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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Whole genome sequence of the soybean aphid, Aphis glycines.
Jacob A Wenger,Bryan J. Cassone,Fabrice Legeai,J. Spencer Johnston,Raman Bansal,Ashley D. Yates,Brad S. Coates,V. A. C. Pavinato,Andy Michel,Andy Michel +9 more
TL;DR: The whole genome sequence of a fourth aphid is presented, the soybean aphid (Aphis glycines), which is an extreme specialist and an important invasive pest of soybean (Glycine max) and contains the smallest known aphid genome to date, based on updated genome sizes for 19 aphid species.
Journal ArticleDOI
Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis , and Ixodes scapularis Ticks.
Rafal Tokarz,Stephen Sameroff,Teresa Tagliafierro,Komal Jain,Simon H. Williams,D. Moses Cucura,Ilia Rochlin,Javier Monzón,Giovanna Carpi,Danielle M. Tufts,Maria A. Diuk-Wasser,Jory Brinkerhoff,W. Ian Lipkin +12 more
TL;DR: This work reports a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including Ixodes scapularis, Amblyomma americanum, and Dermacentor variabilis, collected in New York, Connecticut, and Virginia in 2015 and 2016.
Journal ArticleDOI
Genetic diversity and genome-wide association analysis of cooking time in dry bean ( Phaseolus vulgaris L.)
TL;DR: Fivefold diversity for cooking time found in a panel of 206 P. vulgaris accessions and regions on chromosomes Pv02, Pv03, and Pv06 associated with cooking time are revealed, suggesting with additional experimentation, it may be possible to use this spectroscopy method to non-destructively identify fast cooking lines as part of a breeding program.
Journal ArticleDOI
Two subclasses of odorant-binding proteins in Spodoptera exigua display structural conservation and functional divergence.
Nai-Yong Liu,Nai-Yong Liu,F. Yang,Kun Yang,Peng He,X.-H. Niu,Wei Xu,Alisha Anderson,Shuang-Lin Dong +8 more
TL;DR: Of the three SexiPBPs, SexiPBP1 may play the most important role in female sex pheromone reception, and additionally all three SexoPBP/GOBPs can detect some plant odorants, while SexiGOBP2 may be involved in the detection of female sexpheromones in addition to plant odants.
Journal ArticleDOI
Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast.
Ulschan Scheler,Wolfgang Brandt,Andrea Porzel,Kathleen Rothe,David Manzano,Dragana Božić,Dimitra Papaefthimiou,Gerd Ulrich Balcke,Anja Henning,Swanhild Lohse,Sylvestre Marillonnet,Angelos K. Kanellis,Albert Ferrer,Alain Tissier +13 more
TL;DR: The elucidation of the complete biosynthetic pathway of carnosic acid and its reconstitution in yeast cells is described and opportunities for the metabolic engineering of phenolic diterpenes are opened.
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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