 more
TL;DR: It is shown that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees, and species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline.
Journal ArticleDOI
Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.
Meng Li,Brett J. Baker,Brett J. Baker,Karthik Anantharaman,Sunit Jain,John A. Breier,Gregory J. Dick +6 more
TL;DR: Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter in deep oceans that might play a critical role in global carbon cycling.
Journal ArticleDOI
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution
Lorenzo Barchi,Marco Pietrella,Luca Venturini,Andrea Minio,Laura Toppino,Alberto Acquadro,Giuseppe Andolfo,G. Aprea,C. Avanzato,Laura Bassolino,Cinzia Comino,Alessandra Dal Molin,Alberto Ferrarini,Louise Chappell Maor,Ezio Portis,Sebastian Reyes-Chin-Wo,Riccardo Rinaldi,T. Sala,Davide Scaglione,Prashant D. Sonawane,Paola Tononi,Efrat Almekias-Siegl,Elisa Zago,Maria Raffaella Ercolano,Asaph Aharoni,Massimo Delledonne,Giovanni Giuliano,Sergio Lanteri,Giuseppe Leonardo Rotino +28 more
TL;DR: The data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric Fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.
Journal ArticleDOI
Bacterial nanocellulose from agro-industrial wastes: low-cost and enhanced production by Komagataeibacter saccharivorans MD1
Deyaa Abol-Fotouh,Mohamed A. Hassan,Hassan Shokry,Anna Roig,Mohamed S. Azab,Abd El-Hady B. Kashyout +5 more
TL;DR: It is substantiated that expensive substrates could be exchanged by agro-industrial wastes for BNC production conserving its remarkable physical and microstructural properties.
Journal ArticleDOI
Current status of viroid taxonomy.
F. Di Serio,Ricardo Flores,J. Th. J. Verhoeven,Shifang Li,Vicente Pallás,John W. Randles,Teruo Sano,Georgios Vidalakis,Robert A. Owens +8 more
TL;DR: The current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group.
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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