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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Ef7 Encodes an ELF3-like Protein and Promotes Rice Flowering by Negatively Regulating the Floral Repressor Gene Ghd7 under Both Short- and Long-Day Conditions
Hiroki Saito,Eri Ogiso-Tanaka,Eri Ogiso-Tanaka,Yutaka Okumoto,Yoshihiro Yoshitake,Haruka Izumi,Takayuki Yokoo,Kazuki Matsubara,Kiyosumi Hori,Masahiro Yano,Hiromo Inoue,Takatoshi Tanisaka +11 more
TL;DR: Results show that Ef7 functions as a floral promoter by repressing Ghd7 expression under both SD and LD conditions, and consequently up-regulates the expression of the downstream Ehd1 and FT-like genes under bothSD andLD conditions.
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Cryptic diversity and discordance in single‐locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)
TL;DR: A large data set of mitochondrial ND4 sequences from horned lizards is compiled to elucidate congruence using four tree‐based (single‐threshold GMYC), multiple‐th threshold GMYC, bPTP, mPTP and one distance‐based species delimitation models, suggesting that the mP TP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.
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Insights on the Evolution of Mycoparasitism from the Genome of Clonostachys rosea
Magnus Karlsson,Mikael Brandström Durling,Jaeyoung Choi,Chatchai Kosawang,Gerald Lackner,Georgios Tzelepis,Kristiina Nygren,Mukesh Dubey,Nathalie N. Kamou,Anthony Levasseur,Antonio Zapparata,Jinhui Wang,Daniel Buchvaldt Amby,Birgit Jensen,Sabrina Sarrocco,Emmanuel Panteris,Anastasia L. Lagopodi,Stefanie Pöggeler,Giovanni Vannacci,David B. Collinge,Dirk Hoffmeister,Bernard Henrissat,Yong-Hwan Lee,Dan Funck Jensen +23 more
TL;DR: The genome sequencing and comparative genome analysis suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea and that the evolution of mycoparasitism as a fungal lifestyle is being studied.
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Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges.
TL;DR: In insights into the biology of these remarkable bacteria using genomic, (meta)proteomic, and chemical methods, the data suggest a metabolic model of Ca.
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Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii
TL;DR: A comparative study of three denitrifying Hyphomicrobium species highlights the potential of H. nitrativorans as an efficient and adaptable bacterium that is able to perform complete denitrification under various conditions.
References
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Journal ArticleDOI
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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