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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Development of an Efficient Bacterial Consortium for the Potential Remediation of Hydrocarbons from Contaminated Sites.
TL;DR: The purpose of the study was to isolate TPH degrading bacterial strains from various petroleum contaminated soil of Assam, India and develop a robust bacterial consortium for bioremediation of crude oil of this native land and the consortium showed degradation up to 84.15% of TPH after 5 weeks of incubation, as revealed from gravimetric analysis.
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Middle East Respiratory Syndrome Coronavirus Quasispecies That Include Homologues of Human Isolates Revealed through Whole-Genome Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia
Thomas Briese,Nischay Mishra,Komal Jain,Iyad S. Zalmout,Omar Jabado,William B. Karesh,Peter Daszak,Osama B. Mohammed,Abdulaziz N. Alagaili,W. Ian Lipkin +9 more
TL;DR: Recovery of MERS-CoV from nasal swabs of dromedaries is reported, which supports the plausibility of a role for dRomedaries in human infection, and whole-genome consensus sequences from dromingaries and humans are indistinguishable.
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Molecular basis of a shattering resistance boosting global dissemination of soybean
Hideyuki Funatsuki,Masaya Suzuki,Aya Hirose,Hiroki Inaba,Tetsuya Yamada,Makita Hajika,Kunihiko Komatsu,Takeshi Katayama,Takashi Sayama,Masao Ishimoto,Kaien Fujino +10 more
TL;DR: A major quantitative trait locus (QTL) controlling pod dehiscence in soybean encodes a dirigent-like protein, designated as Pdh1, which increases dehiscing forces by promoting torsion of dried pod walls, suggesting that pdh1 has played a crucial role in the global expansion of soybean cultivation.
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High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq.
Jonathan L. King,Bobby LaRue,Nicole M.M. Novroski,Monika Stoljarova,Seung Bum Seo,Xiangpei Zeng,David H. Warshauer,Carey Davis,Walther Parson,Antti Sajantila,Bruce Budowle +10 more
TL;DR: An overall increase in haplotype or genetic diversity and random match probability, as well as better haplogroup assignment demonstrates that MPS of the mtGenome using the Illumina MiSeq system is a viable and reliable methodology.
Journal ArticleDOI
Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex
Will Van Treuren,Loganathan Ponnusamy,R. Jory Brinkerhoff,Antonio Gonzalez,Christian M. Parobek,Jonathan J. Juliano,Theodore G. Andreadis,Richard C. Falco,Lorenza Beati Ziegler,Nicholas J. Hathaway,Corinna Keeler,Michael Emch,Jeffrey A. Bailey,R. Michael Roe,Charles S. Apperson,Rob Knight,Steven R Meshnick +16 more
TL;DR: Analysis of the microbiota of ticks captured in 19 locations suggests substantial variations in the Ixodes microbiota in association with geography, species, and sex.
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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