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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Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
Tianzhen Zhang,Yan Hu,Wenkai Jiang,Lei Fang,Xueying Guan,Jiedan Chen,Jinbo Zhang,Christopher A. Saski,Brian E. Scheffler,David M. Stelly,Amanda M. Hulse-Kemp,Qun Wan,Bingliang Liu,Chunxiao Liu,Sen Wang,Mengqiao Pan,Yangkun Wang,Dawei Wang,Wenxue Ye,Lijing Chang,Wenpan Zhang,Qingxin Song,Ryan C. Kirkbride,Xiao-Ya Chen,Elizabeth S. Dennis,Danny J. Llewellyn,Daniel G. Peterson,Peggy Thaxton,Don C. Jones,Qiong Wang,Xiaoyang Xu,Hua Zhang,Huaitong Wu,Lei Zhou,Gaofu Mei,Shuqi Chen,Yue Tian,Dan Xiang,Xinghe Li,Jian Ding,Qiyang Zuo,Linna Tao,Yunchao Liu,Ji Li,Yu Lin,Yuanyuan Hui,Zhisheng Cao,Caiping Cai,Xiefei Zhu,Zhi Jiang,Baoliang Zhou,Wangzhen Guo,Ruiqiang Li,Z. Jeffrey Chen +53 more
TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Journal ArticleDOI
Genetic Analysis of Human Norovirus Strains in Japan in 2016-2017.
Koo Nagasawa,Yuki Matsushima,Takumi Motoya,Fuminori Mizukoshi,Yo Ueki,Naomi Sakon,Koichi Murakami,Tomomi Shimizu,Nobuhiko Okabe,Noriko Nagata,Komei Shirabe,Hiroto Shinomiya,Wataru Suzuki,Makoto Kuroda,Tsuyoshi Sekizuka,Yoshiyuki Suzuki,Akihide Ryo,Kiyotaka Fujita,Kazunori Oishi,Kazuhiko Katayama,Hirokazu Kimura,Hirokazu Kimura +21 more
TL;DR: The time-scale phylogeny suggested that the common ancestors of the 2016 strains VP1 gene and RdRp region diverged in 2006 and 1999, respectively, and that the 2016 strain was the progeny of a pre-2016 GII.2.2 strains.
Journal ArticleDOI
Linking stomatal traits and expression of slow anion channel genes HvSLAH1 and HvSLAC1 with grain yield for increasing salinity tolerance in barley
Xiaohui Liu,Michelle Mak,Mohammad Babla,Feifei Wang,Guang Chen,Filip Veljanoski,Gang Wang,Sergey Shabala,Meixue Zhou,Zhong-Hua Chen +9 more
TL;DR: In this article, a range of physiological (stomata assay, gas exchange, phylogenetic analysis, QTL analysis), and molecular techniques (RT-PCR and qPCR) were employed to investigate stomatal behavior and genotypic variation in barley cultivars and a genetic population in four experimental trials.
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Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses
Shawn R. Lockhart,Kizee A. Etienne,Snigdha Vallabhaneni,Joveria Farooqi,Anuradha Chowdhary,Nelesh P. Govender,Arnaldo Lopes Colombo,Belinda Calvo,Christina A. Cuomo,Christopher A. Desjardins,Elizabeth L. Berkow,Mariana Castanheira,Rindidzani E. Magobo,Kauser Jabeen,Rana Jawad Asghar,Jacques F. Meis,Brendan R Jackson,Tom Chiller,Anastasia P. Litvintseva +18 more
TL;DR: Candida auris is an emerging healthcare-associated pathogen associated with high mortality, and WGS analysis suggests nearly simultaneous, and recent, independent emergence of different clonal populations on 3 continents.
Journal ArticleDOI
Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake Grevelingen
Yvonne A. Lipsewers,Ellen C. Hopmans,Filip J. R. Meysman,Jaap S. Sinninghe Damsté,Laura Villanueva +4 more
TL;DR: The simultaneous presence and activity of organoheterotrophic Denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.
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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