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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Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium
Pagakrong Wanapaisan,Natthariga Laothamteep,Felipe Vejarano,Joydeep Chakraborty,Masaki Shintani,Chanokporn Muangchinda,Tomomi Morita,Chiho Suzuki-Minakuchi,Kengo Inoue,Hideaki Nojiri,Onruthai Pinyakong +10 more
TL;DR: Findings showing that synergistic degradation of pyrene in the consortium will facilitate the application of the defined bacterial consortium in bioremediation are shown.
Journal ArticleDOI
Conversion of carlactone to carlactonoic acid is a conserved function of MAX1 homologs in strigolactone biosynthesis
Kaori Yoneyama,Kaori Yoneyama,Kaori Yoneyama,Narumi Mori,Tomoyasu Sato,Akiyoshi Yoda,Xiaonan Xie,Masanori Okamoto,Masashi Iwanaga,Toshiyuki Ohnishi,Hisashi Nishiwaki,Tadao Asami,Takao Yokota,Kohki Akiyama,Koichi Yoneyama,Takahito Nomura +15 more
TL;DR: CLA was detected in root exudates from poplar and Selaginella, but not ubiquitously in other plants examined in this study, suggesting its role as a species-specific signal in the rhizosphere.
Journal ArticleDOI
Chytrids dominate arctic marine fungal communities.
TL;DR: This work provides the first data from any marine ecosystem in which fungi in the Chytridiomycota dominate fungal communities and are linked in their occurrence to light intensities and algal stress.
Journal ArticleDOI
The Stone Age Plague and Its Persistence in Eurasia
Aida Andrades Valtueña,Alissa Mittnik,Alissa Mittnik,Felix M. Key,Wolfgang Haak,Wolfgang Haak,Raili Allmäe,Andrej Belinskij,Mantas Daubaras,Michal Feldman,Michal Feldman,Rimantas Jankauskas,Ivor Janković,Ken Massy,Mario Novak,Saskia Pfrengle,Sabine Reinhold,Mario Šlaus,Maria A. Spyrou,Maria A. Spyrou,Anna Szécsényi-Nagy,Mari Tõrv,Svend Hansen,Kirsten I. Bos,Kirsten I. Bos,Philipp W. Stockhammer,Philipp W. Stockhammer,Alexander Herbig,Alexander Herbig,Johannes Krause,Johannes Krause +30 more
TL;DR: Six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age are presented and it is proposed that the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasian in parallel with human populations.
Journal ArticleDOI
A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective
Rui-Lin Zhao,Guo-Jie Li,Santiago Sánchez-Ramírez,Santiago Sánchez-Ramírez,Matt Stata,Matt Stata,Zhu-Liang Yang,Gang Wu,Yu-Cheng Dai,Shuang-Hui He,Bao-Kai Cui,Jun-Liang Zhou,Fang Wu,Mao-Qiang He,Jean-Marc Moncalvo,Jean-Marc Moncalvo,Kevin D. Hyde,Kevin D. Hyde +17 more
TL;DR: A phylogenetic overview of Basidiomycota and related phyla in relation to ten years of DNA based phylogenetic studies since the AFTOL publications in 2007 is provided.
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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